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Untangle the broad connections and tight interactions between human microbiota and complex diseases through data-driven approaches
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Development of Microbial Ecological Theory: Stability, Plasticity, and Evolution of Microbial Ecosystems
“How can we develop microbial ecological theory?” The development of microbial ecological theory has a long way to reach its goal. Advances in microbial ecological techniques provide novel insights into microbial ecosystems. Articles in this book are challenging to determine the central and general tenets of the ecological theory that describes the features of microbial ecosystems. Their achievements expand the frontiers of current microbial ecology and propose the next step. Assemblage of these diverse articles hopefully helps to go on this long journey with many avenues for advancement of microbial ecology.
The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling
Recent technological advances in single-cell microbiology, using flow cytometry, microfluidics, x-ray fluorescence microprobes, and single-cell -omics, allow for the observation of individuals within populations. Simultaneously, individual-based models (or more generally agent-based models) allow for individual microbes to be simulated. Bridging these techniques forms the foundation of individual-based ecology of microbes (µIBE). µIBE has elucidated genetic and phenotypic heterogeneity that has important consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, an...
Frontiers in Wolbachia Biology 2023
Wolbachia is likely the most successful endosymbiotic bacteria associated with insects and other arthropods, as well as nematodes. Over the past several decades, its widespread presence across the vast range of arthropod in the terrestrial ecosystem, as well as its various biological attributes, have caused an explosive development in Wolbachia research. These include the induction of striking reproductive phenotypes, namely cytoplasmic incompatibility, male-killing, parthenogenesis induction, and feminization; obligatory and conditional beneficial fitness consequences such as nutrient provisioning and resistance to parasites, pathogens and viruses; essentiality for host growth, development ...
Bioactive Compounds from Microbes
Microorganisms have had a long and surprising history. They were “invisible” until invention of microscope in the 17th century. Until that date, although they were extensively (but inconsciously) employed in food preservation, beer and wine fermentation, cheese, vinegar, yogurt and bread making, as well as being the causative agents of infectious diseases, they were considered as “not-existing”. The work of Pasteur in the middle of the 19th century revealed several biological activities performed by microorganisms including fermentations and pathogenicity. Due to the urgent issue to treat infectious diseases (the main cause of death at those times) the “positive potential” of the...
New Insights into Microbial Ecology through Subtle Nucleotide Variation
The 16S ribosomal RNA gene commonly serves as a molecular marker for investigating microbial community composition and structure. Vast amounts of 16S rRNA amplicon data generated from environmental samples thanks to the recent advances in sequencing technologies allowed microbial ecologists to explore microbial community dynamics over temporal and spatial scales deeper than ever before. However, widely used methods for the analysis of bacterial communities generally ignore subtle nucleotide variations among high-throughput sequencing reads and often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial datasets. Lack of proper partitioning of the sequencing data into relevant units often masks important ecological patterns. Our research topic contains articles that use oligotyping to demonstrate the importantance of high-resolution analyses of marker gene data, and providides further evidence why microbial ecologists should open the "black box" of OTUs identified through arbitrary sequence similarity thresholds.
Insect Microbiome: From Diversity To Applications
Insects are by far the most diverse and abundant animal group with respect to the number of species globally, in ecological habitats and in biomass. The ecological and evolutionary success of insects depends in part on their countless relationships with beneficial microorganisms, which are known to influence all aspects of their physiology, ecology, and evolution. These symbiotic associations are known to: (a) enhance nutrient-poor diets, (b) aid digestion of recalcitrant food components, (c) protect from predators, parasites, and pathogens, (d) contribute to inter- and intraspecific communication, (e) affect efficiency as disease vectors and (f) govern mating and reproductive systems. Chara...
Novel Approaches in Microbiome Analyses and Data Visualization
High-throughput sequencing technologies are widely used to study microbial ecology across species and habitats in order to understand the impacts of microbial communities on host health, metabolism, and the environment. Due to the dynamic nature of microbial communities, longitudinal microbiome analyses play an essential role in these types of investigations. Key questions in microbiome studies aim at identifying specific microbial taxa, enterotypes, genes, or metabolites associated with specific outcomes, as well as potential factors that influence microbial communities. However, the characteristics of microbiome data, such as sparsity and skewedness, combined with the nature of data collec...
