UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE
Study programmes & Course catalogue
for academic year 2025/2026
UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE
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Course: The 'unknown unknowns' of arthropod-microbes interactions

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Course title The 'unknown unknowns' of arthropod-microbes interactions
Course code KMB/609
Organizational form of instruction Lecture + Practice
Level of course Doctoral
Year of study not specified
Semester Summer
Number of ECTS credits 2
Language of instruction English
Status of course Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Lukeš Julius, prof. RNDr. CSc.
  • Cabezas Cruz Alejandro, Dr. Ph.D.
Course content
1. The journey of the microbe (Dr. Alejandro Cabezas-Cruz - INRAE, France) 2. Forces shaping the arthropod microbiome (Dr. Alejandra Wu-Chuang - INRAE, France) 3. The role of host-microbe cross-talk in regulating arthropod innate immunity (Dr. Ryan Rego - Institute of Parasitology, Czech Republic) 4. Vector-pathogen-microbiome interactions (Dr. Alejandro Cabezas-Cruz - INRAE, France) 5. Introduction to microbiome analysis (Dr. Dasiel Obregón Alvarez - University of Guelph, Canada) 6. Introduction to microbiome analysis using artificial intelligence (Dr. Fabien Vorimore - ANSES, France) 7. Introduction to network analysis (Prof. Agustín Estrada-Pe?a - University of Zaragoza, Spain) 8. Trans-kingdom molecular communication (Dr. Alejandro Cabezas-Cruz - INRAE, France) 9. Ecosystem Holobiont: importance of arthropod-microbes integration for the ecosystem (Dr. Micaela Tosi - University of Guelph, Canada) 10. Host-microbe interactions through evolutionary time (Dr. Kim Hoang - University of Oxford, UK) Practical lesson 1: 16S rRNA amplicon sequence analysis Practical lesson 2: Data analysis based on Artificial Intelligence

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Written action (comprehensive tests, clauses), Work with multi-media resources (texts, internet, IT technologies), Case studies
  • Semestral paper - 20 hours per semester
  • Preparation for classes - 10 hours per semester
  • Class attendance - 26 hours per semester
Learning outcomes
Conflict and cooperation result from arthropod-microbes interactions. Evolutionary and ecological analyses revealed a continuum in which free-living microbes can become part of arthropod microbiota, then facultative symbionts and at a later stage such interactions can result in obligate symbiosis. Interestingly, obligate symbionts can escape the arthropod hosts and become pathogens with life cycles involving vertebrate and invertebrate hosts. While microbes are recognized as a driving force in arthropod evolution and ecological diversification, some researchers recently argued that some arthropod species are not necessarily associated with microbes. This stirs debate and reclaims a deeper understanding of the evolutionary and ecological conditions that determine ancient arthropod-microbe assembles and the emergence of novel arthropod-microbe interactions. On the root of arthropod-microbes interactions is transkingdom communication which allows molecular signals of one species to be recognized by the other and respond in consequence. For terrestrial life, the soil is a matrix that influences the microbial composition associated with plants and arthropods. In recent years, special attention has been given to the role of microbes in the vectorial competence of arthropod vectors. Sequencing technologies have enabled the exploration of the microbial complexity contained in the environment and arthropod hosts. The study of arthropod-microbes interactions requires skills in data analysis. Arthropod-microbes interaction has become an exciting research area bringing unparalleled innovation with practical uses in society. The aims of the course are: (1) To provide a theoretical basis to understand the scope of arthropod-microbes interactions in nature. (2) To motivate students to explore the contribution of microbes in the biological systems they study. (3) To provide practical tools so they can design experiments including microbiome analysis and carry amplicon sequence analysis.
The course will provide a theoretical basis for understanding the range of arthropod-microbe interactions in nature.
Prerequisites
Basic PC skills, basic knowledge of bioinformatics
UCH/CV036
----- or -----
UCH/036 and KMB/023 and KMB/250

Assessment methods and criteria
Seminar work

Exam in form of evaluated short manuscript-style report from the data analysis.
Recommended literature
  • Alexis A. Smith et al. Cross-Species Interferon Signaling Boosts Microbicidal Activity within the Tick Vector.
  • Andrea Swei and Jessica Y Kwan. Tick microbiome and pathogen acquisition altered by host blood meal.
  • Anton M. Potapov et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates.
  • Benjamin J Callahan et al. DADA 2 : high-resolution sample inference from Iillumina amplicon data.
  • Bolyen et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
  • Congmin Zhu et al. Determine independent gut microbiotadiseases association by eliminating the effects of human lifestyle factors.
  • Constanza Schapheer, Roseli Pellens and Rosa Scherson. Arthropod-Microbiota Integration: Its Importance for Ecosystem Conservation.
  • Danielle NA Lesperance and Nichole A Broderick. Microbiomes as modulators of Drosophila melanogaster homeostasis and disease.
  • David C. Coleman and Diana H. Wall. Soil Fauna: Occurrence, Biodiversity, and Roles in Ecosystem Function.
  • Filip Husnik and Patrick J Keeling. The fate of obligate endosymbionts: reduction, integration, or extinction.
  • Georgia C. Drew , Emily J. Stevens and Kayla C. King. Microbial evolution and transitions along the parasite mutualist continuum.
  • Gina Garland et al. A closer look at the functions behind ecosystem multifunctionality: A review.
  • Girish Neelakanta et al. Anaplasma phagocytophilum induces Ixodes scapularis ticks to express an antifreeze glycoprotein gene that enhances their survival in the cold.
  • Gordon M. Bennett and Nancy A. Moran. Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole.
  • Gregory D.D. Hurst and Alistair C. Darby. The inherited microbiota of arthropods, and their importance in understanding resistance and immunity.
  • Gregory S. Gavelis and Gillian H. Gile. How did cyanobacteria first embark on the path to becoming plastids?: lessons from protist symbioses.
  • Jacob T. Nearing et al. Microbiome differential abundance methods produce different results across 38 datasets.
  • Kayla C. King and Michael B. Bonsall. The evolutionary and coevolutionary consequences of defensive microbes for host-parasite interactions.
  • Kayla C King. Rapid evolution of microbe-mediated protection against pathogens in a worm host.
  • Kim L. Hoang*, Levi T. Morran and Nicole M. Gerardo. Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal?Microbe Interactions.
  • Nabil M. Abrahama et al. Pathogen-mediated manipulation of arthropod microbiota to promote infection.
  • Nicole M Gerardo and Benjamin J Parker. Mechanisms of symbiont-conferred protection against natural enemies: an ecological and evolutionary framework.
  • Paolo Gabrieli et al. Mosquito Trilogy: Microbiota, Immunity and Pathogens, and Their Implications for the Control of Disease Transmission.
  • Shinichiro Enomoto, Abhishek Chari, Adam Larsen Clayton, Colin Dale. Quorum Sensing Attenuates Virulence in Sodalis praecaptivus.
  • Sourabh Samaddar, Liron Marnin, L. Rainer Butler and Joao H.F. Pedra. Immunometabolism in Arthropod Vectors: Redefining Interspecies Relationships.
  • Sukanya Narasimhan et al. Gut Microbiota of the Tick Vector Ixodes scapularis Modulate Colonization of the Lyme Disease Spirochete.
  • Will Van Treuren et al. Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex.
  • Xiaoling Pan et al. The bacterium Wolbachia exploits host innate immunity to establish a symbiotic relationship with the dengue vector mosquito Aedes aegypti.
  • Yong-Xin Liu et al. A practical guide to amplicon and metagenomic analysis of microbiome data.
  • Ziyuan Jiang et al. Accurate diagnosis of atopic dermatitis by combining transcriptome and microbiota data with supervised machine learning.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE, date of update: 21.05.2025 23:50. Data created for academic year 2025/2026