scholarly journals In vitrocommunity synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

2018 ◽  
Author(s):  
Jakob Herschend ◽  
Klaus Koren ◽  
Henriette L. Røder ◽  
Asker Brejnrod ◽  
Michael Kühl ◽  
...  

AbstractComposition and development of naturally occurring microbial communities is defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause community synergies where the community is able to outperform it single species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here we show how pH stabilisation of the environment through the metabolic activity of specific community members acts as a positive inter-species interaction drivingin vitrocommunity synergy in a model consortium of four co-isolated soil bacteria:Microbacterium oxydans,Xanthomonas retroflexus,Stenotrophomonas rhizophilaandPaenibacillus amylolyticus. Using micro-sensor pH measurements to show how individual species change the local pH micro-environment, and how co-cultivation leads to a stabilised pH regime over time. Specifically,in vitroacid production fromPaenibacillus amylolyticusand alkali production primarily fromXanthomonas retroflexuslead to an overall pH stabilisation of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on media type and media concentration, however similar pH drift from the individual species could be observed across media variants.ImportanceWe show thatin vitrometabolic activity of individual members of a synthetic, co- isolated model community presenting community synergistic growth arises through the inter-species interaction of pH stabilization of the community micro-environment. The observed inter-species interaction is highly media specific and most pronounced under high nutrient availability. This adds to the growing diversity of identified community interactions leading to enhanced community growth.

2018 ◽  
Vol 84 (21) ◽  
Author(s):  
Jakob Herschend ◽  
Klaus Koren ◽  
Henriette L. Røder ◽  
Asker Brejnrod ◽  
Michael Kühl ◽  
...  

ABSTRACTThe composition and development of naturally occurring microbial communities are defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause synergies, where the community is able to outperform its single-species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here, we show how opposite pH drift induced by specific community members leads to pH stabilization of the microenvironment, acting as a positive interspecies interaction, drivingin vitrocommunity synergy in a model consortium of four coisolated soil bacteria,Microbacterium oxydans,Xanthomonas retroflexus,Stenotrophomonas rhizophila, andPaenibacillus amylolyticus. We use microsensor pH measurements to show how individual species change the local pH microenvironment and how cocultivation leads to a stabilized pH regime over time. Specifically,in vitroacid production fromP. amylolyticusand alkali production primarily fromX. retroflexusled to an overall pH stabilization of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on medium type and concentration; however, similar pH drift from the individual species could be observed across medium variants.IMPORTANCEUnderstanding interspecies interactions in bacterial communities is important for unraveling species dynamics in naturally occurring communities. These dynamics are fundamental for identifying evolutionary drivers and for the development of efficient biotechnological industry applications. Recently, pH interplay among community members has been identified as a factor affecting community development, and pH stabilization has been demonstrated to result in enhanced community growth. The use of model communities in which the effect of changing pH level can be attributed to specific species contributes to the investigation of community developmental drivers. This contributes to assessment of the extent of emergent behavior and members' contributions to community development. Here, we show that pH stabilization of the microenvironmentin vitroin a synthetic coisolated model community results in synergistic growth. This observation adds to the growing diversity of community interactions leading to enhanced community growth and hints toward pH as a strong driver for community development in diverse environments.


2020 ◽  
Author(s):  
Jack Hassall ◽  
Meera Unnikrishnan

AbstractInteractions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro tools to monitor community responses to pathogens at a single-species level. We have developed a multi-species community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a qPCR-based approach. Introduction of the major nosocomial gut pathogen, Clostridiodes difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp in prevention of C. difficile colonisation. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community.


Author(s):  
Joana Castro ◽  
Ângela Lima ◽  
Lúcia G. V. Sousa ◽  
Aliona S. Rosca ◽  
Christina A. Muzny ◽  
...  

Bacterial Vaginosis (BV) involves the presence of a multi-species biofilm adhered to vaginal epithelial cells, but its in-depth study has been limited due to the complexity of the bacterial community, which makes the design of in vitro models challenging. Perhaps the most common experimental technique to quantify biofilms is the crystal violet (CV) staining method. Despite its widespread utilization, the CV method is not without flaws. While biofilm CV quantification within the same strain in different conditions is normally accepted, assessing multi-species biofilms formation by CV staining might provide significant bias. For BV research, determining possible synergism or antagonism between species is a fundamental step for assessing the roles of individual species in BV development. Herein, we provide our perspective on how CV fails to properly quantify an in vitro triple-species biofilm composed of Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, and Prevotella bivia, three common BV-associated bacteria thought to play key roles in incident BV pathogenesis. We compared the CV method with total colony forming units (CFU) and fluorescence microscopy cell count methods. Not surprisingly, when comparing single-species biofilms, the relationship between biofilm biomass, total number of cells, and total cultivable cells was very different between each tested method, and also varied with the time of incubation. Thus, despite its wide utilization for single-species biofilm quantification, the CV method should not be considered for accurate quantification of multi-species biofilms in BV pathogenesis research.


Author(s):  
Bettina Thalinger ◽  
Kristy Deiner ◽  
Lynsey R. Harper ◽  
Helen C. Rees ◽  
Rosetta C. Blackman ◽  
...  

AbstractThe use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to interpretation of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Their general applicability, uncertainties and limitations often remain undetermined. The absence of clear guidelines prevents targeted eDNA assays from being incorporated into species monitoring and policy, thus their establishment will be key for the future implementation of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, such as “in silico analysis”, and arranged on a 5-level validation scale from “incomplete” to “operational”. Additionally, minimum validation criteria were defined for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. The majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The total number of reported variables ranged from 20% to 76% and deviated both between and within levels. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.


2019 ◽  
Author(s):  
Wenfa Ng

Microbes play important roles in human health and disease either as individual species or as a consortium. While medical microbiology has traditionally associated a single species with a specific disease, recent knowledge of the diversity of microbes present at different sites of the body has opened our eyes to the dynamic interactions between species, and how community interactions amongst microbes could potentiate disease. More importantly, clinical manifestations of disease symptoms have been hypothesized to arise from cross-interactions between metabolites and signalling molecules secreted by microbes not in direct communication with each other. Such myriad and entangled interactions raise important questions on clinicians and researchers’ quest to understand the aetiologies of disease and underpinnings of their progression. Doing so require profiling the microbes present and their community structure, to which mass spectrometry metabolomics could lend a lens. Nevertheless, how do we associate specific diseases to one or two microbiome which may be at different body sites? Do we have the analytical and bioinformatic toolkit to do so? A review paper in Nature (“Microbiome-wide association studies link dynamic microbial consortia to disease”) seek to illuminate this question. But from the clinical perspective, is associating a microbiome to a specific disease useful, particularly for multifactorial diseases such as metabolic syndrome? To a limited extent, the answer is yes, for it provides an initial direction towards understanding the molecular mechanisms at play in disease manifestations as well as the complex interplay between microbe and host in pathological processes. At a deeper level, however, dynamic changes in microbiome community composition and structure with changing environmental conditions and host physiology meant that tracing the specific steps important to disease processes might be more fruitfully accomplished through the bottom-up approach rather than the top-down methodology inherent in microbiome profiling. Specifically, sets of molecular processes are likely impacted in complex diseases which translate to dysfunctional enzymes, or metabolic pathways and signalling cascades in overdrive. Teasing the complex web of metabolic cum signalling pathways apart in seeking to understand the specific molecular effectors important in disease necessitates a combination of molecular biology and biochemistry techniques coupled with contemporary discovery tools in omics. Such information would provide downstream leads for therapeutic development, which microbiome-wide association studies lend a first pointer. Collectively, associating a microbiome to specific disease states provide a list of candidate microbes that could be aetiological agents of disease, from which further biochemical and molecular biology investigations would uncover the underlying disease mechanisms.


mSphere ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Jack Hassall ◽  
Jeffrey K. J. Cheng ◽  
Meera Unnikrishnan

ABSTRACT Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro models to monitor community responses to pathogens at a single-species level. We have developed a multispecies community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a quantitative PCR (qPCR)-based approach. Introduction of the major nosocomial gut pathogen, Clostridioides difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp. in prevention of C. difficile colonization. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community. IMPORTANCE Studying interactions between bacterial species that reside in the human gut is crucial for gaining a better insight into how they provide protection from pathogen colonization. In vitro models of multispecies bacterial communities wherein behaviors of single species can be accurately tracked are key to such studies. Here, we have developed a synthetic, trackable, gut microbiota community which reduces growth of the human gut pathogen Clostridioides difficile. We report that Bacteroides spp. within this community respond by multiplying in the presence of this pathogen, resulting in reduction of C. difficile growth. Defined in vitro communities that can be tailored to include different species are well suited to functional genomic approaches and are valuable tools for understanding interbacterial interactions.


2019 ◽  
Author(s):  
Wenfa Ng

Microbes play important roles in human health and disease either as individual species or as a consortium. While medical microbiology has traditionally associated a single species with a specific disease, recent knowledge of the diversity of microbes present at different sites of the body has opened our eyes to the dynamic interactions between species, and how community interactions amongst microbes could potentiate disease. More importantly, clinical manifestations of disease symptoms have been hypothesized to arise from cross-interactions between metabolites and signalling molecules secreted by microbes not in direct communication with each other. Such myriad and entangled interactions raise important questions on clinicians and researchers’ quest to understand the aetiologies of disease and underpinnings of their progression. Doing so require profiling the microbes present and their community structure, to which mass spectrometry metabolomics could lend a lens. Nevertheless, how do we associate specific diseases to one or two microbiome which may be at different body sites? Do we have the analytical and bioinformatic toolkit to do so? A review paper in Nature (“Microbiome-wide association studies link dynamic microbial consortia to disease”) seek to illuminate this question. But from the clinical perspective, is associating a microbiome to a specific disease useful, particularly for multifactorial diseases such as metabolic syndrome? To a limited extent, the answer is yes, for it provides an initial direction towards understanding the molecular mechanisms at play in disease manifestations as well as the complex interplay between microbe and host in pathological processes. At a deeper level, however, dynamic changes in microbiome community composition and structure with changing environmental conditions and host physiology meant that tracing the specific steps important to disease processes might be more fruitfully accomplished through the bottom-up approach rather than the top-down methodology inherent in microbiome profiling. Specifically, sets of molecular processes are likely impacted in complex diseases which translate to dysfunctional enzymes, or metabolic pathways and signalling cascades in overdrive. Teasing the complex web of metabolic cum signalling pathways apart in seeking to understand the specific molecular effectors important in disease necessitates a combination of molecular biology and biochemistry techniques coupled with contemporary discovery tools in omics. Such information would provide downstream leads for therapeutic development, which microbiome-wide association studies lend a first pointer. Collectively, associating a microbiome to specific disease states provide a list of candidate microbes that could be aetiological agents of disease, from which further biochemical and molecular biology investigations would uncover the underlying disease mechanisms.


Author(s):  
Mary Beth Downs ◽  
Wilson Ribot ◽  
Joseph W. Farchaus

Many bacteria possess surface layers (S-layers) that consist of a two-dimensional protein lattice external to the cell envelope. These S-layer arrays are usually composed of a single species of protein or glycoprotein and are not covalently linked to the underlying cell wall. When removed from the cell, S-layer proteins often reassemble into a lattice identical to that found on the cell, even without supporting cell wall fragments. S-layers exist at the interface between the cell and its environment and probably serve as molecular sieves that exclude destructive macromolecules while allowing passage of small nutrients and secreted proteins. Some S-layers are refractory to ingestion by macrophages and, generally, bacteria are more virulent when S-layers are present.When grown in rich medium under aerobic conditions, B. anthracis strain Delta Sterne-1 secretes large amounts of a proteinaceous extractable antigen 1 (EA1) into the growth medium. Immunocytochemistry with rabbit polyclonal anti-EAl antibody made against the secreted protein and gold-conjugated goat anti-rabbit IgG showed that EAI was localized at the cell surface (fig 1), which suggests its role as an S-layer protein.


1993 ◽  
Vol 69 (01) ◽  
pp. 021-024 ◽  
Author(s):  
Shawn Tinlin ◽  
Sandra Webster ◽  
Alan R Giles

SummaryThe development of inhibitors to factor VIII in patients with haemophilia A remains as a serious complication of replacement therapy. An apparently analogous condition has been described in a canine model of haemophilia A (Giles et al., Blood 1984; 63:451). These animals and their relatives have now been followed for 10 years. The observation that the propensity for inhibitor development was not related to the ancestral factor VIII gene has been confirmed by the demonstration of vertical transmission through three generations of the segment of the family related to a normal (non-carrier) female that was introduced for breeding purposes. Haemophilic animals unrelated to this animal have not developed functionally significant factor VIII inhibitors despite intensive factor VIII replacement. Two animals have shown occasional laboratory evidence of factor VIII inhibition but this has not been translated into clinical significant inhibition in vivo as assessed by clinical response and F.VIII recovery and survival characteristics. Substantial heterogeneity of inhibitor expression both in vitro and in vivo has been observed between animals and in individual animals over time. Spontaneous loss of inhibitors has been observed without any therapies designed to induce tolerance, etc., being instituted. There is also phenotypic evidence of polyclonality of the immune response with variable expression over time in a given animal. These observations may have relevance to the human condition both in determining the pathogenetic factors involved in this condition and in highlighting the heterogeneity of its expression which suggests the need for caution in the interpretation of the outcome of interventions designed to modulate inhibitor activity.


Author(s):  
О.В. Шамова ◽  
М.С. Жаркова ◽  
П.М. Копейкин ◽  
Д.С. Орлов ◽  
Е.А. Корнева

Антимикробные пептиды (АМП) системы врожденного иммунитета - соединения, играющие важную роль в патогенезе инфекционных заболеваний, так как обладают свойством инактивировать широкий спектр патогенных бактерий, обеспечивая противомикробную защиту живых организмов. В настоящее время АМП рассматриваются как потенциальные соединения-корректоры инфекционной патологии, вызываемой антибиотикорезистентными бактериями (АБР). Цель данной работы состояла в изученим механизмов антибактериального действия трех пептидов, принадлежащих к семейству бактенецинов - ChBac3.4, ChBac5 и mini-ChBac7.5Nb. Эти химически синтезированные пептиды являются аналогами природных пролин-богатых АМП, обнаруженных в лейкоцитах домашней козы Capra hircus и проявляющих высокую антимикробную активность, в том числе и в отношении грамотрицательных АБР. Методы. Минимальные ингибирующие и минимальные бактерицидные концентрации пептидов (МИК и МБК) определяли методом серийных разведений в жидкой питательной среде с последующим высевом на плотную питательную среду. Эффекты пептидов на проницаемость цитоплазматической мембраны бактерий для хромогенного маркера исследовали с использованием генетически модифицированного штамма Escherichia coli ML35p. Действие бактенецинов на метаболическую активность бактерий изучали с применением маркера резазурина. Результаты. Показано, что все исследованные пептиды проявляют высокую антимикробную активность в отношении Escherichia coli ML35p и антибиотикоустойчивых штаммов Escherichia coli ESBL и Acinetobacter baumannii in vitro, но их действие на бактериальные клетки разное. Использован комплекс методик, позволяющих наблюдать в режиме реального времени динамику действия бактенецинов в различных концентрациях (включая их МИК и МБК) на барьерную функцию цитоплазматической мембраны и на интенсивность метаболизма бактериальных клеток, что дало возможность выявить различия в характере воздействия бактенецинов, отличающихся по структуре молекулы, на исследуемые микроорганизмы. Установлено, что действие каждого из трех исследованных бактенецинов в бактерицидных концентрациях отличается по эффективности нарушения целостности бактериальных мембран и в скорости подавления метаболизма клеток. Заключение. Полученная информация дополнит существующие фундаментальные представления о механизмах действия пролин-богатых пептидов врожденного иммунитета, а также послужит основой для биотехнологических исследований, направленных на разработку на базе этих соединений новых антибиотических препаратов для коррекции инфекционных заболеваний, вызываемых АБР и являющимися причинами тяжелых внутрибольничных инфекций. Antimicrobial peptides (AMPs) of the innate immunity are compounds that play an important role in pathogenesis of infectious diseases due to their ability to inactivate a broad array of pathogenic bacteria, thereby providing anti-microbial host defense. AMPs are currently considered promising compounds for treatment of infectious diseases caused by antibiotic-resistant bacteria. The aim of this study was to investigate molecular mechanisms of the antibacterial action of three peptides from the bactenecin family, ChBac3.4, ChBac5, and mini-ChBac7.5Nb. These chemically synthesized peptides are analogues of natural proline-rich AMPs previously discovered by the authors of the present study in leukocytes of the domestic goat, Capra hircus. These peptides exhibit a high antimicrobial activity, in particular, against antibiotic-resistant gram-negative bacteria. Methods. Minimum inhibitory and minimum bactericidal concentrations of the peptides (MIC and MBC) were determined using the broth microdilution assay followed by subculturing on agar plates. Effects of the AMPs on bacterial cytoplasmic membrane permeability for a chromogenic marker were explored using a genetically modified strain, Escherichia coli ML35p. The effect of bactenecins on bacterial metabolic activity was studied using a resazurin marker. Results. All the studied peptides showed a high in vitro antimicrobial activity against Escherichia coli ML35p and antibiotic-resistant strains, Escherichia coli ESBL and Acinetobacter baumannii, but differed in features of their action on bacterial cells. The used combination of techniques allowed the real-time monitoring of effects of bactenecin at different concentrations (including their MIC and MBC) on the cell membrane barrier function and metabolic activity of bacteria. The differences in effects of these three structurally different bactenecins on the studied microorganisms implied that these peptides at bactericidal concentrations differed in their capability for disintegrating bacterial cell membranes and rate of inhibiting bacterial metabolism. Conclusion. The obtained information will supplement the existing basic concepts on mechanisms involved in effects of proline-rich peptides of the innate immunity. This information will also stimulate biotechnological research aimed at development of new antibiotics for treatment of infectious diseases, such as severe in-hospital infections, caused by antibiotic-resistant strains.


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