scholarly journals Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles

2020 ◽  
Author(s):  
Antoni Luque ◽  
Cynthia Silveira
Keyword(s):  
Microbial Communities ◽  
Meta Analysis ◽  
Community Diversity ◽  
Biophysical Model ◽  
Environmental Drivers ◽  
Lambda Phage ◽  
Human Gut ◽  
Poor Growth ◽  
Phage Adsorption ◽  
Adsorption Rates

AbstractTemperate phages can integrate in their bacterial host genome to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbial-dense environment of the mammalian-gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored in microbial communities with low densities. Here we hypothesized that phage coinfections—the most studied molecular mechanism of lysogeny in lambda phage—increases at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection and stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from marine and gut microbiomes. Based on lambda experiments, a Poisson process assessed the probability of lysogeny via coinfection in these ecosystems. In 90% of the sampled marine ecosystems, lysogeny stayed below 10% of the bacterial community. In contrast, 25% of the sampled gut communities stayed above 25% of lysogeny, representing an estimated nine trillion lysogens formed via phage coinfection in the human gut every day. The prevalence of lysogeny in the gut was a consequence of the higher densities and faster adsorption rates. In marine communities, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitments times. Our study suggests that physical mechanisms can favor coinfection and cause lysogeny at poor growth conditions (long commitment times) and in rich environments (high densities and adsorption rates).ImportancePhage integration in bacterial genomes manipulate microbial dynamics from the oceans to the human gut. This phage-bacteria interaction, called lysogeny, is well-studied in laboratory models, but its environmental drivers remain unclear. Here we quantified the frequency of lysogeny via phage coinfection—the most studied mechanism of lysogeny—by developing a biophysical model that incorporated a meta-analysis of the properties of marine and gut microbiomes. Lysogeny was found to be more frequent in high-productive environments like the gut, due to higher phage and bacterial densities and faster phage adsorption rates. At low cell densities, lysogeny via coinfection was possible for hosts with long duplication times. Our research bridges the molecular understanding of lysogeny with the ecology of complex microbial communities.

scholarly journals Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Antoni Luque ◽  
Cynthia B. Silveira
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Biophysical Model ◽  
Environmental Drivers ◽  
Microbial Dynamics ◽  
Human Gut ◽  
Phage Adsorption ◽  
Cell Densities ◽  
Adsorption Rates ◽  
Laboratory Models

The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.

scholarly journals Influence of pig farming on human Gut Microbiota: role of airborne microbial communities

Gut Microbes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 1-13
Author(s):  
Julia Moor ◽  
Tsering Wüthrich ◽  
Suzanne Aebi ◽  
Nadezda Mostacci ◽  
Gudrun Overesch ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Pig Farming

scholarly journals The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities

2019 ◽  
Vol 9 ◽  
Author(s):  
Jennifer D. Rocca ◽  
Marie Simonin ◽  
Joanna R. Blaszczak ◽  
Jessica G. Ernakovich ◽  
Sean M. Gibbons ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Meta Analysis ◽  
Environmental Stressors

scholarly journals Systematic review and meta-analysis of 50 years of coral disease research visualized through the scope of network theory

2018 ◽  
Author(s):  
Luis M. Montilla ◽  
Alfredo Ascanio ◽  
Alejandra Verde ◽  
Aldo Croquer
Keyword(s):  
Research Effort ◽  
Coral Disease ◽  
Meta Analysis ◽  
Limited Range ◽  
Environmental Drivers ◽  
Network Nodes ◽  
Host Genus ◽  
Disease Research ◽  
Multiple Processes ◽  
Black Band

AbstractCoral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. To gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: 1) studied disease(s); 2) host genus; 3) marine ecoregion(s) associated with the study site; and 4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g. bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research.

scholarly journals Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Isabelle Laforest-Lapointe ◽  
Marie-Claire Arrieta
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput Sequencing ◽  
Sequencing Technology ◽  
Human Gut ◽  
Microbial Eukaryotes ◽  
Host Health ◽  
High Level ◽  
Eukaryotic Organisms ◽  
New Evidence

ABSTRACTHuman-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

scholarly journals Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e62578 ◽  
Author(s):  
Lukasz Krych ◽  
Camilla H. F. Hansen ◽  
Axel K. Hansen ◽  
Frans W. J. van den Berg ◽  
Dennis S. Nielsen
Keyword(s):  
Gut Microbiome ◽  
Meta Analysis ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis

2021 ◽  
Vol 146 ◽  
pp. 106234
Author(s):  
Maria Luíza S. Suhadolnik ◽  
Patrícia S. Costa ◽  
Giovanni M. Castro ◽  
Francisco P. Lobo ◽  
Andréa M.A. Nascimento
Keyword(s):  
Meta Analysis ◽  
Environmental Drivers ◽  
Iron Redox

scholarly journals Outlier Detection for Minor Compositional Variations in Taxonomic Abundance Data

2019 ◽  
Vol 9 (7) ◽  
pp. 1355
Author(s):  
Koji Ishiya ◽  
Sachiyo Aburatani
Keyword(s):  
Microbial Communities ◽  
Natural Environments ◽  
Human Gut ◽  
Short Term ◽  
Computational Framework ◽  
Dietary Changes ◽  
Compositional Changes ◽  
Compositional Variations ◽  
Living Organisms ◽  
Shed Light

To understand the activities of complex microbial communities in various natural environments and living organisms, we need to capture the compositional changes in their taxonomic abundance. Here, we propose a new computational framework to detect compositional changes in microorganisms, including minor bacteria. This framework is designed to statistically assess relative variations in taxonomic abundance. By using this approach, we detected compositional changes in the human gut microbiome that might be associated with short-term human dietary changes. Our approach can shed light on the compositional changes of minor microorganisms that are easily overlooked.

scholarly journals New View on Dietary Fiber Selection for Predictable Shifts in Gut Microbiota

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
T. M. Cantu-Jungles ◽  
B. R. Hamaker
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Dietary Fiber ◽  
Physical Characteristics ◽  
Dietary Fibers ◽  
Human Gut ◽  
Microbial Composition ◽  
Human Gut Microbiota ◽  
Selection For ◽  
Fiber Selection

ABSTRACT Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate. The use of such fibers as prebiotics targeted to specific microbes would result in predictable shifts independent of the background microbial composition.

scholarly journals Titanium Dioxide Nanoparticles Elicit Lower Direct Inhibitory Effect on Human Gut Microbiota Than Silver Nanoparticles

2019 ◽  
Vol 172 (2) ◽  
pp. 411-416 ◽  
Author(s):  
Richard T Agans ◽  
Alex Gordon ◽  
Saber Hussain ◽  
Oleg Paliy
Keyword(s):  
Silver Nanoparticles ◽  
Titanium Dioxide ◽  
Gut Microbiota ◽  
Titanium Dioxide Nanoparticles ◽  
Close Association ◽  
Community Diversity ◽  
Bacterial Cells ◽  
Human Gut ◽  
Human Gut Microbiota

Abstract Due to continued technological development, people increasingly come in contact with engineered nanomaterials (ENMs) that are now used in foods and many industrial applications. Many ENMs have historically been shown to possess antimicrobial properties, which has sparked concern for how dietary nanomaterials impact gastrointestinal health via microbial dysbiosis. We employed an in vitro Human Gut Simulator system to examine interactions of dietary nano titanium dioxide (TiO2) with human gut microbiota. Electron microscopy indicated a close association of TiO2 particles with bacterial cells. Addition of TiO2 to microbial communities led to a modest reduction in community density but had no impact on community diversity and evenness. In contrast, administration of known antimicrobial silver nanoparticles (NPs) in a control experiment resulted in a drastic reduction of population density. In both cases, communities recovered once the addition of nanomaterials was ceased. Constrained ordination analysis of community profiles revealed that simulated colonic region was the primary determinant of microbiota composition. Accordingly, predicted community functional capacity and measured production of short-chain fatty acids were not changed significantly upon microbiota exposure to TiO2. We conclude that tested TiO2 NPs have limited direct effect on human gut microbiota.

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