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 Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools

2020 ◽  
Vol 21 (4) ◽  
pp. 240-252 ◽  
Author(s):  
Gislaine Fongaro ◽  
Guilherme Augusto Maia ◽  
Paula Rogovski ◽  
Rafael Dorighello Cadamuro ◽  
Joana Camila Lopes ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Hydrothermal Vents ◽  
High Salinity ◽  
Soda Lakes ◽  
Natural Environments ◽  
Ph Conditions ◽  
Extremophile Microorganism ◽  
Shed Light

: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.

scholarly journals Multi-omic Characterization of Intraspecies Variation in Laboratory and Natural Environments

mSystems ◽  
2021 ◽  
Vol 6 (4) ◽  
Author(s):  
Megan G. Behringer
Keyword(s):  
Microbial Communities ◽  
Ecosystem Function ◽  
Interspecific Variation ◽  
Natural Environments ◽  
Species Relationships ◽  
Human Gut ◽  
Intraspecies Variation ◽  
Subglacial Lake

Investigation of microbial communities has led to many advances in our understanding of ecosystem function, whether that ecosystem is a subglacial lake or the human gut. Within these communities, much emphasis has been placed on interspecific variation and between-species relationships.

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 Deconstruction of Lignin: From Enzymes to Microorganisms

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2299
Author(s):  
Jéssica P. Silva ◽  
Alonso R. P. Ticona ◽  
Pedro R. V. Hamann ◽  
Betania F. Quirino ◽  
Eliane F. Noronha
Keyword(s):  
Microbial Communities ◽  
Metabolic Pathways ◽  
Low Cost ◽  
Direct Analysis ◽  
Industrial Applications ◽  
Natural Environments ◽  
Lignocellulosic Residues ◽  
Complementary Techniques ◽  
Plant Polymer ◽  
Powerful Strategy

Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.

scholarly journals Enhancing Nature Connection and Positive Affect in Children through Mindful Engagement with Natural Environments

2021 ◽  
Vol 18 (9) ◽  
pp. 4785
Author(s):  
Alexia Barrable ◽  
David Booth ◽  
Dylan Adams ◽  
Gary Beauchamp
Keyword(s):  
Negative Affect ◽  
Positive Affect ◽  
Positive Relationship ◽  
Nature Reserve ◽  
Empirical Studies ◽  
Medium Effect ◽  
Natural Environments ◽  
Short Term ◽  
Nature Connection ◽  
Mindful Engagement

Nature connection, which describes a positive relationship between humans and the rest of nature, has been recognised as a worthwhile goal of all education. Given its association with wellbeing, as well as the fact that it can predict ecological behaviours in children, there have been several calls for it to become central to environmental education, and an important tool in tackling climate change. Previous research has reported the success of short-term interventions in increasing nature connection in children, but to date no empirical studies have looked at how mindful engagement with nature can promote both nature connection and positive affect. This study took place in a nature reserve in Wales and included n = 74 children, aged 9–10, who took part in three mindful activities. Pre- and post- measures included nature connection and positive/negative affect. Analysis showed a significant small to medium effect of the activity on nature connection. Moreover, positive affect significantly increased post-activity, while negative affect showed a small decrease.

scholarly journals Applying ecological resistance and resilience to dissect bacterial antibiotic responses

2018 ◽  
Vol 4 (12) ◽  
pp. eaau1873 ◽  
Author(s):  
Hannah R. Meredith ◽  
Virgile Andreani ◽  
Helena R. Ma ◽  
Allison J. Lopatkin ◽  
Anna J. Lee ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Antibiotic Treatment ◽  
Bacterial Pathogens ◽  
Ecological Systems ◽  
Essential Property ◽  
Short Term ◽  
Bacterial Response ◽  
Ecological Resistance ◽  
Combination Treatments ◽  
Lactam Antibiotic

An essential property of microbial communities is the ability to survive a disturbance. Survival can be achieved through resistance, the ability to absorb effects of a disturbance without a notable change, or resilience, the ability to recover after being perturbed by a disturbance. These concepts have long been applied to the analysis of ecological systems, although their interpretations are often subject to debate. Here, we show that this framework readily lends itself to the dissection of the bacterial response to antibiotic treatment, where both terms can be unambiguously defined. The ability to tolerate the antibiotic treatment in the short term corresponds to resistance, which primarily depends on traits associated with individual cells. In contrast, the ability to recover after being perturbed by an antibiotic corresponds to resilience, which primarily depends on traits associated with the population. This framework effectively reveals the phenotypic signatures of bacterial pathogens expressing extended-spectrum β-lactamases (ESBLs) when treated by a β-lactam antibiotic. Our analysis has implications for optimizing treatment of these pathogens using a combination of a β-lactam and a β-lactamase (Bla) inhibitor. In particular, our results underscore the need to dynamically optimize combination treatments based on the quantitative features of the bacterial response to the antibiotic or the Bla inhibitor.

scholarly journals Report on the 3rd International Conference on Flood Recovery, Innovation and Response (FRIAR) 2012

2012 ◽  
Vol 43 (3) ◽  
Author(s):  
Daniele De Wrachien ◽  
David Proverbs
Keyword(s):  
Natural Disasters ◽  
Discharge Capacity ◽  
Heavy Precipitation ◽  
Flood Damage ◽  
Economic Losses ◽  
Natural Environments ◽  
Short Term ◽  
Loss Of Life ◽  
International Conference ◽  
Semiarid Areas

The terms flood or flooding are often used in different ways. According to the International Commission on Irrigation and Drainage (ICID), <em>flooding is defined as the overflowing or failing of the normal confines of a river, stream, lake, canal, sea or accumulation of water as a result of heavy precipitation where drains are lacking or their discharge capacity is exceeded</em>. The occurrence of floods is the most frequent amongst all natural disasters. Although flooding is a serious hazard in humid regions, it can also be devastating in semiarid areas, where high rates of runoff following storms produce widespread flood damage down valley. These hazards involve tragic loss of life, damage to buildings and natural environments, and massive short-term disruption to the lives of the affected population. One-third of the annual natural disasters and economic losses, and more than half of the respective victims are flood-related.

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 Rewetting of Three Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes Through Environmental Filtering

2019 ◽  
Author(s):  
Micha Weil ◽  
Haitao Wang ◽  
Mia Bengtsson ◽  
Daniel Köhn ◽  
Anke Günther ◽  
...  
Keyword(s):  
Community Composition ◽  
Ecosystem Respiration ◽  
Abiotic Factors ◽  
Environmental Filtering ◽  
Network Analyses ◽  
Respiration Rates ◽  
Control Community ◽  
Methane Fluxes ◽  
Compositional Changes ◽  
Shed Light

AbstractDrained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are biotic and abiotic factors that control community composition.We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent rewetting. Also, abiotic soil properties including moisture, dissolved organic matter, methane fluxes and ecosystem respiration rates.The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundance of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses we identified soil moisture as major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than tenfold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering.

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

2021 ◽  
Author(s):  
Shira Houwenhuyse ◽  
Lore Bulteel ◽  
Naina Goel ◽  
Isabel Vanoverberghe ◽  
Ellen Decaestecker
Keyword(s):  
Body Size ◽  
Microbial Communities ◽  
Daphnia Magna ◽  
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.

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