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 Exercise and the Microbiome: Mechanistic Perspectives of the Impact of Exercise on the Gut-Vascular Axis

mSystems ◽  
2021 ◽  
Vol 6 (4) ◽  
Author(s):  
Marc D. Cook ◽  
Taylor Hogue
Keyword(s):  
Health Outcomes ◽  
Microbial Communities ◽  
Human Health ◽  
Metabolic Profiling ◽  
Vascular Health ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions ◽  
The Impact ◽  
Disease Understanding

Given the participation of the microbiome in human health and disease, understanding the context of host-microbe interactions involved in vascular pathophysiology is now evolving through identifying microbial communities, specific taxa, and metabolic profiling which can be coupled to human health outcomes. Exercise has been used to define mechanisms related to improved vascular health, which may involve the microbiome.

scholarly journals Plant-Derived Extracellular Vesicles: Current Findings,Challenges, and Future Applications

Membranes ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 411
Author(s):  
Nader Kameli ◽  
Anya Dragojlovic-Kerkache ◽  
Paul Savelkoul ◽  
Frank R. Stassen
Keyword(s):  
Human Health ◽  
Extracellular Vesicles ◽  
Preliminary Results ◽  
In Vivo Experiments ◽  
Health And Disease ◽  
Conducting Research ◽  
Protocol Standardization ◽  
Insight Into

In recent years, plant-derived extracellular vesicles (PDEVs) have gained the interest of many experts in fields such as microbiology and immunology, and research in this field has exponentially increased. These nano-sized particles have provided researchers with a number of interesting findings, making their application in human health and disease very promising. Both in vitro and in vivo experiments have shown that PDEVs can exhibit a multitude of effects, suggesting that these vesicles may have many potential future applications, including therapeutics and nano-delivery of compounds. While the preliminary results are promising, there are still some challenges to face, such as a lack of protocol standardization, as well as knowledge gaps that need to be filled. This review aims to discuss various aspects of PDEV knowledge, including their preliminary findings, challenges, and future uses, giving insight into the complexity of conducting research in this field.

scholarly journals Understanding the host-microbe interactions using metabolic modeling

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Jack Jansma ◽  
Sahar El Aidy
Keyword(s):  
Human Health ◽  
Flux Balance Analysis ◽  
Bacterial Species ◽  
Flux Balance ◽  
Interaction Field ◽  
In Silico Simulation ◽  
Balance Analysis ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Genome Scale

AbstractThe human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challenging to elucidate, limiting development in the treatment for a variety of diseases associated with microbiota dysbiosis. Using in silico simulation methods based on flux balance analysis, those interactions can be better investigated. Flux balance analysis uses an annotated genome-scale reconstruction of a metabolic network to determine the distribution of metabolic fluxes that represent the complete metabolism of a bacterium in a certain metabolic environment such as the gut. Simulation of a set of bacterial species in a shared metabolic environment can enable the study of the effect of numerous perturbations, such as dietary changes or addition of a probiotic species in a personalized manner. This review aims to introduce to experimental biologists the possible applications of flux balance analysis in the host-microbiota interaction field and discusses its potential use to improve human health.

scholarly journals Fecal Virome Transplantation

2021 ◽  
Author(s):  
Derek Lin ◽  
Henry C. Lin
Keyword(s):  
Immune System ◽  
Human Health ◽  
Bacterial Communities ◽  
Therapeutic Potential ◽  
Large Population ◽  
Current Understanding ◽  
Host Immune System ◽  
Full Extent ◽  
Health And Disease ◽  
Established Role

The gut virome consists of a large population of eukaryotic and prokaryotic viruses that have an emerging role in human health and disease. Growing evidence for the importance of the virome includes recent findings on fecal virome transplantation (FVT) that suggest FVT may have therapeutic potential for the resolution of dysbiosis and treatment of dysbiosis-related disorders. Most viruses in the gut virome are bacteriophages (phages), which have a well-established role in regulating bacterial communities across environments. Phages also influence health and disease by interacting directly with the host immune system. The full extent to which gut phages should be considered as both a target and a tool for microbiome modulation remains to be seen. This chapter will explore the current understanding of the gut virome and the therapeutic potential for FVT.

scholarly journals Mucosal microbial parasites/symbionts in health and disease: an integrative overview

Parasitology ◽  
2019 ◽  
Vol 146 (9) ◽  
pp. 1109-1115 ◽  
Author(s):  
Robert P. Hirt
Keyword(s):  
Host Interactions ◽  
Detection Techniques ◽  
Symbiotic Relationships ◽  
Life Styles ◽  
Mucosal Surfaces ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions ◽  
Species Being

AbstractMicrobial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host–parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites–microbiota–host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host–microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host–microbe interactions in both human health and disease.

scholarly journals Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Ragnhild I Vestrum ◽  
Kari J K Attramadal ◽  
Olav Vadstein ◽  
Madeleine Stenshorne Gundersen ◽  
Ingrid Bakke
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Atlantic Cod ◽  
Animal Health ◽  
Striking Difference ◽  
Ecological Processes ◽  
Opportunistic Bacteria ◽  
Atlantic Cod Larvae ◽  
Microbe Interactions ◽  
Host Microbe Interactions

ABSTRACT Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host–microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host–microbe interactions and improved fish health and survival.

scholarly journals Inferring directional relationships in microbial communities using signed Bayesian networks

BMC Genomics ◽  
2020 ◽  
Vol 21 (S6) ◽  
Author(s):  
Musfiqur Sazal ◽  
Kalai Mathee ◽  
Daniel Ruiz-Perez ◽  
Trevor Cickovski ◽  
Giri Narasimhan
Keyword(s):  
Microbial Community ◽  
Bayesian Networks ◽  
Bayesian Network ◽  
Microbial Communities ◽  
Community Analysis ◽  
Vital Role ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Colonization Patterns ◽  
Host Microbe Interactions

Abstract Background Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community. Unlike the previously proposed Co-occurrence Networks (CoNs), BNs are based on conditional dependencies and can help in revealing complex associations. Results In this paper, we propose a way of combining a BN and a CoN to construct a signed Bayesian Network (sBN). We report a surprising association between directed edges in signed BNs and known colonization orders. Conclusions BNs are powerful tools for community analysis and extracting influences and colonization patterns, even though the analysis only uses an abundance matrix with no temporal information. We conclude that directed edges in sBNs when combined with negative correlations are consistent with and strongly suggestive of colonization order.

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 A community perspective on the concept of marine holobionts: current status, challenges, and future directions

2019 ◽  
Author(s):  
Simon M Dittami ◽  
Enrique Arboleda ◽  
Jean-Christophe Auguet ◽  
Arite Bigalke ◽  
Enora Briand ◽  
...  
Keyword(s):  
Complex Systems ◽  
Marine Ecosystems ◽  
Model Systems ◽  
Current Status ◽  
Future Directions ◽  
Stable Relationship ◽  
Living Together ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Experimental Model Systems

Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a stable relationship, form the holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences with comparisons to terrestrial sciences where appropriate. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g. the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. The most significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This will be crucial to decipher the roles of marine holobionts in biogeochemical cycles, but also developing concrete applications of the holobiont concept e.g. to increase yield or disease resistance in aquacultures or to protect and restore marine ecosystems through management projects.

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.

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