Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel

AbstractMultispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources—particularly oxygen—and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.

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4 SPECIES OF BACTERIA DETERMINISTICALLY FORM A STABLE BIOFILM IN A MILLIFLUIDIC CHANNEL: ASSEMBLY PRINCIPLES

10.1101/2021.04.16.440159 ◽

2021 ◽

Author(s):

Amaury Monmeyran ◽

Wafa Benyoussef ◽

Philippe Thomen ◽

Narimane Dahmane ◽

Aurelie Baliarda ◽

...

Keyword(s):

Environmental Changes ◽

Environmental Parameters ◽

Individual Species ◽

Interspecies Interactions ◽

Laboratory Setup ◽

Quantitative Measurements ◽

Channel Assembly ◽

Emergence Of Complexity ◽

And Control ◽

Assembly Principles

Multispecies microbial adherent communities are widespread in nature and organisms but the principles of their assembly and development remain unclear. Yet, the demand to understand and predict the responses of such living communities to environmental changes is increasing, calling for new approaches. Here, we test the possibility to establish a simplified but relevant model of multispecies biofilm in a laboratory setup enabling in situ real-time monitoring of the community development and control of the environmental parameters in order to decipher the mechanisms underlying the formation of the community. Using video-microscopy and species combinatorial approach, we assess the global and individual species spatiotemporal development in millifluidic channels under constant flow of nutrients. Based on quantitative measurements of expansion kinetics, local dynamics and spatial distribution, we demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians and Rhodocyclus sp.) form a dynamical community that deterministically reaches its equilibrium after about 30 hours of growth. We evidence the emergence of complexity in this simplified community as reported by spatial heterogeneity rise and non-monotonic developmental kinetics. We find interspecies interactions consisting in competition for resources - in particular oxygen - and both direct and indirect physical interactions but no positive feedback. Thereby, we introduce a model of multispecies adherent community where effective couplings result from individual species quest for fitness optimization in a moving and heterogenous environment. This control and the understanding of this simplified experimental model shall open new avenues to apprehend adherent bacterial communities behavior in a context of rapid global change.

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MiSiC, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities

eLife ◽

10.7554/elife.65151 ◽

2021 ◽

Vol 10 ◽

Author(s):

Swapnesh Panigrahi ◽

Dorothée Murat ◽

Antoine Le Gall ◽

Eugénie Martineau ◽

Kelly Goldlust ◽

...

Keyword(s):

Deep Learning ◽

Bacterial Communities ◽

Cell Biology ◽

Imaging Modality ◽

Interaction Model ◽

Cell Segmentation ◽

Bacterial Cells ◽

Interspecies Interactions ◽

Prey Interaction ◽

Simple Implementation

Studies of bacterial communities, biofilms and microbiomes, are multiplying due to their impact on health and ecology. Live imaging of microbial communities requires new tools for the robust identification of bacterial cells in dense and often inter-species populations, sometimes over very large scales. Here, we developed MiSiC, a general deep-learning-based 2D segmentation method that automatically segments single bacteria in complex images of interacting bacterial communities with very little parameter adjustment, independent of the microscopy settings and imaging modality. Using a bacterial predator-prey interaction model, we demonstrate that MiSiC enables the analysis of interspecies interactions, resolving processes at subcellular scales and discriminating between species in millimeter size datasets. The simple implementation of MiSiC and the relatively low need in computing power make its use broadly accessible to fields interested in bacterial interactions and cell biology.

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Ecology and evolution of antimicrobial resistance in bacterial communities

The ISME Journal ◽

10.1038/s41396-020-00832-7 ◽

2020 ◽

Author(s):

Michael J. Bottery ◽

Jonathan W. Pitchford ◽

Ville-Petri Friman

Keyword(s):

Antibiotic Resistance ◽

Microbial Community ◽

Bacterial Communities ◽

Emergent Property ◽

Future Research ◽

Individual Species ◽

Ecological Context ◽

Interspecies Interactions ◽

Complete Understanding ◽

Resistance Evolution

AbstractAccumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by the presence of other interacting microbes. These interactions are not typically accounted for when determining pathogen sensitivity to antibiotics. In this perspective, we argue that resistance and evolutionary responses to antibiotic treatments should not be considered only a trait of an individual bacteria species but also an emergent property of the microbial community in which pathogens are embedded. We outline how interspecies interactions can affect the responses of individual species and communities to antibiotic treatment, and how these responses could affect the strength of selection, potentially changing the trajectory of resistance evolution. Finally, we identify key areas of future research which will allow for a more complete understanding of antibiotic resistance in bacterial communities. We emphasise that acknowledging the ecological context, i.e. the interactions that occur between pathogens and within communities, could help the development of more efficient and effective antibiotic treatments.

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Contrasting patterns of bacterial communities in the rearing water and gut of Penaeus vannamei in response to exogenous glucose addition

Marine Life Science & Technology ◽

10.1007/s42995-021-00124-9 ◽

2022 ◽

Author(s):

Lei Huang ◽

Haipeng Guo ◽

Zidan Liu ◽

Chen Chen ◽

Kai Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Communities ◽

Carbon Sources ◽

Operational Taxonomic Unit ◽

Diversity Indices ◽

Response Patterns ◽

Interspecies Interactions ◽

Glucose Addition ◽

Growth And Survival ◽

Α Diversity

AbstractSupplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria.

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Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods

10.1101/651612 ◽

2019 ◽

Author(s):

Sten Anslan ◽

Huan Li ◽

Sven Künzel ◽

Miguel Vences

Keyword(s):

Bacterial Communities ◽

Sample Type ◽

Gut Content ◽

Cold Temperatures ◽

Fecal Samples ◽

Non Invasive ◽

Preservation Methods ◽

Preservation Method ◽

Aquatic Vertebrates ◽

Study Species

AbstractSample type and preservation methods are likely to influence microbiome analysis results. Relatively few studies have explored the differences between feces and gut as well as ethanol-stored and frozen samples. Here, we sampled the same individuals of three aquatic vertebrates from the Qinghai-Tibetan Plateau non-invasively for feces, and subsequently for hindgut through dissection. Our study species, two fishes (Gymnocypris cf. namensis and Triplophysa sp.) and one amphibian (tadpoles of Nanorana parkeri), were all collected at the same time and site. Gut and fecal samples were stored in ethanol, and additionally, part of the gut samples were frozen, but temporarily thawed during transport as it often happens under difficult field conditions. Our results showed that both substrate (gut content vs. feces) as well as preservation method can influence the analysis of intestinal microbiomes. Frozen gut samples strongly differed from ethanol-stored samples, and especially in Nanorana most frozen samples were dominated (in relative abundance) by a set of Proteobacteria OTUs that were completely absent from the ethanol-stored samples. This blooming of contaminant bacteria occurred after less than 12 h of thawing, thus caution should be taken when constancy of cold temperatures cannot be maintained in the field for sample preservation purposes. Among ethanol-stored samples, bacterial communities from feces differed from those recovered from guts, but in part recovered similar patterns, such as a higher bacterial richness in the more herbivorous Nanorana tadpoles. Although our results argue against combining gut and fecal samples in analyses of host-specific microbiome differences, they also confirm that non-invasive sampling of feces can provide useful information of gut microbiomes in aquatic vertebrates, which may be important especially when working with endangered species.

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Characterising the Photoplethysmography Pulse Waveform for Use in Human Neuroscience: The Hybrid Excess and Decay (HED) Model

10.1101/2021.08.19.456935 ◽

2021 ◽

Author(s):

Simon Williamson ◽

Lucie Daniel-Watanabe ◽

Johanna Finnemann ◽

Craig Powell ◽

Adam Teed ◽

...

Keyword(s):

Pulse Wave ◽

Blood Oxygenation ◽

Pulse Waveform ◽

Relevant Model ◽

Systematic Analysis ◽

Invasive Approach ◽

Non Invasive ◽

Sympathomimetic Drug ◽

Wave Morphology ◽

High Degree

Photoplethysmography (PPG) offers a widely-used, convenient and non-invasive approach to monitoring basic indices of cardiovascular function such as heart rate and blood oxygenation. However, while the pulse waveform, generated by PPG comprises features that are shaped by physiological and psychological factors, it is frequently overlooked in analyses of such data. We suggest that studies could be enriched by exploiting the possibilities afforded by a systematic analysis of PPG waveforms. To do this we initially require a robust and automated means of characterising it, thereby allowing us to examine variations across individuals and between different physiological and psychological contexts. We present a psychophysiologically-relevant model, the Hybrid Excess and Decay (HED) Model, which characterises pulse wave morphology in terms of three underlying pressure waves and a decay function. We show that these parameters capture PPG data with a high degree of precision and, moreover, are sensitive to specific, physiologically-relevant changes within individuals. We present the theoretical and practical basis for the model and demonstrate its performance when applied to a pharmacological dataset of 105 participants receiving intravenous administrations of the sympathomimetic drug isoproterenol (Isoprenaline). We conclude by discussing the possible value in using the HED model to complement standard measures of PPG outputs.

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Influence of interspecies interactions on the spatial organization of dual species bacterial communities

Biofilm ◽

10.1016/j.bioflm.2020.100035 ◽

2020 ◽

Vol 2 ◽

pp. 100035 ◽

Cited By ~ 1

Author(s):

Sean C. Booth ◽

Scott A. Rice

Keyword(s):

Bacterial Communities ◽

Spatial Organization ◽

Interspecies Interactions

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In vitro reconstitution of the polymicrobial community associated with CF airway infections

Access Microbiology ◽

10.1099/acmi.ac2020.po0314 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Thomas O’Brien ◽

Martin Welch

Keyword(s):

Cell Number ◽

Fungal Species ◽

Experimental Models ◽

Stable Steady State ◽

Interspecies Interactions ◽

Airway Infections ◽

Number Species ◽

Bacteria And Fungi ◽

Dynamic Community

The airways of persons with cystic fibrosis (CF) provide a nutritionally rich environment that is prone to colonisation by a diverse and dynamic community of microbes (including both bacteria and fungi). Traditionally, Pseudomonas aeruginosa (PA) was thought to be the dominant pathogen associated with CF airway infections. However, it is becoming increasingly clear that interspecies interactions play a crucial role in modulating the physiology and gene expression profile(s) of the protagonists, and also impact on the response to therapeutic intervention. However, there are currently no suitable experimental models that permit long-term successful co-cultivation of PA with other CF-associated pathogens. Simply mixing bacterial or fungal species together and hoping for the best is not a recipe for success, since PA rapidly outcompetes most other species when grown in batch culture. In this work, we rectify this by describing a “3Rs-compliant” continuous-flow in vitro co-culture model. Using our model, it is possible to maintain remarkably stable steady-state co-cultures of major CF-associated pathogens (PA, Staphylococcus aureus and Candida albicans). Our findings reveal that even numerically minor (0.1%, by cell number) species can have a profound impact on quorum sensing and virulence factor production by PA. Furthermore, we show that complete polymicrobial communities derived from CF sputum can be inoculated directly into the model, thus enabling the recapitulation of the entire microbiome associated with CF airway infections to be studied under physiologically relevant conditions.

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Interspecies bacterial competition determines community assembly in the C. elegans intestine

10.1101/535633 ◽

2019 ◽

Cited By ~ 6

Author(s):

Anthony Ortiz Lopez ◽

Nicole M. Vega ◽

Jeff Gore

Keyword(s):

Community Assembly ◽

Bacterial Communities ◽

Bacterial Species ◽

Valuable Insight ◽

Interspecies Interactions ◽

Bottom Up ◽

C Elegans ◽

Bacterial Competition ◽

Average Fraction ◽

And Function

AbstractFrom insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. However, the complexity of these gut microbiomes and their hosts often constrains our ability to understand how these bacterial communities assemble and function. In order to elucidate basic principles of community assembly in a host intestine, we study the assembly of the microbiome of Caenorhabditis elegans with a bottom-up approach. We colonize the gut of the worm C. elegans with 11 bacterial species individually, in all possible pairs, and in selected trios, and we find an organized mixture of coexistence and competitive exclusion that indicates a hierarchical structure in the bacterial interactions. The capacity of a bacterial species fed in monoculture to colonize the C. elegans intestine correlates with its average fraction in co-culture experiments, yet fails to predict its abundance in many two- and three-species microbiomes. Hence, the bacterial fractional abundances in co-culture experiments—pairwise outcomes—are influenced by interspecies interactions. These pairwise outcomes accurately predict the trio outcomes in the worm intestine, further highlighting the importance of pairwise interactions in determining community composition. We also find that the C. elegans gut environment influences the outcome of co-culture experiments, and demonstrate that the low intestinal pH is one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and composition of complex microbial communities.

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Interspecies bacterial competition regulates community assembly in the C. elegans intestine

The ISME Journal ◽

10.1038/s41396-021-00910-4 ◽

2021 ◽

Author(s):

Anthony Ortiz ◽

Nicole M. Vega ◽

Christoph Ratzke ◽

Jeff Gore

Keyword(s):

Community Assembly ◽

Bacterial Communities ◽

Mapk Pathway ◽

Dominant Role ◽

Bacterial Species ◽

Environmental Filtering ◽

Community Diversity ◽

Interspecies Interactions ◽

C Elegans ◽

And Function

AbstractFrom insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

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