84 results on '"microbial interactions"'
Search Results
2. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.
- Author
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Long, Philip E, Williams, Kenneth H, Hubbard, Susan S, and Banfield, Jillian F
- Subjects
Carbon ,Sulfur ,Nitrogen ,Gases ,Soil ,Soil Microbiology ,Ecosystem ,Biodiversity ,Greenhouse Effect ,Atmosphere ,Climate ,Symbiosis ,Geologic Sediments ,Metabolic Networks and Pathways ,Metagenomics ,Microbial Interactions ,Nitrogen Cycle ,Microbial Consortia ,Groundwater ,Genome ,Microbial ,greenhouse gases ,metagenome ,reaction pathway ,subsurface biogeochemistry ,Genome ,Microbial ,Microbiology ,Medical Microbiology - Abstract
Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.
- Published
- 2016
3. Ecology of the respiratory tract microbiome.
- Author
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Pérez-Cobas AE, Rodríguez-Beltrán J, Baquero F, and Coque TM
- Subjects
- Humans, Ecology, Microbial Interactions, Models, Theoretical, Respiratory System, Ecosystem, Microbiota
- Abstract
A thriving multi-kingdom microbial ecosystem inhabits the respiratory tract: the respiratory tract microbiome (RTM). In recent years, the contribution of the RTM to human health has become a crucial research aspect. However, research into the key ecological processes, such as robustness, resilience, and microbial interaction networks, has only recently started. This review leans on an ecological framework to interpret the human RTM and determine how the ecosystem functions and assembles. Specifically, the review illustrates the ecological RTM models and discusses microbiome establishment, community structure, diversity stability, and critical microbial interactions. Lastly, the review outlines the RTM responses to ecological disturbances, as well as the promising approaches for restoring ecological balance., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
- Published
- 2023
- Full Text
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4. The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria.
- Author
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Tyc,, Olaf, Song, Chunxu, Dickschat, Jeroen S., Vos, Michiel, and Garbeva, Paolina
- Subjects
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VOLATILE organic compounds , *METABOLITES , *SOIL microbiology , *ANALYTICAL chemistry , *NUCLEOTIDE sequencing - Abstract
The rich diversity of secondary metabolites produced by soil bacteria has been appreciated for over a century, and advances in chemical analysis and genome sequencing continue to greatly advance our understanding of this biochemical complexity. However, we are just at the beginning of understanding the physicochemical properties of bacterial metabolites, the factors that govern their production and ecological roles. Interspecific interactions and competitor sensing are among the main biotic factors affecting the production of bacterial secondary metabolites. Many soil bacteria produce both volatile and soluble compounds. In contrast to soluble compounds, volatile organic compounds can diffuse easily through air- and gas-filled pores in the soil and likely play an important role in long-distance microbial interactions. In this review we provide an overview of the most important soluble and volatile classes of secondary metabolites produced by soil bacteria, their ecological roles, and their possible synergistic effects. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
5. Disentangling Interactions in the Microbiome: A Network Perspective.
- Author
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Layeghifard, Mehdi, Hwang, David M., and Guttman, David S.
- Subjects
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HUMAN microbiota , *HOST-parasite relationships , *INDIVIDUALIZED medicine , *PUBLIC health , *ENVIRONMENTAL health - Abstract
Microbiota are now widely recognized as being central players in the health of all organisms and ecosystems, and subsequently have been the subject of intense study. However, analyzing and converting microbiome data into meaningful biological insights remain very challenging. In this review, we highlight recent advances in network theory and their applicability to microbiome research. We discuss emerging graph theoretical concepts and approaches used in other research disciplines and demonstrate how they are well suited for enhancing our understanding of the higher-order interactions that occur within microbiomes. Network-based analytical approaches have the potential to help disentangle complex polymicrobial and microbe–host interactions, and thereby further the applicability of microbiome research to personalized medicine, public health, environmental and industrial applications, and agriculture. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
6. Conceptualizing microbe-plasmid communities as complex adaptive systems.
- Author
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Pilosof S
- Subjects
- Plasmids genetics, Microbial Interactions, Ecology, Microbiota
- Abstract
Plasmids shape microbial communities' diversity, structure, and function. Nevertheless, we lack a mechanistic understanding of how community structure and dynamics emerge from local microbe-plasmid interactions and coevolution. Addressing this gap is challenging because multiple processes operate simultaneously at multiple levels of organization. For example, immunity operates between a plasmid and a cell, but incompatibility mechanisms regulate coexistence between plasmids. Conceptualizing microbe-plasmid communities as complex adaptive systems is a promising approach to overcoming these challenges. I illustrate how agent-based evolutionary modeling, extended by network analysis, can be used to quantify the relative importance of local processes governing community dynamics. These theoretical developments can advance our understanding of plasmid ecology and evolution, especially when combined with empirical data., Competing Interests: Declaration of interests There are no interests to declare., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
7. Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease
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Corey P. Parlet, Morgan M. Brown, and Alexander R. Horswill
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Microbiology (medical) ,Staphylococcus aureus ,Staphylococcus ,Disease ,Colonisation resistance ,Skin infection ,Biology ,medicine.disease_cause ,Microbiology ,Article ,03 medical and health sciences ,Immune system ,Virology ,medicine ,Humans ,Colonization ,Skin ,030304 developmental biology ,0303 health sciences ,integumentary system ,030306 microbiology ,Microbiota ,Antimicrobial ,medicine.disease ,Quorum sensing ,Infectious Diseases ,Host-Pathogen Interactions ,Microbial Interactions ,Staphylococcal Skin Infections - Abstract
Commensal organisms that constitute the skin microbiota play a pivotal role in the orchestration of cutaneous homeostasis and immune competence. This balance can be promptly offset by the expansion of the opportunistic pathogen Staphylococcus aureus, which is responsible for the majority of bacterial skin infections. S. aureus carriage is also known to be a precondition for its transmission and pathogenesis. Recent reports suggest that skin-dwelling coagulase-negative staphylococci (CoNS) can prime the skin immune system to limit the colonization potential of invaders, and they can directly compete through production of antimicrobial molecules or through signaling antagonism. We review recent advances in these CoNS colonization resistance mechanisms, which may serve to aid development of pharmacologic and probiotic intervention strategies to limit S. aureus skin colonization and disease.
- Published
- 2019
8. Host, symbionts, and the microbiome
- Author
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Joana Falcão Salles, Leo W. Beukeboom, Pina Brinker, Michael C. Fontaine, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Beukeboom lab, Fontaine lab, and Falcao Salles lab
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Microbiology (medical) ,Metacommunity ,DYNAMICS ,Environment ,Biology ,Microbiology ,Mosquitoes ,03 medical and health sciences ,Symbiosis ,Virology ,INFECTION ,Animals ,Humans ,WOLBACHIA ,Microbiome ,CYTOPLASMIC INCOMPATIBILITY ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Host (biology) ,Microbiota ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,fungi ,GUT MICROBIOTA ,Integrated approach ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,EVOLUTION ,Insects ,COMMUNITY ,DROSOPHILA ,Infectious Diseases ,Phenotype ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Evolutionary biology ,ENDOSYMBIONTS ,Host-Pathogen Interactions ,Microbial Interactions ,Wolbachia ,AEDES-AEGYPTI ,Cytoplasmic incompatibility - Abstract
International audience; Symbiosis between microbial associates and a host is a ubiquitous feature of life on earth, modulating host phenotypes. In addition to endosymbionts, organisms harbour a collection of host-associated microbes, the microbiome that can impact important host traits. In this opinion article we argue that the mutual influences of the microbiome and endosymbionts, as well as their combined influence on the host, are still understudied. Focusing on the endosymbiont Wolbachia, we present growing evidence indicating that host phenotypic effects are exerted in interaction with the remainder microbiome and the host. We thus advocate that only through an integrated approach that considers multiple interacting partners and environmental influences will we be able to gain a better understanding of host–microbe associations.
- Published
- 2019
9. Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity
- Author
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Gautam Dantas and Eric C. Keen
- Subjects
0301 basic medicine ,Microbiology (medical) ,Host immunity ,Prophages ,030106 microbiology ,Bacterial Physiological Phenomena ,Microbiology ,Article ,Bacteriophage ,03 medical and health sciences ,Virology ,Lysogenic cycle ,Animals ,Humans ,Bacteriophages ,Human virome ,Symbiosis ,Lysogeny ,Prophage ,Bacteria ,Host Microbial Interactions ,biology ,Microbiota ,Human microbiome ,biology.organism_classification ,Commensalism ,Phenotype ,030104 developmental biology ,Infectious Diseases ,Evolutionary biology ,Models, Animal ,Microbial Interactions - Abstract
Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the ‘virome’) play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages’ interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.
- Published
- 2018
10. Towards a General Understanding of Bacterial Interactions
- Author
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Madhav P. Thakur, Lutz Becks, Mark van Kleunen, and Zhijie Zhang
- Subjects
Microbiology (medical) ,0303 health sciences ,Bacteria ,Ecology ,030306 microbiology ,Ecology (disciplines) ,Microbiota ,Interaction strength ,Bacterial Physiological Phenomena ,Biology ,Microbiology ,03 medical and health sciences ,Infectious Diseases ,Community context ,Microbial ecology ,Virology ,ddc:570 ,Microbial Interactions ,Interaction range ,030304 developmental biology - Abstract
Understanding the general rules of microbial interactions is central for advancing microbial ecology. Recent studies show that interaction range, interaction strength, and community context determine bacterial interactions and the coexistence and evolution of bacteria. We highlight how these factors could contribute to a general understanding of bacterial interactions. published
- Published
- 2020
11. Metabolic Heterogeneity and Cross-Feeding in Bacterial Multicellular Systems
- Author
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Christopher P. Kempes, Lars E. P. Dietrich, Alexa Price-Whelan, and Christopher R. Evans
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Microbiology (medical) ,0303 health sciences ,Bacteria ,030306 microbiology ,Metabolic heterogeneity ,Microfluidics ,Biofilm ,Computational biology ,Biology ,Bacterial growth ,Bacterial Physiological Phenomena ,Microbiology ,Article ,03 medical and health sciences ,Multicellular organism ,Infectious Diseases ,Molecular level ,Virology ,Biofilms ,Drug Resistance, Bacterial ,Microbial Interactions ,Metabolic Networks and Pathways ,030304 developmental biology - Abstract
Cells in assemblages differentiate and perform distinct roles. Though many pathways of differentiation are understood at the molecular level in multicellular eukaryotes, the elucidation of similar processes in bacterial assemblages is recent and ongoing. Here, we discuss examples of bacterial differentiation, focusing on cases in which distinct metabolisms coexist and those that exhibit cross-feeding, with one subpopulation producing substrates that are metabolized by a second subpopulation. We describe several studies of single-species systems, then segue to studies of multi-species metabolic heterogeneity and cross-feeding in the clinical setting. Many of the studies described exemplify the application of new techniques and modeling approaches that provide insights into metabolic interactions relevant for bacterial growth outside the laboratory.
- Published
- 2020
12. Of Mice and Men....and Plants: Comparative Genomics of the Dual Lifestyles of Enteric Pathogens
- Author
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Marcos H. de Moraes and Max Teplitski
- Subjects
0301 basic medicine ,Microbiology (medical) ,Salmonella ,Virulence Factors ,030106 microbiology ,Virulence ,Human pathogen ,Context (language use) ,Biology ,medicine.disease_cause ,Communicable Diseases ,Microbiology ,Disease Outbreaks ,Mice ,03 medical and health sciences ,Virology ,Endophytes ,Escherichia coli ,Type III Secretion Systems ,medicine ,Animals ,Humans ,Colonization ,Life Style ,Plant Diseases ,Comparative genomics ,Genetics ,Genes, Essential ,Polymorphism, Genetic ,Indoleacetic Acids ,Outbreak ,Genomics ,Plants ,Gastroenteritis ,Disease Models, Animal ,Infectious Diseases ,Regulon ,Microbial Interactions ,Genome, Bacterial - Abstract
Outbreaks of gastrointestinal illness, linked to the consumption of fruits, vegetables, and sprouts, continue to capture the attention of the general public and scientists. The recurrence of these outbreaks, despite heightened producer and consumer awareness, combined with improved sanitation protocols and technology, can be explained by the hypothesis that enteric pathogens, such as nontyphoidal Salmonella spp. and enterovirulent Escherichia coli, have evolved to exploit plants as alternative hosts. This review explores the genetic and genomic context for this hypothesis. Even though gastroenteritis outbreaks associated with the consumption of produce have been caused by a limited number of strains or serovars, robust evidence in support of the polymorphism hypothesis is lacking. While some housekeeping genes with additional virulence functions in animal models contribute to the fitness of enterics within plants, canonical virulence determinants required for animal infections, such as the type III secretion system (T3SS) and effectors, by and large, are of little consequence in interactions with plants. Conversely, despite possessing some functions more commonly found in phytobacteria, human enteric pathogens do not appear to rely on the same strategies for plant colonization. Instead, it is likely that nontyphoidal Salmonella and enterovirulent E. coli have evolved a set of functions distinct from its virulence regulon and from those used by phytopathogens.
- Published
- 2018
13. Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments
- Author
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Hyun Koo, Robert A. Burne, Hui Wu, and William H. Bowen
- Subjects
0301 basic medicine ,Microbiology (medical) ,Dietary Sugars ,030106 microbiology ,Dental Plaque ,Dental Caries ,Biology ,Matrix (biology) ,Polymicrobial biofilms ,Microbiology ,Article ,Extracellular matrix ,03 medical and health sciences ,Virology ,Humans ,Disease process ,Virulence ,Microbiota ,Biofilm ,Biofilm matrix ,Commensalism ,stomatognathic diseases ,Infectious Diseases ,Cellular Microenvironment ,Biofilms ,Host-Pathogen Interactions ,Microbial Interactions ,Tooth Tissue - Abstract
Biofilms are microbial communities embedded within an extracellular matrix, forming a highly organized structure that causes many human infections. Dental caries (tooth-decay) is a polymicrobial biofilm disease driven by the diet and microbiota-matrix interactions that occur on a solid surface. Sugars fuel the emergence of pathogens, the assembly of the matrix, and the acidification of the biofilm microenvironment, promoting ecological changes and concerted multispecies efforts that are conducive for acid damage of the mineralized tooth tissue. Here, we discuss recent advances on the role of the biofilm matrix and interactions between opportunistic pathogens and commensals in the pathogenesis of dental caries. In addition, we highlight the importance of matrix-producing organisms in fostering a pathogenic habitat where inter-species competition and synergies occur to drive the disease process, which could have implications to other infections associated with polymicrobial biofilms
- Published
- 2018
14. Archaea Are Interactive Components of Complex Microbiomes
- Author
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Julian Taffner, Ruth A. Schmitz, Christine Moissl-Eichinger, Gabriele Berg, Manuela R. Pausan, and Corinna Bang
- Subjects
0301 basic medicine ,Microbiology (medical) ,Thaumarchaeota ,Microbial Consortia ,030106 microbiology ,Euryarchaeota ,Microbiology ,03 medical and health sciences ,Syntrophy ,Virology ,Animals ,Humans ,Microbiome ,Symbiosis ,Keystone species ,Ecosystem ,Phylogeny ,Soil Microbiology ,Mouth ,Ecology ,biology ,Microbiota ,Eukaryota ,Biodiversity ,Ruminants ,Plants ,biology.organism_classification ,Archaea ,Halophile ,Gastrointestinal Microbiome ,Halobacteriales ,Gastrointestinal Tract ,Holobiont ,030104 developmental biology ,Infectious Diseases ,Health ,Biofilms ,Viruses ,Microbial Interactions - Abstract
Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.
- Published
- 2018
15. Oral Biofilm Architecture at the Microbial Scale.
- Author
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Ferrer, Maria D. and Mira, Alex
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- *
FLUORESCENCE in situ hybridization , *SPECTRAL imaging , *BIOFILMS , *BACTERIA classification , *HUMAN microbiota , *BACTERIAL communities , *PHYSIOLOGY - Abstract
The application of Spectral Imaging FISH to oral biofilm samples has permitted the direct, simultaneous observation of up to nine different bacterial taxa. This has revealed a complex yet organized microbial architecture, identifying the key microorganisms in the community and detecting the existing interspecies physical interactions at the micron scale. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
16. Streptomyces Exploration: Competition, Volatile Communication and New Bacterial Behaviours
- Author
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Marie A. Elliot and Stephanie Jones
- Subjects
0301 basic medicine ,Microbiology (medical) ,media_common.quotation_subject ,Biology ,Bacterial Physiological Phenomena ,Microbiology ,Streptomyces ,Competition (biology) ,03 medical and health sciences ,Bacterial Proteins ,Virology ,Botany ,media_common ,Volatile Organic Compounds ,Bacteria ,Ecology ,Solid surface ,Fungi ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Anti-Bacterial Agents ,030104 developmental biology ,Infectious Diseases ,Microbial Interactions ,Genome, Bacterial - Abstract
Streptomyces bacteria are prolific producers of specialized metabolites, and have a well studied, complex life cycle. Recent work has revealed a new type of Streptomyces growth termed 'exploration' - so named for the ability of explorer cells to rapidly traverse solid surfaces. Streptomyces exploration is stimulated by fungal interactions, and is associated with the production of an alkaline volatile organic compound (VOC) capable of inducing exploration by other streptomycetes. Here, we examine Streptomyces exploration from the perspectives of interkingdom interactions, pH-induced morphological switches, and VOC-mediated communication. The phenotypic diversity that can be revealed through microbial interactions and VOC exposure is providing us with insight into novel modes of microbial development, and an opportunity to exploit VOCs to stimulate desired microbial behaviours.
- Published
- 2017
17. Cultivation-Free Raman Spectroscopic Investigations of Bacteria
- Author
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Björn Lorenz, Stephan Stöckel, Jürgen Popp, Christina Wichmann, and Petra Rösch
- Subjects
0301 basic medicine ,Microbiology (medical) ,Stable-isotope probing ,Nanotechnology ,Biology ,Spectrum Analysis, Raman ,01 natural sciences ,Microbiology ,03 medical and health sciences ,symbols.namesake ,Virology ,Statistical analysis ,Bacteria ,010401 analytical chemistry ,technology, industry, and agriculture ,biology.organism_classification ,0104 chemical sciences ,Phenotype ,030104 developmental biology ,Infectious Diseases ,Isotope Labeling ,symbols ,Microbial Interactions ,Single-Cell Analysis ,Raman spectroscopy - Abstract
Raman spectroscopy is currently advertised as a hot and ambitious technology that has all of the features needed to characterize and identify bacteria. Raman spectroscopy is rapid, easy to use, noninvasive, and it could complement established microbiological and biomolecular methods in the near future. To bring this vision closer to reality, ongoing research is being conducted on spectral fingerprinting. This can yield a wealth of information, from even single bacteria from various habitats which can be further improved by combining Raman spectroscopy with methods such as stable isotope probing to elucidate microbial interactions. In conjunction with extensive statistical analysis, Raman spectroscopy will allow identification of (non)pathogenic bacteria at different taxonomic levels.
- Published
- 2017
18. The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases
- Author
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Lisa Y. Stein
- Subjects
Microbiology (medical) ,Greenhouse Effect ,Biogeochemical cycle ,Climate Change ,Microbial metabolism ,Nitrous Oxide ,Context (language use) ,Biology ,Microbiology ,Methane ,03 medical and health sciences ,chemistry.chemical_compound ,Greenhouse Gases ,Soil ,Virology ,Environmental Microbiology ,Ecosystem ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Atmosphere ,Nitrous oxide ,Infectious Diseases ,chemistry ,13. Climate action ,Environmental chemistry ,Greenhouse gas ,Microbial Interactions ,Gases ,Flux (metabolism) - Abstract
The production and consumption of the potent greenhouse gases, nitrous oxide and methane, are largely controlled by microorganisms that have long been assigned to defined functional guilds. However, our understanding of how microbial and biogeochemical processes interact to control the flux of these gases has expanded in recent years. The consumption and production of nitrous oxide and methane are functionally intertwined and engage a range of other biogeochemically active molecules from oxic to anoxic ecosystems. Abiotic processes, such as reaction of nitrogen oxides with metals, have a strong influence on microorganisms and play an equally significant role in greenhouse gas flux. The complex enzymology and physiology of microbial greenhouse gas metabolism are explored and discussed in the context of geochemistry and climate change.
- Published
- 2019
19. Making the Best of Aggression: The Many Dimensions of Bacterial Toxin Regulation
- Author
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Diego L. González, Despoina A. I. Mavridou, and Medical Research Council
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Microbiology (medical) ,Biochemistry & Molecular Biology ,toxin regulation ,STRESS ,GENES ,Population ,Bacterial Toxins ,INHIBITION ,type VI secretion system ,VI SECRETION SYSTEM ,Molecular systems ,Biology ,Bacterial Physiological Phenomena ,Microbiology ,03 medical and health sciences ,bacteriocin ,antibacterial toxins ,1108 Medical Microbiology ,Virology ,medicine ,TRANSCRIPTION ,education ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Microbial toxins ,Science & Technology ,030306 microbiology ,Aggression ,INDUCTION ,PSEUDOMONAS-AERUGINOSA ,contact-dependent inhibition system ,Competitor analysis ,SOS RESPONSE ,Infectious Diseases ,GROWTH ,Microbial Interactions ,bacterial competition ,medicine.symptom ,Life Sciences & Biomedicine ,Neuroscience ,BEHAVIOR ,0605 Microbiology - Abstract
Most bacteria use toxins to exclude competitors. As the synthesis and delivery of these molecules entail considerable costs for the producers, their expression is tightly regulated, often by molecular systems detecting physiological stresses or environment-specific cues. However, the ecological connection between such systems and competitive behaviors is not always clear. Here, we review the regulation of antibacterial toxins and propose a conceptual framework organizing the decision-making processes controlling toxin production. As bacteria are unable to precisely identify their competitors, we argue that toxin regulation primarily responds to cues directly or indirectly associated with the presence of competing strains. The density and fitness of the producing population also play a role in the decision-making process. Overall, we contend that optimal toxin production strategies involve monitoring of both self and foe.
- Published
- 2019
20. Contribution of the Mucosal Microbiota to Bovine Respiratory Health
- Author
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James Lowe, Brian Aldridge, and Mohamed Zeineldin
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Microbiology (medical) ,Respiratory System ,Respiratory Tract Diseases ,Bovine respiratory disease ,Cattle Diseases ,Disease ,Biology ,Complex ecosystem ,Microbiology ,03 medical and health sciences ,Virology ,medicine ,Animals ,Homeostasis ,Microbiome ,Respiratory system ,Respiratory health ,030304 developmental biology ,0303 health sciences ,Mucous Membrane ,030306 microbiology ,Microbiota ,High-Throughput Nucleotide Sequencing ,medicine.disease ,Infectious Diseases ,medicine.anatomical_structure ,Immunology ,Dysbiosis ,Microbial Interactions ,Cattle ,Respiratory tract - Abstract
Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patterns and a progressive dysbiosis. The ecological factors that shape the respiratory microbiota, and the influence of these complex communities on bovine respiratory health, are a rich area for research exploration. Here, we review the current status of understanding of the bovine respiratory microbiota, the factors that influence its development and stability, its role in maintaining mucosal homeostasis, and ultimately its contribution to bovine health and disease. Finally, we explore the limitations of current research approaches to the microbiome and discuss potential directions for future research that can help us better understand the role of the respiratory microbiota in the health, welfare, and productivity of livestock.
- Published
- 2019
21. Trophic Regulations of the Soil Microbiome
- Author
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Madhav P. Thakur, Stefan Geisen, and Terrestrial Ecology (TE)
- Subjects
Microbiology (medical) ,predators ,Food Chain ,Climate Change ,Biology ,complex mixtures ,Microbiology ,Predation ,03 medical and health sciences ,Soil ,NIOO ,Virology ,Animals ,Ecosystem ,Global environmental change ,Microbiome ,bacteria ,Soil Microbiology ,030304 developmental biology ,Apex predator ,Trophic level ,Abiotic component ,0303 health sciences ,Bacteria ,030306 microbiology ,Ecology ,Microbiota ,Community structure ,Fungi ,Microbiomes ,Plants ,Structure and function ,Infectious Diseases ,climate change ,food webs ,Predatory Behavior ,top-down control ,Microbial Interactions ,fungi - Abstract
The soil microbiome regulates vital ecosystem functions ranging from primary production to soil carbon sequestration. Yet, we have only begun to understand the factors regulating the soil microbiome. While the importance of abiotic factors is increasingly recognized, the roles of trophic regulations in driving the structure and function of the soil microbiome remain less explored. Here, we review the current understanding of how and when microbial and top predators of the soil shape the community structure and function of the soil microbiome via both direct and indirect effects. We finally highlight that the structure and function of the soil microbiome depend on the interactive effects among predation, plant inputs, and abiotic variables present in the soil.
- Published
- 2019
22. Stress as a Normal Cue in the Symbiotic Environment
- Author
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Edward G. Ruby and Julia A. Schwartzman
- Subjects
0301 basic medicine ,Microbiology (medical) ,Microorganism ,Environment ,Biology ,Microbiology ,Article ,Fight-or-flight response ,03 medical and health sciences ,Symbiosis ,Stress, Physiological ,Virology ,Animals ,Ecology ,Host (biology) ,Microbiota ,fungi ,Plants ,Multicellular organism ,030104 developmental biology ,Infectious Diseases ,Host-Pathogen Interactions ,Microbial Interactions ,Cues ,Molecular exchange - Abstract
All multicellular hosts form associations with groups of microorganisms. These microbial communities can be taxonomically diverse and dynamic, and their persistence is due to robust, and sometimes co-evolved, host microbe and microbe microbe interactions. Chemical and physical sources of stress are prominently situated in this molecular exchange, as cues for cellular responses in symbiotic microbes. Stress in the symbiotic environment may arise from three sources: host tissues, microbe-induced immune responses, or other microbes in the host environment. The responses of microbes to these stresses can be general or highly specialized, and collectively may contribute to the stability of the symbiotic system. In this review, we highlight recent work that emphasizes the role of stress as a cue in the symbiotic environment of plants and animals.
- Published
- 2016
23. Sugar Coating the Envelope : Glycoconjugates for Microbe-Host Crosstalk
- Author
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Willem M. de Vos and Hanne L. P. Tytgat
- Subjects
0301 basic medicine ,Microbiology (medical) ,Glycan ,Glycosylation ,Glycoconjugate ,Glycobiology ,Bacterial Physiological Phenomena ,Campylobacter jejuni ,Microbiology ,Pilus ,03 medical and health sciences ,chemistry.chemical_compound ,Species Specificity ,Polysaccharides ,Microbiologie ,Virology ,Humans ,VLAG ,Glycoproteins ,chemistry.chemical_classification ,Bacteria ,biology ,Microbiota ,Pili ,biology.organism_classification ,Gastrointestinal Microbiome ,Crosstalk (biology) ,030104 developmental biology ,Infectious Diseases ,chemistry ,Biochemistry ,Host-Pathogen Interactions ,biology.protein ,Microbial Interactions ,Microbiota-host interactions ,Glycoconjugates - Abstract
Tremendous progress has been made on mapping the mainly bacterial members of the human intestinal microbiota. Knowledge on what is out there, or rather what is inside, needs to be complemented with insight on how these bacteria interact with their biotic environment. Bacterial glycoconjugates, that is, the collection of all glycan-modified molecules, are ideal modulators of such interactions. Their enormous versatility and diversity results in a species-specific glycan barcode, providing a range of ligands for host interaction. Recent reports on the functional importance of glycosylation of important bacterial ligands in beneficial and pathogenic species underpin this. Glycoconjugates, and glycoproteins in particular, are an underappreciated, potentially crucial, factor in understanding bacteria-host interactions of old friends and foes. Glycoconjugates generate a species-specific barcode on the bacterial cell surface. The extreme diversity of bacterial glycoconjugates renders them ideal ligands to establish specific interactions with the environment.Host cells are covered with lectin receptors designed to discriminate between self and non-self glycoconjugates and signal to the immune system.Most ground has been covered by research on glycoconjugates of species on the pathogenic side of the bacterial spectrum. Glycosylation seems to be closely intertwined with virulence. By the same token, glycosylation can be closely intertwined with symbiotic interactions of beneficial species.Glycosylation of cell surface molecules of (beneficial) bacteria might play a crucial, yet underappreciated, role in microbiota-host interactions and offer unique insights in the understanding of these specific interactions.
- Published
- 2016
24. Experimental systems biology approaches reveal interaction mechanisms in model multispecies communities.
- Author
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Khare A
- Subjects
- Genomics, Systems Biology, Microbial Interactions, Microbiota
- Abstract
Interactions between microorganisms in multispecies communities are thought to have substantial consequences for the community. Identifying the molecules and genetic pathways that contribute to such interplay is thus crucial to understand as well as modulate community dynamics. Here I focus on recent studies that utilize experimental systems biology techniques to study these phenomena in simplified model microbial communities. These unbiased biochemical and genomic approaches have identified novel interactions and described the underlying genetic and molecular mechanisms. I discuss the insights provided by these studies, describe innovative strategies used to investigate less tractable organisms and environments, and highlight the utility of integrating these and more targeted methods to comprehensively characterize interactions between species in microbial communities., Competing Interests: Declaration of interests There are no interests to declare., (Published by Elsevier Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
25. Early-Life Microbiota Perturbations and Behavioral Effects
- Author
-
Antonia P. Francis and Maria Gloria Dominguez-Bello
- Subjects
Microbiology (medical) ,0303 health sciences ,030306 microbiology ,Offspring ,Transmission (medicine) ,Microbiota ,fungi ,Age Factors ,Infant ,Biology ,Affect (psychology) ,Microbiology ,Early life ,Developmental psychology ,03 medical and health sciences ,Infectious Diseases ,Child Development ,Virology ,Host-Pathogen Interactions ,Cognitive development ,Animals ,Humans ,Microbial Interactions ,030304 developmental biology ,A determinant - Abstract
The maternal environment, during the prenatal and postnatal periods, is a determinant of offspring development and health. Perturbations during these periods can affect maternal behaviors and maternal–infant bonding, and also impair transmission of maternal microbiota to the offspring. Impaired microbiota has been associated with alterations of offspring cognitive development and behavior.
- Published
- 2018
26. Bacteroides thetaiotaomicron
- Author
-
Nathan T. Porter, Ana S. Luis, and Eric C. Martens
- Subjects
0301 basic medicine ,Microbiology (medical) ,Dietary Fiber ,Host Microbial Interactions ,030106 microbiology ,Microbiology ,Gastrointestinal Microbiome ,Gastrointestinal Tract ,03 medical and health sciences ,Bacteroides thetaiotaomicron ,030104 developmental biology ,Infectious Diseases ,Polysaccharides ,Virology ,Plant Cells ,Fermentation ,Humans ,Microbial Interactions ,Symbiosis - Abstract
This infographic on Bacteroides thetaiotaomicron (Bt) explores the ability of this microbe to digest a broad array of complex carbohydrates, alter its surface features, and its emerging role in gastrointestinal diseases. The infographic of Bacteroides thetaiotaomicron (Bt) illustrates two key facets of its symbiotic lifestyle in the human gut: a broad ability to digest dietary fiber polysaccharides and host glycans, and a dynamic cell-surface architecture that promotes both interactions with and evasion of the host immune system. The starch-utilization system (Sus) is a cell-surface and periplasmic system involved in starch cleavage and transport. Over 80 additional Sus-like systems utilize substrates ranging from host glycans to plant cell wall pectins. Bt has evolved intricate strategies to interact with other microbes or its host, including modification of its surface. Some nutrient utilization pathways select for or directly trigger changes in capsular polysaccharide (CPS) expression. Like other fermentative members of the gut microbiome, Bt produces host absorbable short-chain and organic acids, which can all be absorbed by the host as a source of energy.
- Published
- 2018
27. The potential impact of coinfection on antimicrobial chemotherapy and drug resistance
- Author
-
Michael J. Mina, Emily Griffiths, Roger D. Kouyos, Ruthie Birger, C. Jessica E. Metcalf, Bryan T. Grenfell, Ted Cohen, Silvie Huijben, Victoriya V. Volkova, University of Zurich, and Birger, Ruthie B
- Subjects
Drug ,Microbiology (medical) ,media_common.quotation_subject ,610 Medicine & health ,Drug resistance ,Biology ,Models, Biological ,Microbiology ,Article ,2726 Microbiology (medical) ,10234 Clinic for Infectious Diseases ,Virology ,Antimicrobial chemotherapy ,medicine ,Animals ,Humans ,Immunologic Factors ,media_common ,Potential impact ,Animal health ,Coinfection ,2404 Microbiology ,Drug Resistance, Microbial ,2725 Infectious Diseases ,Immune modulation ,medicine.disease ,3. Good health ,Antimicrobial drug ,Infectious Diseases ,Host-Pathogen Interactions ,Immunology ,2406 Virology ,Microbial Interactions - Abstract
Across a range of pathogens, resistance to chemotherapy is a growing problem in both public health and animal health. Despite the ubiquity of coinfection, and its potential effects on within-host biology, the role played by coinfecting pathogens on the evolution of resistance and efficacy of antimicrobial chemotherapy is rarely considered. In this review, we provide an overview of the mechanisms of interaction of coinfecting pathogens, ranging from immune modulation and resource modulation, to drug interactions. We discuss their potential implications for the evolution of resistance, providing evidence in the rare cases where it is available. Overall, our review indicates that the impact of coinfection has the potential to be considerable, suggesting that this should be taken into account when designing antimicrobial drug treatments.
- Published
- 2015
- Full Text
- View/download PDF
28. Biofilms: Microbial Cities Wherein Flow Shapes Competition
- Author
-
Liang Yang, Su Chuen Chew, School of Biological Sciences, and Singapore Centre for Environmental Life Sciences Engineering
- Subjects
0301 basic medicine ,Microbiology (medical) ,media_common.quotation_subject ,030106 microbiology ,Biology ,Bacterial Physiological Phenomena ,Microbiology ,Competition (biology) ,03 medical and health sciences ,Extracellular polymeric substance ,Biopolymers ,Virology ,Phenotypic diversity ,media_common ,Bacteria ,Ecology ,Biofilm ,Substrate (biology) ,biology.organism_classification ,030104 developmental biology ,Infectious Diseases ,Phenotype ,Biofilms ,Pseudomonas aeruginosa ,Hydrodynamics ,Microbial Interactions ,human activities ,Hydrodynamic flow - Abstract
The phenotypic diversity in biofilms allows bacteria to adapt to changing environmental conditions. Stochastic gene expression and structural differentiation are believed to confer phenotypic diversity. However, two recent publications demonstrate how hydrodynamic flow and substrate topography can also alter the competitive outcomes of different bacterial phenotypes, increasing biofilm phenotypic variation. MOE (Min. of Education, S’pore) Accepted version
- Published
- 2017
29. Polybacterial human disease: the ills of social networking
- Author
-
Short, Francesca L., Murdoch, Sarah L., and Ryan, Robert P.
- Subjects
Microbiology (medical) ,metatranscriptomics ,Bacteria ,Virulence ,cell–cell signaling ,polymicrobial infection ,synergy ,Review ,Bacterial Infections ,Microbiology ,Models, Biological ,infection ,Anti-Bacterial Agents ,Infectious Diseases ,polybacterial disease ,Virology ,Humans ,Microbial Interactions ,Signal Transduction - Abstract
Highlights • Bacteria are typically found within complex microbial communities in nature. • Molecular interactions between co-infecting bacteria can profoundly affect disease prognosis and treatment. • In vivo models and genomic tools are providing new insights into interbacterial behavior during infection. • There is potential to target interbacterial interactions as part of a therapeutic strategy., Polybacterial diseases involve multiple organisms that act collectively to facilitate disease progression. Although this phenomenon was highlighted early in the 20th century, recent technological advances in diagnostics have led to the appreciation that many infections are far more complex than originally believed. Furthermore, it is apparent that although most treatments focus on the dominant bacterial species in an infection, other microbes, including commensals, can have a profound impact on both the response to therapy and virulence. Very little is known about the molecular mechanisms that underpin interactions between bacteria during such infections. Here, we discuss recent studies identifying and characterizing mechanisms of bacterial interaction and the biological processes they govern during certain diseases. We also highlight how possible strategies for targeting these interbacterial interactions may afford a route towards development of new therapies, with consequences for disease control.
- Published
- 2014
30. Are CDI Systems Multicolored, Facultative, Helping Greenbeards?
- Author
-
Elizabeth S. Danka, Peggy A. Cotter, and Erin C. Garcia
- Subjects
0301 basic medicine ,Microbiology (medical) ,genetic structures ,Burkholderia ,media_common.quotation_subject ,030106 microbiology ,Molecular evidence ,Biology ,Microbiology ,Competition (biology) ,Article ,03 medical and health sciences ,Bacterial Proteins ,Virology ,Escherichia coli ,Animals ,media_common ,Genetics ,Facultative ,Contact Inhibition ,Escherichia coli Proteins ,Biofilm ,Membrane Proteins ,Specific immunity ,Bacterial strain ,030104 developmental biology ,Infectious Diseases ,Biofilms ,Microbial Interactions ,Function (biology) ,Social behavior ,Signal Transduction - Abstract
Competitive and cooperative interactions between organisms, including bacteria, can significantly impact the composition of a community and the fitness of its members, as well as the fitness of their hosts when communities are living on or within other organisms. Understanding the underlying mechanisms is critical to the development of strategies to control microbiological communities that impact animal and plant health and also for understanding the evolution of social behaviors, which has been challenging for evolutionary biologists. Contact-dependent growth inhibition (CDI) is a phenomenon defined by the delivery of a protein toxin to the cytoplasm of neighboring bacteria upon cell-cell contact, resulting in growth inhibition or death unless a specific immunity protein is present. CDI was first described based on observations of interbacterial killing and has been assumed to function primarily as a means of eliminating competitor cells. However, recent molecular evidence indicates that multiple levels of specificity restrict CDI toxin delivery and activity to the same bacterial strain, and that CDI system proteins can mediate cooperative behaviors among 'self' cells, a phenomenon called contact-dependent signaling (CDS). Here we review these recent findings and discuss potential biological and evolutionary implications of CDI system-mediated interbacterial competition and cooperation.
- Published
- 2016
31. Influence of bacterial interactions on pneumococcal colonization of the nasopharynx
- Author
-
Keith P. Klugman, Jorge E. Vidal, and Joshua R. Shak
- Subjects
Microbiology (medical) ,Serotype ,Biology ,medicine.disease_cause ,Microbiology ,Article ,Pneumococcal Infections ,stomatognathic system ,Nasopharynx ,Virology ,Streptococcus pneumoniae ,otorhinolaryngologic diseases ,medicine ,Humans ,Coinfection ,respiratory system ,medicine.disease ,Pneumococcal infections ,Infectious Diseases ,Otitis ,Carriage ,Carrier State ,Immunology ,Microbial Interactions ,medicine.symptom ,Pneumonia (non-human) ,Meningitis - Abstract
Streptococcus pneumoniae (the pneumococcus) is a common commensal inhabitant of the nasopharynx and a frequent etiologic agent in serious diseases such as pneumonia, otitis media, bacteremia, and meningitis. Multiple pneumococcal strains can colonize the nasopharynx, which is also home to many other bacterial species. Intraspecies and interspecies interactions influence pneumococcal carriage in important ways. Co-colonization by two or more pneumococcal strains has implications for vaccine serotype replacement, carriage detection, and pneumonia diagnostics. Interactions between the pneumococcus and other bacterial species alter carriage prevalence, modulate virulence, and affect biofilm formation. By examining these interactions, this review highlights how the bacterial ecosystem of the nasopharynx changes the nature and course of pneumococcal carriage.
- Published
- 2013
32. Unseen players shape benthic competition on coral reefs
- Author
-
Forest Rohwer and Katie L. Barott
- Subjects
Microbiology (medical) ,Coral ,Population Dynamics ,Biology ,Microbiology ,Algae ,Virology ,Animals ,Seawater ,natural sciences ,Organic matter ,Organic Chemicals ,chemistry.chemical_classification ,geography ,geography.geographical_feature_category ,Bacteria ,Coral Reefs ,Ecology ,fungi ,technology, industry, and agriculture ,Coralline algae ,Coral reef ,biochemical phenomena, metabolism, and nutrition ,Anthozoa ,Seaweed ,biology.organism_classification ,Biota ,Holobiont ,Infectious Diseases ,chemistry ,Benthic zone ,Viruses ,Microbial Interactions ,Crustose ,geographic locations - Abstract
Recent work has shown that hydrophilic and hydrophobic organic matter (OM) from algae disrupts the function of the coral holobiont and promotes the invasion of opportunistic pathogens, leading to coral morbidity and mortality. Here we refer to these dynamics as the (3)DAM [dissolved organic matter (DOM), direct contact, disease, algae and microbes] model. There is considerable complexity in coral-algae interactions; turf algae and macroalgae promote heterotrophic microbial overgrowth of coral, macroalgae also directly harm the corals via hydrophobic OM, whereas crustose coralline algae generally encourage benign microbial communities. In addition, complex flow patterns transport OM and pathogens from algae to downstream corals, and direct algal contact enhances their delivery. These invisible players (microbes, viruses, and OM) are important drivers of coral reefs because they have non-linear responses to disturbances and are the first to change in response to perturbations, providing near real-time trajectories for a coral reef, a vital metric for conservation and restoration.
- Published
- 2012
33. Disentangling Interactions in the Microbiome: A Network Perspective
- Author
-
David M. Hwang, David S. Guttman, and Mehdi Layeghifard
- Subjects
0301 basic medicine ,Microbiology (medical) ,030106 microbiology ,microbial clusters ,microbiome ,Network theory ,Biology ,microbial interactions ,Microbiology ,Models, Biological ,Article ,03 medical and health sciences ,Virology ,Animals ,Humans ,Microbiome ,Microbiological Phenomena ,business.industry ,Ecology ,Microbiota ,Data science ,030104 developmental biology ,Infectious Diseases ,network ,Personalized medicine ,business ,keystone species - Abstract
Microbiota are now widely recognized as being central players in the health of all organisms and ecosystems, and subsequently have been the subject of intense study. However, analyzing and converting microbiome data into meaningful biological insights remain very challenging. In this review, we highlight recent advances in network theory and their applicability to microbiome research. We discuss emerging graph theoretical concepts and approaches used in other research disciplines and demonstrate how they are well suited for enhancing our understanding of the higher-order interactions that occur within microbiomes. Network-based analytical approaches have the potential to help disentangle complex polymicrobial and microbe–host interactions, and thereby further the applicability of microbiome research to personalized medicine, public health, environmental and industrial applications, and agriculture., Trends Polymicrobial communities (microbiota) are complex, dynamic, and ubiquitous. Microbiota play a central role in host health and development. For example, dysbiotic shifts in the composition of the human microbiome have been linked to a wide variety of health issues, such as obesity, diabetes, eczema, heart disease, asthma, colitis, etc. The complexity of microbiomes motivates a movement from reductionist approaches that focus on individual pathogens in isolation to more holistic approaches that focus on interactions among members of the community and their hosts. Network theory has emerged as an extremely promising approach for modelling complex biological systems with multifaceted interactions between members, such as microbiota. Networks enhance the analysis of polymicrobial interactions within microbiota and their role in health, disease, and development.
- Published
- 2016
34. Host-Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization
- Author
-
Michelle E. Mulcahy and Rachel M. McLoughlin
- Subjects
0301 basic medicine ,Microbiology (medical) ,Staphylococcus aureus ,030106 microbiology ,Population ,Rodentia ,Biology ,Adaptive Immunity ,Nose ,medicine.disease_cause ,Microbiology ,Bacterial Adhesion ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Risk Factors ,Virology ,otorhinolaryngologic diseases ,medicine ,Animals ,Humans ,Nasal colonization ,education ,education.field_of_study ,Microbiota ,Epithelial Cells ,respiratory system ,Staphylococcal Infections ,Acquired immune system ,Nasal epithelium ,Immunity, Innate ,Anterior nares ,Crosstalk (biology) ,Disease Models, Animal ,Nasal Mucosa ,Infectious Diseases ,medicine.anatomical_structure ,Immunology ,Carrier State ,Host-Pathogen Interactions ,Microbial Interactions ,Nasal Cavity ,030215 immunology - Abstract
Staphylococcus aureus persistently colonizes the anterior nares of approximately one fifth of the population and nasal carriage is a significant risk factor for infection. Recent advances have significantly refined our understanding of S. aureus–host communication during nasal colonization. Novel bacterial adherence mechanisms in the nasal epithelium have been identified, and novel roles for both the innate and the adaptive immune response in controlling S. aureus nasal colonization have been defined, through the use of both human and rodent models. It is clear that S. aureus maintains a unique, complex relationship with the host immune system and that S. aureus nasal colonization is overall a multifactorial process which is as yet incompletely understood.
- Published
- 2016
35. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
- Author
-
Philip E. Long, Kenneth H. Williams, Susan S. Hubbard, and Jillian F. Banfield
- Subjects
0301 basic medicine ,Microbiology (medical) ,Greenhouse Effect ,Biogeochemical cycle ,Geologic Sediments ,Nitrogen ,Climate ,Microbial Consortia ,Biology ,Microbiology ,metagenome ,subsurface biogeochemistry ,03 medical and health sciences ,Soil ,Microbial ,Virology ,greenhouse gases ,Symbiosis ,Life Below Water ,Groundwater ,Organism ,Ecosystem ,Soil Microbiology ,Total organic carbon ,Genome ,Ecology ,Atmosphere ,reaction pathway ,Biodiversity ,Nitrogen Cycle ,Carbon ,Trace gas ,Climate Action ,Genome, Microbial ,030104 developmental biology ,Infectious Diseases ,Metagenomics ,Medical Microbiology ,Greenhouse gas ,Microbial Interactions ,Gases ,Surface water ,Metabolic Networks and Pathways ,Sulfur - Abstract
© 2016 Elsevier Ltd Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes–such as the nitrogen cycle–that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.
- Published
- 2016
36. Incoming pathogens team up with harmless ‘resident’ bacteria
- Author
-
Daniel Passos da Silva and Vittorio Venturi
- Subjects
Microbiology (medical) ,Bacteria ,biology ,Host (biology) ,Bacterial Infections ,Bacterial Physiological Phenomena ,Commensalism ,Evasion (ethics) ,biology.organism_classification ,Microbiology ,Infectious Diseases ,Immune system ,Disease severity ,Virology ,Animals ,Humans ,Microbial Interactions - Abstract
Microbial diseases occur as a result of multifarious host-pathogen interactions. However, invading pathogens encounter a large number of different harmless and beneficial bacterial species, which colonize and reside in the host. Surprisingly, there has been little study of the possible interactions between incoming pathogens and the resident bacterial community. Recent studies have revealed that resident bacteria assist different types of incoming pathogens via a wide variety of mechanisms including cell-cell signaling, metabolic interactions, evasion of the immune response and a resident-to-pathogen switch. This calls for serious consideration of pathogen-microbe interactions in the host with respect to disease severity and progression.
- Published
- 2012
37. Studying Bacterial Multispecies Biofilms: Where to Start?
- Author
-
Mette Burmølle, Henriette Lyng Røder, and Søren J. Sørensen
- Subjects
0301 basic medicine ,Microbiology (medical) ,High prevalence ,Bacteria ,Ecology ,Multispecies biofilms ,Ecology (disciplines) ,030106 microbiology ,Microbial Consortia ,Biofilm ,Bacterial Physiological Phenomena ,Biology ,Environment ,Microbiology ,03 medical and health sciences ,Infectious Diseases ,Virology ,Biofilms ,Microbial Interactions - Abstract
The high prevalence and significance of multispecies biofilms have now been demonstrated in various bacterial habitats with medical, industrial, and ecological relevance. It is highly evident that several species of bacteria coexist and interact in biofilms, which highlights the need for evaluating the approaches used to study these complex communities. This review focuses on the establishment of multispecies biofilms in vitro, interspecies interactions in microhabitats, and how to select communities for evaluation. Studies have used different experimental approaches; here we evaluate the benefits and drawbacks of varying the degree of complexity. This review aims to facilitate multispecies biofilm research in order to expand the current limited knowledge on interspecies interactions.
- Published
- 2015
38. Moving From One to Many
- Author
-
Gail Teitzel
- Subjects
Microbiological Techniques ,Microbiology (medical) ,Microscopy ,Bacteria ,Spectrum Analysis ,Biology ,Microbiology ,Host-Parasite Interactions ,Visual arts ,Infectious Diseases ,Virology ,Viruses ,Disease Transmission, Infectious ,Humans ,Microbial Interactions ,Spectrum analysis ,Disease transmission ,Metabolic Networks and Pathways - Abstract
One of the things that drew me to microbiology was microscopy: you could take a small aliquot from a test tube that smelled both a little salty and a little like soup broth and put it under a microscope and focus down and suddenly see how it was teeming with life. I could see the little rod shapes of Pseudomonas aeruginosa swimming around, and it was endlessly fascinating to peer down into their smaller world to see what they were doing, how they formed communities, and how this changed in response to stress.
- Published
- 2017
39. Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions
- Author
-
Tim J. Daniell, Bruce D.L. Fitt, Adrian C. Newton, Dale R. Walters, and Simon D. Atkins
- Subjects
Microbiology (medical) ,Ecological niche ,Mutualism (biology) ,Bacteria ,Ecology ,food and beverages ,Parasitism ,Plants ,Biology ,Microbiology ,Disease control ,Plant Physiological Phenomena ,Infectious Diseases ,Symbiosis ,Virology ,Host-Pathogen Interactions ,Trophic mutualism ,Microbial Interactions ,Plant Diseases ,Trophic level - Abstract
Microbe-host interactions can be categorised as pathogenic, parasitic or mutualistic, but in practice few examples exactly fit these descriptions. New molecular methods are providing insights into the dynamics of microbe-host interactions, with most microbes changing their relationship with their host at different life-cycle stages or in response to changing environmental conditions. Microbes can transition between the trophic states of pathogenesis and symbiosis and/or between mutualism and parasitism. In plant-based systems, an understanding of the true ecological niche of organisms and the dynamic state of their trophic interactions with their hosts has important implications for agriculture, including crop rotation, disease control and risk management.
- Published
- 2010
40. Label or Concept - What Is a Pathobiont?
- Author
-
Jochum L and Stecher B
- Subjects
- Animals, Bacteria genetics, Host-Pathogen Interactions, Humans, Microbial Interactions, Symbiosis, Bacterial Physiological Phenomena, Gastrointestinal Microbiome
- Abstract
An increasing number of microorganisms are classified as 'pathobionts' (i.e., organisms that can cause harm under certain circumstances) but there exist no universally used criteria for this definition. In particular, the term is often used for categorizing disease-associated taxa without proof of 'causality'. This creates confusion and distracts from explicitly searching for beneficial functions of these organisms that they may in fact have. Here, we discuss why this term in its current use, and its apparent simplicity, may obscure the complexity of microbe-host and microbe-microbe interactions that define (the status of) the gut ecosystem., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
41. Towards a General Understanding of Bacterial Interactions.
- Author
-
Zhang Z, van Kleunen M, Becks L, and Thakur MP
- Subjects
- Bacteria genetics, Ecology, Microbiota, Bacterial Physiological Phenomena, Microbial Interactions
- Abstract
Understanding the general rules of microbial interactions is central for advancing microbial ecology. Recent studies show that interaction range, interaction strength, and community context determine bacterial interactions and the coexistence and evolution of bacteria. We highlight how these factors could contribute to a general understanding of bacterial interactions., (Copyright © 2020 Elsevier Ltd. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
42. Metabolic Heterogeneity and Cross-Feeding in Bacterial Multicellular Systems.
- Author
-
Evans CR, Kempes CP, Price-Whelan A, and Dietrich LEP
- Subjects
- Bacterial Physiological Phenomena, Drug Resistance, Bacterial, Microfluidics methods, Bacteria growth & development, Bacteria metabolism, Biofilms growth & development, Metabolic Networks and Pathways, Microbial Interactions
- Abstract
Cells in assemblages differentiate and perform distinct roles. Though many pathways of differentiation are understood at the molecular level in multicellular eukaryotes, the elucidation of similar processes in bacterial assemblages is recent and ongoing. Here, we discuss examples of bacterial differentiation, focusing on cases in which distinct metabolisms coexist and those that exhibit cross-feeding, with one subpopulation producing substrates that are metabolized by a second subpopulation. We describe several studies of single-species systems, then segue to studies of multispecies metabolic heterogeneity and cross-feeding in the clinical setting. Many of the studies described exemplify the application of new techniques and modeling approaches that provide insights into metabolic interactions relevant for bacterial growth outside the laboratory., (Copyright © 2020 Elsevier Ltd. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
43. Making the Best of Aggression: The Many Dimensions of Bacterial Toxin Regulation.
- Author
-
Gonzalez D and Mavridou DAI
- Subjects
- Bacterial Physiological Phenomena, Bacterial Toxins metabolism, Microbial Interactions
- Abstract
Most bacteria use toxins to exclude competitors. As the synthesis and delivery of these molecules entail considerable costs for the producers, their expression is tightly regulated, often by molecular systems detecting physiological stresses or environment-specific cues. However, the ecological connection between such systems and competitive behaviors is not always clear. Here, we review the regulation of antibacterial toxins and propose a conceptual framework organizing the decision-making processes controlling toxin production. As bacteria are unable to precisely identify their competitors, we argue that toxin regulation primarily responds to cues directly or indirectly associated with the presence of competing strains. The density and fitness of the producing population also play a role in the decision-making process. Overall, we contend that optimal toxin production strategies involve monitoring of both self and foe., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
44. Multispecies Swarms of Social Microorganisms as Moving Ecosystems
- Author
-
Alin Finkelshtein, Gil Ariel, Eshel Ben-Jacob, and Colin J. Ingham
- Subjects
0301 basic medicine ,Microbiology (medical) ,Microorganism ,030106 microbiology ,Microbial Consortia ,Swarming (honey bee) ,Biology ,Bacterial Physiological Phenomena ,Microbiology ,Competitive advantage ,Models, Biological ,03 medical and health sciences ,Microbial ecology ,Virology ,Environmental Microbiology ,Ecosystem ,Bacteria ,Ecology ,Swarm behaviour ,030104 developmental biology ,Infectious Diseases ,Habitat ,Flagella ,Biological dispersal ,Microbial Interactions - Abstract
Microorganisms use collective migration to cross barriers and reach new habitats, and the ability to form motile swarms offers a competitive advantage. Traditionally, dispersal by microbial swarm propagation has been studied in monoculture. Microorganisms can facilitate other species' dispersal by forming multispecies swarms, with mutual benefits. One party (the transporter) moves a sessile partner (the cargo). This results in asymmetric associations ranging from temporary marriages of convenience to long-term fellow travellers. In the context of the 'microbial market', the parties offer very different services in exchange. We discuss bacteria transporting bacteria, eukaryotic microorganisms moving bacteria, and bacteria facilitating the spread of eukaryotes - and ask what the benefits are, the methods of study, and the consequences of multispecies, swarming logistics networks.
- Published
- 2015
45. Fate, activity, and impact of ingested bacteria within the human gut microbiota
- Author
-
Johan E. T. van Hylckama Vlieg and Muriel Derrien
- Subjects
Microbiology (medical) ,Biology ,Gut flora ,Bacterial Physiological Phenomena ,Microbiology ,Eating ,Human gut ,transient microbiome ,Virology ,Humans ,clinical studies ,Microbiome ,ingested bacteria ,Potential impact ,Clinical Trials as Topic ,gut microbiota ,Host (biology) ,Probiotics ,digestive, oral, and skin physiology ,Propionibacteriaceae ,biology.organism_classification ,Fatty Acids, Volatile ,Gut microbiome ,Diet ,Gastrointestinal Microbiome ,Gastrointestinal Tract ,Lactobacillus ,Infectious Diseases ,Microbial population biology ,Microbial Interactions ,Bifidobacterium ,Bacteria - Abstract
The human gut contains a highly diverse microbial community that is essentially an open ecosystem, despite being deeply embedded within the human body. Food-associated fermentative bacteria, including probiotics, are major sources of ingested bacteria that may temporarily complement resident microbial communities, thus forming part of our transient microbiome. Here, we review data on the fate and activity of ingested bacteria and, in particular, lactobacilli and bifidobacteria in the gastrointestinal (GI) tract and their impact on the composition and metabolism of the gut microbiome with a focus on data from clinical studies. In addition, we discuss the mechanisms involved and the potential impact on the host's health.
- Published
- 2014
46. The target cell genus does not matter
- Author
-
Sophie Bleves, Thibault G. Sana, Romé Voulhoux, Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Microbiology (medical) ,media_common.quotation_subject ,Cell ,education ,Virulence ,Biology ,Phospholipase ,medicine.disease_cause ,Bacterial Physiological Phenomena ,Microbiology ,Virology ,medicine ,Phospholipase D ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Internalization ,media_common ,chemistry.chemical_classification ,Effector ,Host (biology) ,Pseudomonas aeruginosa ,Infectious Diseases ,medicine.anatomical_structure ,Enzyme ,Eukaryotic Cells ,chemistry ,Host-Pathogen Interactions ,Microbial Interactions ,Signal Transduction - Abstract
International audience; Two type VI secreted phospholipases D of Pseudomonas aeruginosa were identified as trans-kingdom virulence effectors, targeting both prokaryotic and eukaryotic host cells. Each of them triggers killing bacterial competitors and internalization into non-phagocytic cells. These type VI lipolytic enzymes are widely distributed among pathogens and may constitute a conserved strategy.
- Published
- 2014
47. Contribution of the Mucosal Microbiota to Bovine Respiratory Health.
- Author
-
Zeineldin M, Lowe J, and Aldridge B
- Subjects
- Animals, Cattle, Dysbiosis, High-Throughput Nucleotide Sequencing, Homeostasis, Microbial Interactions, Microbiota genetics, Cattle Diseases microbiology, Microbiota physiology, Mucous Membrane microbiology, Respiratory System microbiology, Respiratory Tract Diseases microbiology
- Abstract
Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patterns and a progressive dysbiosis. The ecological factors that shape the respiratory microbiota, and the influence of these complex communities on bovine respiratory health, are a rich area for research exploration. Here, we review the current status of understanding of the bovine respiratory microbiota, the factors that influence its development and stability, its role in maintaining mucosal homeostasis, and ultimately its contribution to bovine health and disease. Finally, we explore the limitations of current research approaches to the microbiome and discuss potential directions for future research that can help us better understand the role of the respiratory microbiota in the health, welfare, and productivity of livestock., (Published by Elsevier Ltd.)
- Published
- 2019
- Full Text
- View/download PDF
48. Early-Life Microbiota Perturbations and Behavioral Effects.
- Author
-
Francis AP and Dominguez-Bello MG
- Subjects
- Age Factors, Animals, Child Development, Humans, Infant, Host-Pathogen Interactions, Microbial Interactions, Microbiota
- Abstract
The maternal environment, during the prenatal and postnatal periods, is a determinant of offspring development and health. Perturbations during these periods can affect maternal behaviors and maternal-infant bonding, and also impair transmission of maternal microbiota to the offspring. Impaired microbiota has been associated with alterations of offspring cognitive development and behavior., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
49. Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease.
- Author
-
Parlet CP, Brown MM, and Horswill AR
- Subjects
- Humans, Microbiota, Skin immunology, Staphylococcal Skin Infections immunology, Host-Pathogen Interactions immunology, Microbial Interactions, Skin microbiology, Staphylococcal Skin Infections microbiology, Staphylococcus physiology, Staphylococcus aureus physiology
- Abstract
Commensal organisms that constitute the skin microbiota play a pivotal role in the orchestration of cutaneous homeostasis and immune competence. This balance can be promptly offset by the expansion of the opportunistic pathogen Staphylococcus aureus, which is responsible for the majority of bacterial skin infections. S. aureus carriage is also known to be a precondition for its transmission and pathogenesis. Recent reports suggest that skin-dwelling coagulase-negative staphylococci (CoNS) can prime the skin immune system to limit the colonization potential of invaders, and they can directly compete through production of antimicrobial molecules or through signaling antagonism. We review recent advances in these CoNS colonization resistance mechanisms, which may serve to aid development of pharmacologic and probiotic intervention strategies to limit S. aureus skin colonization and disease., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
50. Host, Symbionts, and the Microbiome: The Missing Tripartite Interaction.
- Author
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Brinker P, Fontaine MC, Beukeboom LW, and Falcao Salles J
- Subjects
- Animals, Environment, Humans, Microbial Interactions, Host-Pathogen Interactions, Microbiota, Symbiosis
- Abstract
Symbiosis between microbial associates and a host is a ubiquitous feature of life on earth, modulating host phenotypes. In addition to endosymbionts, organisms harbour a collection of host-associated microbes, the microbiome that can impact important host traits. In this opinion article we argue that the mutual influences of the microbiome and endosymbionts, as well as their combined influence on the host, are still understudied. Focusing on the endosymbiont Wolbachia, we present growing evidence indicating that host phenotypic effects are exerted in interaction with the remainder microbiome and the host. We thus advocate that only through an integrated approach that considers multiple interacting partners and environmental influences will we be able to gain a better understanding of host-microbe associations., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
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