scholarly journals Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 602
Author(s):  
Baltasar Mayo ◽  
Javier Rodríguez ◽  
Lucía Vázquez ◽  
Ana Belén Flórez
Keyword(s):  
Microbial Communities ◽  
Abiotic Factors ◽  
Microbial Interactions ◽  
Competitive Interactions ◽  
Quality And Safety ◽  
Improve Quality ◽  
Basic Principles ◽  
Functional Consequences ◽  
Experimental Use ◽  
Synthetic Microbial Communities

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of “synthetic” microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

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.

scholarly journals Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales

2018 ◽  
Vol 115 (28) ◽  
pp. E6585-E6594 ◽  
Author(s):  
Mikayla A. Borton ◽  
David W. Hoyt ◽  
Simon Roux ◽  
Rebecca A. Daly ◽  
Susan A. Welch ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Management Practices ◽  
The United States ◽  
Microbial Interactions ◽  
Competitive Interactions ◽  
Industrial Processes ◽  
Laboratory Findings ◽  
Microbial Ecosystem ◽  
Field Investigations

Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth’s surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show thatHalanaerobium,Geotoga, andMethanohalophilusstrain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.

scholarly journals The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

2018 ◽  
Vol 35 (13) ◽  
pp. 2332-2334 ◽  
Author(s):  
Federico Baldini ◽  
Almut Heinken ◽  
Laurent Heirendt ◽  
Stefania Magnusdottir ◽  
Ronan M T Fleming ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Genome ◽  
Metagenomic Data ◽  
Metabolic Interactions ◽  
Constraint Based Modeling ◽  
Genome Scale

Abstract Motivation The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes. Results To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox. Availability and implementation The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

scholarly journals Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

2022 ◽  
Author(s):  
Gayathri Sambamoorthy ◽  
Karthik Raman
Keyword(s):  
Microbial Communities ◽  
In Silico ◽  
Microbial Interactions ◽  
Interaction Patterns ◽  
Wild Type ◽  
Community Function ◽  
Evolutionary Forces ◽  
In Silico Studies ◽  
Wide Range ◽  
In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions

2018 ◽  
Vol 54 (3) ◽  
pp. 363-372 ◽  
Author(s):  
Xingang Zhou ◽  
Jianhui Zhang ◽  
Dandan Pan ◽  
Xin Ge ◽  
Xue Jin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Interactions

Competition between native and non-native plants.

2020 ◽  
pp. 291-307
Author(s):  
Elizabeth M. Wandrag ◽  
◽  
Jane A. Catford ◽  
◽  
◽  
...  
Keyword(s):  
Plant Species ◽  
Plant Communities ◽  
Native Species ◽  
Abiotic Factors ◽  
Invasion Biology ◽  
Competitive Interactions ◽  
Native Plant ◽  
Native Plant Species ◽  
New Locations ◽  
Strength Of Competition

The introduction of species to new locations leads to novel competitive interactions between resident native and newly-arriving non-native species. The nature of these competitive interactions can influence the suitability of the environment for the survival, reproduction and spread of non-native plant species, and the impact those species have on native plant communities. Indeed, the large literature on competition among plants reflects its importance in shaping the composition of plant communities, including the invasion success of non-native species. While competition and invasion theory have historically developed in parallel, the increasing recognition of the synergism between the two themes has led to new insights into how non-native plant species invade native plant communities, and the impacts they have on those plant communities. This chapter provides an entry point into the aspects of competition theory that can help explain the success, dominance and impacts of invasive species. It focuses on resource competition, which arises wherever the resources necessary for establishment, survival, reproduction and spread are in limited supply. It highlights key hypotheses developed in invasion biology that relate to ideas of competition, outlines biotic and abiotic factors that influence the strength of competition and species' relative competitive abilities, and describes when and how competition between non-native and native plant species can influence invasion outcomes. Understanding the processes that influence the strength of competition between non-native and native plant species is a necessary step towards understanding the causes and consequences of biological invasions.

Agency Action: Introducing Control and Flexibility

2020 ◽  
pp. 137-146
Author(s):  
Stephen J. Swensen ◽  
Tait D. Shanafelt
Keyword(s):  
Health Care Professionals ◽  
Quality And Safety ◽  
Improve Quality ◽  
Flexible Work ◽  
Standard Work ◽  
Collaborative Environment ◽  
Degree Of Control ◽  
Good For ◽  
Agency Action ◽  
Mental And Physical Health

There is a healthy tension between standard work, which is controlled, and flexible work. Standardization of processes that improve quality and safety is good for patients. Flexible work in other areas is good for employees’ mental and physical health. Executed properly, standard and flexible work can be complementary. In a collaborative environment, leaders and organizations create increased flexibility for health care professionals when they focus more on outcomes than on specific processes. How decisions are made at all levels of the organization substantially determines the degree of control and flexibility in the workplace.

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