scholarly journals Formation of Phage Lysis Patterns and Implications on Co-Propagation of Phages and Motile Host Bacteria

2019 ◽  
Author(s):  
Xiaochu Li ◽  
Floricel Gonzalez ◽  
Nathaniel Esteves ◽  
Birgit E. Scharf ◽  
Jing Chen
Keyword(s):  
Mathematical Model ◽  
Microbial Community ◽  
Microbial Communities ◽  
Biological Properties ◽  
Scientific Basis ◽  
Nutrient Level ◽  
Natural Environments ◽  
Extrinsic Factors ◽  
Inhibition Of Proliferation ◽  
Set Up

AbstractCoexistence of bacteriophages, or phages, and their host bacteria plays an important role in maintaining the microbial communities. In natural environments with limited nutrients, motile bacteria can actively migrate towards locations of richer resources. Although phages are not motile themselves, they can infect motile bacterial hosts and spread in space via the hosts. Therefore, in a migrating microbial community coexistence of bacteria and phages implies their co-propagation in space. Here, we combine an experimental approach and mathematical modeling to explore how phages and their motile host bacteria coexist and co-propagate. When lytic phages encountered motile host bacteria in our experimental set up, a sector-shaped lysis zone formed. Our mathematical model indicates that local nutrient depletion and the resulting inhibition of proliferation and motility of bacteria and phages are the key to formation of the observed lysis pattern. The model further reveals the straight radial boundaries in the lysis pattern as a tell-tale sign for coexistence and co-propagation of bacteria and phages. Emergence of such a pattern, albeit insensitive to extrinsic factors, requires a balance between intrinsic biological properties of phages and bacteria, which likely results from co-evolution of phages and bacteria.Author summaryCoexistence of phages and their bacterial hosts is important for maintaining the microbial communities. In a migrating microbial community, coexistence between phages and host bacteria implies that they co-propagate in space. Here we report a novel phage lysis pattern that is indicative of this co-propagation. The corresponding mathematical model we developed highlights a crucial dependence of the lysis pattern and implied phage-bacteria co-propagation on intrinsic properties allowing proliferation and spreading of the microbes in space. Remarkably, extrinsic factors, such as overall nutrient level, do not influence phage-bacteria coexistence and co-propagation. Findings from this work have strong implications for dispersal of phages mediated by motile bacterial communities, which will provide scientific basis for the fast-growing applications of phages.

scholarly journals Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states

2020 ◽  
Vol 375 (1794) ◽  
pp. 20190112 ◽  
Author(s):  
Richard D. Bardgett ◽  
Tancredi Caruso
Keyword(s):  
Climate Change ◽  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Climate Extremes ◽  
Alternative States ◽  
Community Responses ◽  
Extrinsic Factors ◽  
Soil Microbial

A major challenge for advancing our understanding of the functional role of soil microbial communities is to link changes in their structure and function under climate change. To address this challenge requires new understanding of the mechanisms that underlie the capacity of soil microbial communities to resist and recover from climate extremes. Here, we synthesize emerging understanding of the intrinsic and extrinsic factors that influence the resistance and resilience of soil microbial communities to climate extremes, with a focus on drought, and identify drivers that might trigger abrupt changes to alternative states. We highlight research challenges and propose a path for advancing our understanding of the resistance and resilience of soil microbial communities to climate extremes, and of their vulnerability to transitions to alternative states, including the use of trait-based approaches. We identify a need for new approaches to quantify resistance and resilience of soil microbial communities, and to identify thresholds for transitions to alternative states. We show how high-resolution time series coupled with gradient designs will enable detecting response patterns to interacting drivers. Finally, to account for extrinsic factors, we suggest that future studies should use environmental gradients to track soil microbial community responses to climate extremes in space and time. This article is part of the theme issue ‘Climate change and ecosystems: threats, opportunities and solutions’.

scholarly journals Stressor interactions under differential exogenous microbial exposure in Daphnia magna_version2

2021 ◽  
Author(s):  
Shira Houwenhuyse ◽  
Lore Bulteel ◽  
Naina Goel ◽  
Isabel Vanoverberghe ◽  
Ellen Decaestecker
Keyword(s):  
Body Size ◽  
Microbial Community ◽  
Microbial Communities ◽  
Stress Responses ◽  
Multiple Stressors ◽  
Natural Environments ◽  
Laboratory Setting ◽  
Natural Conditions ◽  
Aspergillus Aculeatus ◽  
Diverse Microbial Community

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory setting often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated how stressor responses differed between laboratory and natural conditions in Daphnia magna when exposed to single or multiple stressors. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows that natural environments have a more diverse microbial community compared with laboratory conditions, which was ultimately reflected in the gut microbiomes after inoculation. Stressor responses in Daphnia were affected by their bacterial environment for survival, but not for fecundity and body size. Fecuntiy and body size did show a main stressor effect, which could possibly be linked with stessor-specific microbiomes (for Microcystis and the combined stressor treatment). In addition, genotype-specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.

scholarly journals MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways

2021 ◽  
Vol 22 (20) ◽  
pp. 10992
Author(s):  
Daniel Walke ◽  
Kay Schallert ◽  
Prasanna Ramesh ◽  
Dirk Benndorf ◽  
Emanuel Lange ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Web Application ◽  
Functional Characterization ◽  
Single Species ◽  
Central Carbon Metabolism ◽  
Biological Pathways ◽  
Community Data ◽  
Set Up ◽  
User Friendly

Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versality of microbial metabolism and a still-increasing number of newly biological pathways, linkage to standard pathway maps such as the KEGG central carbon metabolism is often problematic. We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called ‘Pathway-Creator’ and ‘Pathway-Calculator’. The ‘Pathway-Creator’ enables an easy set-up of user-defined pathways with specific taxonomic constraints. The ‘Pathway-Calculator’ automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. The MPA_Pathway_Tool is implemented in Java and ReactJS.

Mathematical model of determining the index of fractal structures for estimating efficiency of probiotic fodder additives for microbiotes of the gut intestin

2020 ◽  
Vol 1 (4) ◽  
pp. 22-30
Author(s):  
N. I. Vorob'ev ◽  
◽  
I. N. Nikonov ◽  
M. V. Selina ◽  
◽  
...  
Keyword(s):  
Mathematical Model ◽  
Microbial Community ◽  
Microbial Communities ◽  
Feed Additives ◽  
The Self ◽  
Lactobacillus Fermentum ◽  
Self Organization ◽  
Fractal Structures

The work is devoted to the study of the self-organization of microbial communities in the intestines of chickens in different conditions of keeping and feeding chickens and the development on this basis of a mathematical model for determining the index of fractal structures to assess the effectiveness of probiotic feed additives on the microbiota of the intestines of chickens. The experience with chicken diets showed that the level of self-organization of microbial communities in the intestines of chickens depends on the probiotics used. The best indicator of the organization of the microbial community is the experimental version with a probiotic based on Lactobacillus fermentum. It was shown that the index values of the fractal structures of microbial communities in the intestines of chickens when using various probiotic preparations for different experimental schemes are as follows: OP1 – 0,292; OP1 + Probiotic 1 – 0,286; OP1 + Probiotic 2 – 0,354 and the developed mathematical model can be used to evaluate the effectiveness of probiotic feed additives on the microbiota of chicken intestines.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

Research on Dynamic Balance Method of Precision Centrifuge

2014 ◽  
Vol 945-949 ◽  
pp. 777-780
Author(s):  
Tao Liu ◽  
Yong Xu ◽  
Bo Yuan Mao
Keyword(s):  
Mathematical Model ◽  
Balance Control ◽  
Dynamic Balance ◽  
Dynamic Balancing ◽  
Structure Characteristics ◽  
Balance System ◽  
Simulation Results ◽  
Set Up ◽  
System Controller ◽  
The Mathematical Model

Firstly, according to the structure characteristics of precision centrifuge, the mathematical model of its dynamic balancing system was set up, and the dynamic balancing scheme of double test surfaces, double emendation surfaces were established. Then the dynamic balance system controller of precision centrifuge was designed. Simulation results show that the controller designed can completely meet the requirements of precision centrifuge dynamic balance control system.

scholarly journals The role of macrophage polarization and associated mechanisms in regulating the anti-inflammatory action of acupuncture: a literature review and perspectives

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jiaqi Wang ◽  
Shanshan Lu ◽  
Fuming Yang ◽  
Yi Guo ◽  
Zelin Chen ◽  
...  
Keyword(s):  
Macrophage Polarization ◽  
Scientific Basis ◽  
M2 Macrophage ◽  
Extrinsic Factors ◽  
Therapeutic Goals ◽  
Tissue Microenvironment ◽  
Inflammatory Conditions ◽  
Cytokine Levels ◽  
Anti Inflammatory ◽  
Inflammatory Action

AbstractAcupuncture is used in the treatment of a variety of inflammatory conditions and diseases. However, the mechanisms of its anti-inflammatory action are complex and have not been systematically investigated. Macrophages are key components of the innate immune system, thus, balancing the M1/M2 macrophage ratio and modulating cytokine levels in the inflammatory environment may be desirable therapeutic goals. Evidence has shown that acupuncture has anti-inflammatory actions that affect multiple body systems, including the immune, locomotory, endocrine, nervous, digestive, and respiratory systems, by downregulating pro-inflammatory M1 and upregulating anti-inflammatory M2 macrophages, as well as by modulating associated cytokine secretion. Macrophage polarization is controlled by the interlocking pathways of extrinsic factors, the local tissue microenvironment, and the neural-endocrine-immune systems. It has been suggested that polarization of T lymphocytes and cytokine secretions resulting in modulation of the autonomic nervous system and the hypothalamic–pituitary–adrenal axis, may be upstream mechanisms of acupuncture-induced macrophage polarization. We further propose that macrophage polarization could be the principal pathway involved in acupuncture immune regulation and provide the scientific basis for the clinical application of acupuncture in inflammatory conditions.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

scholarly journals Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil System ◽  
Soil Microbial ◽  
Total Soil ◽  
Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

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