scholarly journals Dynamics of the bacterial community associated withPhaeodactylum tricornutumcultures

2016 ◽  
Author(s):  
Fiona Wanjiku Moejes ◽  
Ovidiu Popa ◽  
Antonella Succurro ◽  
Julie Maguire ◽  
Oliver Ebenhöh
Keyword(s):  
Bacterial Community ◽  
Phaeodactylum Tricornutum ◽  
Large Scale ◽  
Model Organism ◽  
Interdisciplinary Approach ◽  
Pennate Diatom ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Insight Into ◽  
Over Time

AbstractThe pennate diatomPhaeodactylum tricornutumis a model organism able to synthesise industrially-relevant molecules. Large-scale monocultures are prone to bio-contamination, however, little is known about the identity of the invading organisms. To gain insight into the bacterial community associated with diatoms, we translated the complexity of a natural system into reproducible experiments where we investigated the microbiome ofP. tricornutumcultures. The results revealed a dynamic bacterial community that changed over time and in differing media conditions. We propose a network of putative interactions betweenP. tricornutumand the main bacterial factions, which is translated into a set of ordinary differential equations constituting a computational dynamic model. The proposed mathematical model is able to capture the population dynamics, further supporting the hypothesised interactions. The interdisciplinary approach implemented provides a framework for understanding the dynamics of diatom-associated microbial communities, and provides a foundation for further systematic investigations of host-microbe interactions.

scholarly journals Dynamics of the Bacterial Community Associated with Phaeodactylum tricornutum Cultures

2017 ◽  
Author(s):  
Fiona Wanjiku Moejes ◽  
Ovidiu Popa ◽  
Antonella Succurro ◽  
Julie Maguire ◽  
Oliver Ebenhöh
Keyword(s):  
Bacterial Community ◽  
Phaeodactylum Tricornutum ◽  
Model Organism ◽  
Culture Collection ◽  
Pennate Diatom ◽  
Natural Systems ◽  
Current State ◽  
Commercial Scale ◽  
Starting Point ◽  
Minimal Media

The pennate diatom Phaeodactylum tricornutum is a model organism able to synthesize industrially-relevant molecules. Commercial-scale cultivation currently requires large monocultures, prone to bio-contamination. However, little is known about the identity of the invading organisms. To reduce the complexity of natural systems, we systematically investigated the microbiome of non-axenic P. tricornutum cultures from a culture collection in reproducible experiments. The results revealed a dynamic bacterial community that developed differently in “complete” and “minimal” media conditions. In complete media, we observed an accelerated “culture crash”, indicating a more stable culture in minimal media. The identification of only four bacterial families as major players within the microbiome suggests specific roles depending on environmental conditions. From our results we propose a network of putative interactions between P. tricornutum and these main bacterial factions. We demonstrate that, even with rather sparse data, a mathematical model can be reconstructed that qualitatively reproduces the observed population dynamics, thus indicating that our hypotheses regarding the molecular interactions are in agreement with experimental data. Whereas the model in its current state is only qualitative, we argue that it serves as a starting point to develop quantitative and predictive mathematical models, which may guide experimental efforts to synthetically construct and monitor stable communities required for robust upscaling strategies.

scholarly journals Chemically Mediated Microbial “Gardening” Capacity of a Seaweed Holobiont Is Dynamic

2020 ◽  
Vol 8 (12) ◽  
pp. 1893
Author(s):  
Mahasweta Saha ◽  
Shawn Dove ◽  
Florian Weinberger
Keyword(s):  
Pathogenic Bacteria ◽  
Abiotic Factors ◽  
Terrestrial Plants ◽  
Beneficial Bacteria ◽  
Low Salinity ◽  
Aquatic Flora ◽  
Salinity Levels ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Over Time

Terrestrial plants are known to “garden” the microbiota of their rhizosphere via released metabolites (that can attract beneficial microbes and deter pathogenic microbes). Such a “gardening” capacity is also known to be dynamic in plants. Although microbial “gardening” has been recently demonstrated for seaweeds, we do not know whether this capacity is a dynamic property in any aquatic flora like in terrestrial plants. Here, we tested the dynamic microbial “gardening” capacity of seaweeds using the model invasive red seaweed Agarophyton vermiculophyllum. Following an initial extraction of surface-associated metabolites (immediately after field collection), we conducted a long-term mesocosm experiment for 5 months to test the effect of two different salinities (low = 8.5 and medium = 16.5) on the microbial “gardening” capacity of the alga over time. We tested “gardening” capacity of A. vermiculophyllum originating from two different salinity levels (after 5 months treatments) in settlement assays against three disease causing pathogenic bacteria and seven protective bacteria. We also compared the capacity of the alga with field-collected samples. Abiotic factors like low salinity significantly increased the capacity of the alga to deter colonization by pathogenic bacteria while medium salinity significantly decreased the capacity of the alga over time when compared to field-collected samples. However, capacity to attract beneficial bacteria significantly decreased at both tested salinity levels when compared to field-collected samples. Dynamic microbial “gardening” capacity of a seaweed to attract beneficial bacteria and deter pathogenic bacteria is demonstrated for the first time. Such a dynamic capacity as found in the current study could also be applicable to other aquatic host–microbe interactions. Our results may provide an attractive direction of research towards manipulation of salinity and other abiotic factors leading to better defended A. vermiculophyllum towards pathogenic bacteria thereby enhancing sustained production of healthy A. vermiculophyllum in farms.

scholarly journals Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Anna Heintz-Buschart ◽  
Patrick May ◽  
Cédric C. Laczny ◽  
Laura A. Lebrun ◽  
Camille Bellora ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Human Health ◽  
Large Scale ◽  
Integrative Approach ◽  
Gastrointestinal Microbiota ◽  
Gastrointestinal Microbiome ◽  
Familial Type ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Abstract The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mellitus (T1DM). Analysis of intra- and inter-individual variation demonstrates that family membership has a pronounced effect on the structural and functional composition of the gastrointestinal microbiome. In the context of T1DM, consistent taxonomic differences were absent across families, but certain human exocrine pancreatic proteins were found at lower levels. The associated microbial functional signatures were linked to metabolic traits in distinct taxa. The methodologies and results provide a foundation for future large-scale integrated multi-omic analyses of the gastrointestinal microbiome in the context of host–microbe interactions in human health and disease.

scholarly journals Structural basis of ligand selectivity by a bacterial adhesin lectin involved in multi- species biofilm formation

2020 ◽  
Author(s):  
Shuaiqi Guo ◽  
Tyler D.R. Vance ◽  
Hossein Zahiri ◽  
Robert Eves ◽  
Corey Stevens ◽  
...  
Keyword(s):  
High Resolution ◽  
Biofilm Formation ◽  
Molecular Basis ◽  
Symbiotic Bacterium ◽  
Structural Basis ◽  
Ligand Selectivity ◽  
End Groups ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Insight Into

AbstractCarbohydrate recognition by lectins governs critical host-microbe interactions. MpPA14 lectin is a domain of a 1.5-MDa adhesin responsible for a symbiotic bacterium-diatom interaction in Antarctica. Here we show MpPA14 binds various monosaccharides, with L-fucose and N-acetyl glucosamine being the strongest ligands (Kd ~ 150 μM). High-resolution structures of MpPA14 with 15 different sugars bound elucidated the molecular basis for the lectin’s apparent binding promiscuity but underlying selectivity. MpPA14 mediates strong Ca2+-dependent interactions with the 3, 4 diols of L-fucopyranose and glucopyranoses, and binds other sugars via their specific minor isomers. Thus, MpPA14 only binds polysaccharides like branched glucans and fucoidans with these free end-groups. Consistent with our findings, adhesion of MpPA14 to diatom cells was selectively blocked by L-fucose, but not by N-acetyl galactosamine. With MpPA14 lectin homologs present in adhesins of several pathogens, our work gives insight into an anti-adhesion strategy to block infection via ligand-based antagonists.

scholarly journals Mammalian lectin arrays for screening host–microbe interactions

2020 ◽  
Vol 295 (14) ◽  
pp. 4541-4555 ◽  
Author(s):  
Sabine A. F. Jégouzo ◽  
Conor Nelson ◽  
Thomas Hardwick ◽  
S. T. Angel Wong ◽  
Noel Kuan Kiat Lau ◽  
...  
Keyword(s):  
Model Organism ◽  
Yeast Cells ◽  
Target Cells ◽  
Binding Studies ◽  
Lectin Array ◽  
Receptor Interactions ◽  
Microbe Interactions ◽  
Lectin Family ◽  
Host Microbe Interactions ◽  
Mammalian Lectin

Many members of the C-type lectin family of glycan-binding receptors have been ascribed roles in the recognition of microorganisms and serve as key receptors in the innate immune response to pathogens. Other mammalian receptors have become targets through which pathogens enter target cells. These receptor roles have often been documented with binding studies involving individual pairs of receptors and microorganisms. To provide a systematic overview of interactions between microbes and the large complement of C-type lectins, here we developed a lectin array and suitable protocols for labeling of microbes that could be used to probe this array. The array contains C-type lectins from cow, chosen as a model organism of agricultural interest for which the relevant pathogen–receptor interactions have not been previously investigated in detail. Screening with yeast cells and various strains of both Gram-positive and -negative bacteria revealed distinct binding patterns, which in some cases could be explained by binding to lipopolysaccharides or capsular polysaccharides, but in other cases they suggested the presence of novel glycan targets on many of the microorganisms. These results are consistent with interactions previously ascribed to the receptors, but they also highlight binding to additional sugar targets that have not previously been recognized. Our findings indicate that mammalian lectin arrays represent unique discovery tools for identifying both novel ligands and new receptor functions.

scholarly journals Immunotopological Analysis of theTreponema denticolaMajor Surface Protein (Msp)

2018 ◽  
Vol 201 (2) ◽  
Author(s):  
Valentina Godovikova ◽  
M. Paula Goetting-Minesky ◽  
John C. Timm ◽  
J. Christopher Fenno
Keyword(s):  
Outer Membrane ◽  
In Silico ◽  
Model Organism ◽  
Surface Protein ◽  
Membrane Topology ◽  
Orthologous Group ◽  
Treponema Denticola ◽  
Functional Relationships ◽  
Microbe Interactions ◽  
Host Microbe Interactions

ABSTRACTTreponema denticola, one of several recognized periodontal pathogens, is a model organism for studyingTreponemaphysiology and host-microbe interactions. Its major surface protein Msp (or MOSP) comprises an oligomeric outer membrane-associated complex that binds fibronectin, has cytotoxic pore-forming activity, and disrupts several intracellular responses. There are two hypotheses regarding native Msp structure and membrane topology. One hypothesis predicts that the entire Msp protein forms a β-barrel structure similar to that of well-studied outer membrane porins of Gram-negative bacteria. The second hypothesis predicts a bipartite Msp with distinct and separate periplasmic N-terminal and porin-like β-barrel C-terminal domains. The bipartite model, based on bioinformatic analysis of the orthologousTreponema pallidumTpr proteins, is supported largely by studies of recombinant TprC and Msp polypeptides. The present study reports immunological studies in bothT. denticolaandEscherichia colibackgrounds to identify a prominent Msp surface epitope (residues 229 to 251 in ATCC 35405) in a domain that differs between strains with otherwise highly conserved Msps. These results were then used to evaluate a series ofin silicostructural models of representativeT. denticolaMsps. The data presented here are consistent with a model of Msp as a large-diameter β-barrel porin. This work adds to the knowledge regarding the diverse Msp-like proteins in oral treponemes and may contribute to an understanding of the evolutionary and potential functional relationships between Msps of oralTreponemaand the orthologous group of Tpr proteins ofT. pallidum.IMPORTANCETreponema denticolais among a small subset of the oral microbiota contributing to severe periodontal disease. Due to its relative genetic tractability,T. denticolais a model organism for studyingTreponemaphysiology and host-microbe interactions.T. denticolaMsp is a highly expressed outer membrane-associated oligomeric protein that binds fibronectin, has cytotoxic pore-forming activity, and disrupts intracellular regulatory pathways. It shares homology with the orthologous group ofT. pallidumTpr proteins, one of which is implicated inT. pallidum in vivoantigenic variation. The outer membrane topologies of both Msp and the Tpr family proteins are unresolved, with conflicting reports on protein domain localization and function. In this study, we combined empirical immunological data derived both from diverseT. denticolastrains and from recombinant Msp expression inE. coliwithin silicopredictive structural modeling ofT. denticolaMsp membrane topology, to move toward resolution of this important issue inTreponemabiology.

scholarly journals Probiotics: Should We Consider it in Therapeutics?

1970 ◽  
Vol 13 (1) ◽  
pp. 55-59
Author(s):  
MD Ismail Patwary ◽  
MD Khalilur Rahman
Keyword(s):  
World Wide ◽  
Medical Field ◽  
Microbial Resistance ◽  
Fast Growing ◽  
Resistance To Antibiotics ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Insight Into

Probiotics are receiving increasing attention in the medical field. This is partly due to the recognition that microbial resistance to antibiotics presents a serious world-wide problem. In addition, fast growing insight into host-microbe interactions opened new routes in the development of rational alternatives in therapy and prevention of diseases as result of the complex procaryotic-eucaryotic evolutionary symphony. Consequently, long existing aspects of probiotics came into focus, and already provide exciting prospects. DOI: http://dx.doi.org/10.3329/jom.v13i1.10049 JOM 2012; 13(1): 55-59

scholarly journals Old and new models for studying host-microbe interactions in health and disease:C. difficileas an example

2017 ◽  
Vol 312 (6) ◽  
pp. G623-G627 ◽  
Author(s):  
Vincent B. Young
Keyword(s):  
Human Health ◽  
Bacterial Communities ◽  
Human Microbiome ◽  
Model Systems ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Indigenous Microbiota ◽  
Pathogenic Microbes ◽  
Host Microbe Interactions ◽  
Insight Into

There has been an explosion of interest in studying the indigenous microbiota, which plays an important role in human health and disease. Traditionally, the study of microbes in relationship to human health involved consideration of individual microbial species that caused classical infectious diseases. With the interest in the human microbiome, an appreciation of the influence that complex communities of microbes can have on their environment has developed. When considering either individual pathogenic microbes or a symbiotic microbial community, researchers have employed a variety of model systems with which they can study the host-microbe interaction. With the use of studies of infections with the toxin-producing bacterium Clostridium difficile as a model for both a pathogen and beneficial bacterial communities as an example, this review will summarize and compare various model systems that can be used to gain insight into the host-microbe interaction.

scholarly journals Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus

2020 ◽  
Author(s):  
Xingkun Jin ◽  
Ziwei Chen ◽  
Yan Shi ◽  
Jian-Fang Gui ◽  
Zhe Zhao
Keyword(s):  
Growth Rate ◽  
Gut Microbiota ◽  
Slow Growth ◽  
Ecological Processes ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Environmental Bacteria ◽  
Feed Source ◽  
Host Microbe Interactions ◽  
Insight Into

ABSTRACTUnderstanding the ecological processes in controlling the assemblage of gut microbiota becomes an essential prerequisite for a more sustainable aquaculture. Here we used 16S rRNA amplicon sequencing to characterize the hindgut microbiota from cultured obscure puffer Takifugu obscurus. The gut microbiota is featured with lower alpha-diversity, greater beta-dispersion and higher average 16S rRNA copy numbers comparing to water and sediment, but far less so to feed. SourceTracker predicted a notable source signature from feed in gut microbiota. Furthermore, effect of varying degrees of feed-associated bacteria on compositional, functional and phylogenetic diversity of gut microbiota were revealed. Coincidently, considerable increase of species richness and feed source proportions both were observed in slow growth fugu, implying a reduced stability in gut microbiota upon bacterial disturbance from feed. Moreover, quantitative ecological analytic framework was applied and the ecological processes underlying such community shift were determined. In the context of lower degree of feed disturbance, homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts. Whilst with the degree of feed disturbance increased, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Altogether, our findings illustrated a clear diversity-function relationships in fugu gut microbiota, and it has implicated in a strong correlation between feed-borne bacteria and host growth rate. These results provide a new insight into aquaculture of fugu and other economically important fishes, as well as a better understanding of host-microbe interactions in the vertebrate gastrointestinal tract.IMPORTANCEEnvironmental bacteria has a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon fugu gut microbiota. As a result, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, which is potentially correlated with the host physiological condition such as gastric evacuation rate. Our findings emphasized the intricate linkage between feed and gut microbiota, and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes, and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.

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