10 research outputs found

    Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system

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    <div><p>An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, <i>Haliotis diversicolor</i>, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.</p></div

    Changes in α-diversity (Shannon-Wiener indexes) of each component in the abalone seed-nursing system over time.

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    <p>Different lengths of colored bars show different developmental stages of the abalone. Green, trochophore stage (0–2 days); Purple, creeping larva stage (2–4 days); Yellow, peristomial shell larva stage (4–12 days); Red, differentiation stage (12–21 days); Blue, juvenile (> 21 days).</p

    Effects of the three bacterial communities on each other in the abalone seed-nursing ecosystem based on a Bray-Curtis similarity percentage (BC%) analysis.

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    <p>A, Abalone; S, Adherent substrate; W, Water; n − 1, time point prior to “n.” Using the A sample as an example, the microbiome of A is influenced by two spatially (Sn-An and Wn-An), one temporally (An-1-An), and two spatio-temporally (Sn-1-An and Wn-1-An) adjacent samples. Wn-1-An (light blue) indicates the BC<sub>Wn-1-An</sub> percentage in a total of five BCs of A; Wn-An (dark blue) indicates the BC<sub>Wn-An</sub>; Sn-1-An percentage (light green) indicates the percentage of BC<sub>Sn-1-An</sub>; Sn-An (dark green) indicates the percentage of BC<sub>Sn-An</sub>; and An-1-An (red) indicates the percentage of BC<sub>An-1-An</sub>. This can be repeated for the additional samples. For details, please refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182590#pone.0182590.g001" target="_blank">Fig 1</a> and Material and Methods.</p

    Principal component analysis of bacterial communities in abalone seed-nursing ecosystem samples.

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    <p>A, with water samples; B, without water samples; blue square, water; green circle, adherent substrate; red triangle, abalone; Arabic numerals, sampling days. Results were plotted using Canoco for Windows 4.5, and the 5,000 most abundant operational taxonomic units of the analyzed samples were used in this analysis. Log transformation (Y' = log (Y + 1)).</p

    PCA plots based on bacterial denaturing gradient gel electrophoresis patterns of the three components in the abalone seed-nursing system.

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    <p>Different colored dots indicate the different developmental stages of the abalone. Green, trochophore stage (0–2 days); Purple, creeping larva stage (2–4 days); Yellow, peristomial shell larva stage (4–12 days); Red, differentiation stage (12–21 days); Blue, juvenile (> 21 days).</p

    Schematic representation of the BC% analysis of the abalone seed-nursing ecosystem.

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    <p>“A,” “S,” and “W” represent different components of the ecosystem with direct microbial exchanges. Comparisons of bacterial communities were only conducted for two samples that were spatially or temporally adjacent, e.g., An-1&An, Wn-1&An, Sn&An. The microbiome of “An” is mainly influenced by five spatially and temporally adjacent samples: Wn-1, An-1, Sn-1, Wn, and Sn. The influence of “W” or “S” was external and that of “An-1” was internal. When the BC values of “An” are considered 100%, the BC percentage (BC%) reflects the strength of the influence on “An”. BC, Bray-Curtis similarity value; A, Abalone; S, Adherent substrate; W, Water; n − 1, Time point prior to “n.”</p

    Common operational taxonomic unit (out) percentages of the three components in the abalone seed-nursing ecosystem samples.

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    <p>A, Abalone; S, Adherent substrate; W, Water. Unique, unique operational taxonomic units (OTUs) in each sample; AW, SW, and AS, common OTUs in two samples; ASW, common OTUs in all three samples. The numbers of OTUs in each sample type: A, 119,722; S, 64,431; W, 49,217.</p

    DataSheet1_Primary exploration of host–microorganism interaction and enteritis treatment with an embedded membrane microfluidic chip of the human intestinal–vascular microsystem.pdf

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    Intestinal flora plays a crucial role in the host’s intestinal health. Imbalances in the intestinal flora, when accompanied by inflammation, affect the host’s intestinal barrier function. Understanding it requires studying how living cells and tissues work in the context of living organs, but it is difficult to form the three-dimensional microstructure intestinal–vascular system by monolayer cell or co-culture cell models, and animal models are costly and slow. The use of microfluidic-based organ chips is a fast, simple, and high-throughput method that not only solves the affinity problem of animal models but the lack of microstructure problem of monolayer cells. In this study, we designed an embedded membrane chip to generate an in vitro gut-on-a-chip model. Human umbilical vein endothelial cells and Caco-2 were cultured in the upper and lower layers of the culture chambers in the microfluidic chip, respectively. The human peripheral blood mononuclear cells were infused into the capillary side at a constant rate using an external pump to simulate the in vitro immune system and the shear stress of blood in vivo. The model exhibited intestine morphology and function after only 5 days of culture, which is significantly less than the 21 days required for static culture in the Transwell¼ chamber. Furthermore, it was observed that drug-resistant bacteria triggered barrier function impairment and inflammation, resulting in enteritis, whereas probiotics (Lactobacillus rhamnosus GG) improved only partially. The use of Amikacin for enteritis is effective, whereas other antibiotic therapies do not work, which are consistent with clinical test results. This model may be used to explore intestinal ecology, host and intestinal flora interactions, and medication assessment.</p

    Microfluidic Device for Efficient Airborne Bacteria Capture and Enrichment

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    Highly efficient capture and enrichment is always the key for rapid analysis of airborne pathogens. Herein we report a simple microfluidic device which is capable of fast and efficient airborne bacteria capture and enrichment. The device was validated with <i>Escherichia coli</i> (<i>E. coli</i>) and <i>Mycobacterium smegmatis</i>. The results showed that the efficiency can reach close to 100% in 9 min. Compared with the traditional sediment method, there is also great improvement with capture limit. In addition, various flow rate and channel lengths have been investigated to obtain the optimized condition. The high capture and enrichment might be due to the chaotic vortex flow created in the microfluidic channel by the staggered herringbone mixer (SHM) structure, which is also confirmed with flow dynamic mimicking. The device is fabricated from polydimethylsiloxane (PDMS), simple, cheap, and disposable, perfect for field application, especially in developing countries with very limited modern instruments
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