Doctoral Study Programme Microbiology

On this website, you will find information for applicants, students, and supervisors of the doctoral study programme Microbiology, relevant to all four faculties where the programme is accredited, and covering the following topics:

Characterization of the Programme, the Graduate Profile and Career Options

The aim of the programme is to provide students with advanced theoretical and practical knowledge in the field of microbiology, enhancing their ability to formulate research problems, and solve them methodically and experimentally, as well as interpret and present their findings

Graduates of the programme are able to independently design and solve research problems. They propose various solutions to problems, critically analyze the obtained data, and interpret the results. They are proficient in microbiological, biochemical, molecular genetic, analytical, and biophysical methods. Graduates effectively present their findings to scientific forums at both national and international conferences and are also able to present them to the general public. They can independently engage in publishing activities, project development, and are capable of evaluating the publications of other authors. They are prepared to work worldwide in research laboratories within international teams.

Career prospects for programme graduates: Functional genomics and proteomics have revealed the unique genetic potential of microorganisms and the extraordinary variability of their life processes. Therefore, microbiology continues to develop rapidly, and its research and practical applications offer many opportunities for graduates both in academia and industry. Graduates find employment primarily in scientific and teaching positions at domestic and foreign universities and scientific institutes engaged in basic and applied microbiological research or related fields, as well as in research and technology centers focused on similar areas. In the non-academic sphere, they are employed in applied research at development facilities and corporate laboratories, for example, in areas such as biotechnological and pharmaceutical production, clinical microbiology - molecular and biochemical diagnostics of infectious diseases, food microbiology, bioremediation, and water management

Institutions Guaranteeing and Supervising the Programme

The programme is co-accredited at three faculties of Charles University (Faculty of Science, First Faculty of Medicine and Second Faculty of Medicine) and five institutes of the Czech Academy of Sciences (Institute of Microbiology, Institute of Physiology, Institute of Organic Chemistry and Biochemistry, Institute of Experimental Medicine, Institute of Animal Physiology and Genetics and Institute of Physics).

In addition to the mentioned faculties and institutions, supervisors from other institutes in the Czech Republic where microbiological topics are studied also sometimes participate in the programme, e.g., Crop Research Institute, among others.

More detailed information about the research groups of the programme's main supervisors can be found here. On the same website, you will also find links to currently offered doctoral (and potentially postdoctoral) positions and Ph.D. topics listed in SIS. However, it is possible (and recommended) that if you are interested in a topic for which there is no current offer, you contact the head of the relevant supervisory Laboratory in advance and arrange an individual consultation.

Requirements for Supervisors / Co-supervisors and Their Responsibilities

The role of supervisors is to guide the doctoral students academically, recommend relevant scientific literature for their projects (particularly at its beginning), teach students how to navigate the professional community and publicly present their research results, and mentor them in imparting knowledge to other students. Additionally, the supervisors help their students establish professional contacts both domestically and internationally, teach them how to secure financial resources for their projects, and ensure the operational and technical support necessary for the doctoral projects (in collaboration with the supervising institution). Supervisors' duties include monitoring the student's academic progress and regularly consulting on the progress and outcomes of the doctoral project (including overseeing the fulfillment of publication requirements set by the Subject Area Board). Supervisors must collaborate with their students to create their Individual Study Plan (ISP) and evaluate its fulfillment annually in the SIS module, submitting this evaluation to the Subject Area Board for approval (see Article Four, Consolidated Rector's Directive No. 19/2018 as amended by Rector's Directive No. 5/2020).

Doctoral supervisors can be academic or research staff members in the fields covered by the programme. They should ensure the quality and proper guidance of the student and have sufficient time to devote to supervising the doctoral student. Supervisors are appointed and dismissed by the dean of the respective faculty based on the recommendation of the Subject Area Board. If a supervisor is not an associate professor or full professor and has not yet supervised a doctoral student in the Microbiology programme at the respective faculty, he/she must be approved by the programme's Subject Area Board and the Scientific Council of the respective faculty (this approval must be obtained separately for each doctoral study programme and each faculty, i.e., even if the individual has been already approved as a supervisor for another DSP at the same faculty or another faculty of the same DSP, a new application must be submitted!).

An applicant for a supervisory role must therefore submit to the programme Guarantor (who will forward the materials to the Subject Area Board for evaluation) the following:

1) Mandatory: An academic CV (including all previous experience in supervising undergraduate, master's, or doctoral students in any programme at any university).

2) Mandatory: A list of publications

3) An optional: Annotation(s) of project(s) the applicant intends to offer to doctoral students (this may include one or more projects; it is recommended to state the existing or anticipated sources of financial support for the research).

For the Faculty of Science, the above documents can be sent directly to the programme Guarantor via email. The medical faculties have additional specific requirements regarding the format of supervisory applications, whether they should be submitted electronically or in print, and what exactly (in addition to the requirements set by the Subject Area Board) must be attached. In such cases, applications are submitted to the department responsible for doctoral studies at the respective faculty. Relevant information can be found on the websites of the respective faculties (First Faculty of Medicine, Second Faculty of Medicine), or you may contact the doctoral studies administrators (First Faculty of Medicine, Second Faculty of Medicine). Note: The approval process can take a considerable amount of time, depending on the meeting dates of the relevant Subject Area Board/Scientific Councils. At the Faculty of Science, new supervisory applicants are only approved twice a year - spring and fall. Once the supervisor is approved and usually only when he/she officially becomes the supervisor of a specific doctoral student, an official appointment letter is sent by the respective department responsible for doctoral studies (typically not before then). However, it is possible to inquire about the approval status with the DSP Guarantor approximately three months after submitting the application).

For co-supervisors, the situation is somewhat similar. A co-supervisor should be a specialist in a specific area that the supervisor's Laboratory cannot adequately cover academically or technically; usually, he/she should not be from the same Laboratory as the supervisor - see Article Five, Consolidated Rector's Directive No. 19/2018 as amended by Rector's Directive No. 5/2020). The assignment of a co-supervisor to a specific student must always be proposed by the student's supervisor and the same rules apply to applications as for supervisory roles, except that a project annotation is not required, but the specific student for whom the co-supervisor is proposed and the reason for the assignment must be provided. Specific forms for such requests can be found at the websites of the departments responsible for doctoral studies at individual faculties.

If a supervisor fails to fulfill their duties significantly or violates Charles University's Code of Ethics in relation to doctoral students, the student should contact the programme Guarantor (as well as the relevant faculty DSP coordinator, see below), who will decide on the appropriate course of action depending on the specific problem and situation. Similarly, the supervisor should contact the programme Guarantor if the situation is reversed. If there is written or email communication between the supervisor and the doctoral student regarding the issue, it is recommended to present it.

Guarantor, Subject Area Board and Faculty Coordinators

Guarantor of the Programme and Chair of the Subject Area Board: Assoc. Prof. RNDr. Radovan Fišer, Ph.D.

Subject Area Board: The current composition of the Subject Area Board can be found here. The Subject Area Board for Microbiology is part of the Coordination Group for the Natural Sciences Doctoral Programmes and the Coordination Group for the Doctoral Programmes in Biomedicine. 

The Coordinators of the Study Programme for the Respective Faculties:

The Admission Process

Applicants to the programme apply for specific topics, so it is necessary for them to coordinate with the relevant supervisor before submitting their application to ensure they can work on the project in the respective Laboratory. It is recommended that the future supervisor also attends the admission interview (medical faculties explicitly require the supervisor's presence). Applicants are also required to submit a sufficiently detailed abstract of their future doctoral project as an appendix to their application.

The official admission process occurs once a year. Applications must be submitted by the end of April. The actual admission process takes place at the end of June. Current admission conditions, specific dates, and information on the required documents and their format, are published annually on the websites of Charles University and the respective faculties (Faculty of Science, First Faculty of Medicine, Second Faculty of Medicine).

At the Faculty of Science, applicants can also apply to the STARS programme, which is annually offered for exceptionally talented students. The programme is associated with an additional scholarship.

The admissions process is conducted in the form of an oral interview . As part of the interview, the candidates will give a brief, approximately five-minute presentation during which they will discuss their proposed doctoral project or outline their general ideas about what they wish to focus on during their doctoral studies. The candidates may also talk about their Master’s theses or other professional experiences. The committee’s questions will follow up on the proposed project and will partially relate to its topic. The candidates should be able to think about how the scientific problem related to the project could be addressed and what obstacles might arise in solving it. Additionally, the committee's questions may also touch on broader areas of microbiology

Some collaborating institutions (e.g., institutes of the Czech Academy of Sciences) also hold their own preliminary rounds of the admission process (usually in January or February) - relevant information can always be found on the websites of these institutes. However, the acceptance during this preliminary round of admission interviews is not in any way binding for the Charles University and does not automatically mean that the applicant will be accepted into the doctoral study programme during the official admission interviews held by the respective Faculty!

Successful applicants will have to officially enroll in the 1st year of their doctoral studies before the start of the academic year (typically at the end of September). Information on how, when, and where these enrollments take place, and what documents need to be submitted, can be found on the websites of the respective faculties (Faculty of Science, First Faculty of Medicine, Second Faculty of Medicine), or by contacting the doctoral studies administrative personnel (see below).

Doctoral Bursaries and Scholarships

All doctoral students studying within the full-time form of the study programme receive a regular monthly bursary once their studies commence (but not if they are studying in the combined form!), throughout the whole standard study period (i.e., four years). However, this bursary is not provided during he official period(s) of interruptions of their study or if the student has previously unsuccessfully attempted a doctoral programme at the Czech Republic (see Scholarship and Bursary Rules of the Charles University). The specific amount of the doctoral bursary is determined by the Dean of the relevant faculty (see the Dean's Measures for the relevant academic year, available here: Faculty of Science, First Faculty of Medicine, Second Faculty of Medicine). The amount of the monthly bursary typically increases after the successful completion of the state doctoral examination. The Dean may also reduce the bursary amount, upon the proposal of the Subject Area Board, in case the student fails to meet certain obligations of his/her individual study plan without proper justification.

In accordance with the Scholarship and Bursary Rules of the Charles University and the internal regulations of the relevant faculty, doctoral students may also receive additional scholarships/bursaries (e.g., Bursary to Support Study in the Czech Republic, Accomodation Bursary, Bursaries in Cases Worthy a Special Consideration, Scholarships for Research, Development and Innovation (RDI) Activities of for Outstanding RDI activities, etc.). At the Faculty of Science, they may also hold a scholarship within the STARS programme. They may also be nominated for one of the annual awards. More details about this aspect of doctoral studies can be found on the websites of the respective faculties (Faculty of Science, First Faculty of Medicine, Second Faculty of Medicine), or by contacting the administrative personnel for doctoral studies (see below). Doctoral students may also become employees of their supervising institution in accordance with applicable legal regulations; however, this option entirely depends on the decisions of the responsible bodies of the relevant institution and is not guaranteed (please inquire directly with your supervisor).

Study Requirements and Individual Curriculum / Study Plan (ISP)

Preparation and Regular Yearly Evaluation of ISP

The Individual Curriculum / Study Plan (ISP) must always be prepared and followed in accordance with the requirements of the Subject Area Board (see below). Detailed, annually updated instructions on the technical aspects of preparing the ISP and conducting its yearly evaluation can be found at the Faculty of Science Study Department's website. All students and their supervisors are also informed about this by email from the Study Information System, or by the administrative personnel for doctoral studies (depending on the respective faculty).

Recommendations from the programme Guarantor regarding the factual content of the ISP both for its preparation and its yearly evaluation, can be found here:

• Preparation of ISP
• Yearly Evaluation of the ISP

Study Duties

Completion of Specialized Lectures/Courses

During the 1st and 2nd year of study, the student must complete two mandatory courses:

1) Advances in Molecular Biology and Genetics (the SIS code MPGS0034, for the First Faculty of Medicine B90041), which is annually organized by the Institute of Molecular Genetics of the Czech Academy of Sciences. The alternative to this course is Advances in Molecular Genetics of Bacteria (MB140P45).

2) Advances in Microbiology (MPGS0013).

If, for serious reasons (e.g., Cotutelle - doctoral studies under dual dissertation supervision) it is not possible to complete one of these mandatory courses, it may be replaced by a similarly demanding course, subject to the approval of the Subject Area Board.

In addition, the doctoral students select two elective lectures/courses to include in their individual study plan in consultation with their supervisor and based on their professional needs. However, these must be lectures/courses with a truly scientific content. "Soft-skills" courses are not accepted as required study obligations in this context, although the doctoral students may still enroll in and complete them if they deem it appropriate.

The options for selecting the additional two lectures/courses apart from the two mandatory ones, are very broad. These include courses offered by the Faculty of Science, e.g., the elective and recommended courses for the Master's programmes taught by the Department of Genetics and Microbiology, subjects recommended for the students of the doctoral study programme Molecular and Cellular Biology, Genetics, and Virology (their list can be found here), courses from similarly research-oriented departments within the Biology or Chemistry sections of the Faculty of Science, as well as courses from the Faculty of Mathematics and Physics or the medical faculties of Charles University. It is, of course, possible to enroll in and complete more specialized courses according to the doctoral student’s needs and interests, as well as the supervisor’s recommendations.

Another requirement is either a certified English exam (FCE, CAE, TOEFL) or an exam at the Institute for Language and Preparatory Studies, Charles University.

Additional currently offerred interesting courses can be also found at the Doctoral Programmes in Biomedicine website, or at Doctoral Study Hub of the Charles University.

Besides the duty to complete the above specified courses, which is directly stipulated by the Subject Area Board of the DSP Microbiology programme, additional specific study duties may be established by the internal regulations of the faculty to which the student is enrolled, and fulfilling these may be mandatory for students of that faculty if explicitly stated in its official regulations. This applies for the students of the First and Second Faculties of Medicine, who must meet the following strictly prescribed obligations (some in a specific year of study), even if not directly required by our Subject Area Board (individual faculties have the right to impose these requirements on their students):

Participation in Scientific Conferences

PhD students in Microbiology are required to give two presentations about their doctoral project during the standard period of study at the annual Microbiology Ph.D. Student Conference, which is conducted in English. Typically, students present in their 2nd year, where they introduce their project, and in their 4th year, where they report on their readiness for the thesis defense and the results obtained.

Besides this, the Subject Area Board strongly recommends that doctoral students actively participate in national and especially international conferences, either through their own presentations or poster sessions. Such participation provides valuable and highly useful experience for further scientific and research activities. Doctoral students should also attend various types of regular doctoral conferences organized by their faculty or supervisory institution; attendance at such conferences may also be a mandatory part of the ISP, if required by the internal regulations of the faculty (see the table above; this may also be required for students who work on their doctoral projects in one of the institutes of the Czech Academy of Sciences where such regular annual doctoral conferences are held).

Participation in Grant Project Preparation

The Subject Area Board recommends that doctoral students prepare and submit their own projects in the yearly competition for grant allocation at Charles University (GA UK). It is also expected that the students are actively involved in the preparation of grant projects at their research institution.

Participation in International Cooperation

Doctoral students should undertake a research internship abroad (with a total duration of at least one month) during their studies. The inclusion of this internship in the ISP is primarily decided by the supervisor, and its realization depends on the possibilities of the respective research institution. If an internship cannot be arranged, doctoral students should engage in international collaboration in another manner, in accordance with the Standards for Study Programmes at Charles University (article 13 of the Rector´s Directive 13/2019 as amended by Rector´s Directive 22/2022).

Information about various programmes that support international mobility, current offers for study stays abroad, internships, etc., can be found at websites of Charles University and the individual faculties (Faculty of Science, First Faculty of Medicine, Second Faculty of Medicine); for further information, contact the administrative personnel at the relevant departments of the respective faculties.

Creative Work and the Publication Activity

The main requirement for creative work is the independent execution of original and high-quality scientific research, resulting in at least two original scientific publications related to the topic of the doctoral project and published during the doctoral study. At least one of these publications must be an original paper where the doctoral student is the first author and has made a significant contribution. Publication outputs must appear in peer-reviewed journals indexed in databases recognized by the international scientific community (e.g., Web of Science, impact factor journals). In exceptional and justified cases (e.g., obtaining a high-quality first-author publication), the Subject Area Board may decide otherwise. For unpublished papers, confirmation that the manuscript has been accepted for publication by a scientific journal must be provided. Shared first authorship can be recognized as first authorship but requires prior approval from the programme Guarantor who will consult the situation with the Subject Area Board. The same applies for cases where the second required publication is of a type other than an "original paper").

Regulations concerning university/faculty affiliation on publications and its correct wording can be found in the appendix to Rector´s Directive 40/2021 as amended by the Rector´s Directive 26/2023, with official English faculty names in Article 5 of Appendix 1 to Constitution of the Charles University. It is also necessary to adhere to the internal regulations of the respective faculty. If a doctoral student is an author of a publication acknowledging support from a GA UK grant he/she is a principal investigator or a co-investigator of (or from other university projects requiring this), the university and faculty affiliation must be stated (otherwise, such a publication would not be recognized for grant fulfillment). All publications with university/faculty affiliation must also be recorded in the OBD database (see Article 11 of Rector´s Directive 40/2021 as amended by the Rector´s Directive 26/2023). For further information on these aspects of publication activities, the programme Guarantor can provide guidance.

Each doctoral student should also establish so-called Personal Identifiers for Researchers, i.e., 1) ORCID; 2) Researcher ID/Publons ID for Web of Science, and possibly 3) Scopus ID (see Article 5 of Rector´s Directive 40/2021 as amended by the Rector´s Directive 26/2023).

State Doctoral Examination (SDE) and Defense of the Ph.D. Thesis

State doctoral examinations and defenses of Ph.D. theses are organized individually; thus, student can apply for them during the whole academic year. Unlike undergraduate and Master’s studies, applications for the SDE or thesis defense are not submitted directly through the SIS, but must be delivered to the administrative department for the doctoral studies of the respective faculty as a printed, completed, and signed application form along with other required documents (links to the relevant websites for these forms are provided below). Students from the First Faculty of Medicine must not only apply for the SDE according to faculty rules but also pass it by the end of the third year of study - see Dean´s Order No. 16/2022 (available in Czech only).

State Doctoral Examination

Doctoral students must apply for the SDE no later than during their third year of study, If unsuccessful, a second attempt must be made no later than during the following academic year.

The State Doctoral Examination assesses the overall knowledge of the students in the field of microbiology, including the breadth and depth of their theoretical understanding at the current level of scientific knowledge. The exam also aims to evaluate their scientific thinking, specifically their ability to grasp the essence of a given problem and propose their own solutions.

As part of the State Doctoral Examination, the student gives a very brief introductory presentation (up to 10 minutes), to familiarize the committee members with his/her research topic.

The State Doctoral Examination further consists of an oral exam comprising two subjects/areas:

1) the Mandatory Subject/Area: Physiology of Microorganisms; Genetics of Microorganisms

2) the Elective Subject/Area (the student chooses one of the offered options based on the topic of their doctoral project): a) Molecular Biology; b) Medical Microbiology; c) Ecology of Microorganisms

The State Doctoral Examination focuses on three levels of the doctoral student's knowledge in microbiology: 1) the level of theoretical knowledge and the ability to navigate the broad scope of the field; 2) understanding of the principles, methods, and techniques currently used in microbiology, both generally and with regard to the doctoral project; 3) detailed knowledge of the specific issues related to the project's focus.

Detailed information about the SDE procedure and the requirements for students related to this examination and application can be found here.

Ph.D. Thesis and Its Defense

The Ph.D. Thesis represents the culmination and main output of the entire doctoral study. It must be an original author’s work allowing an assessment of whether the candidate is prepared for independent scientific work in the respective field. The doctoral students should be able to comprehensively address the scientific problem in appropriate depth and formulate independent opinions and questions arising from the results of their doctoral project.

Before submitting the thesis for defense the doctoral student must 1) complete all study duties listed in the ISP (referring to subjects with SIS codes), 2) successfully pass the state doctoral examination, and 3) to fulfill the requirements on Creative Work and the Publication Activity for either the full or short format of the Ph.D. thesis (see below).

At the Faculty of Science, the student applies for the defense by uploading the thesis text, any appendices (attention to the correct format!), abstracts in Czech and English, and CV directly into the SIS, allowing it to pass through the relevant SIS checks and confirming submission. The administrative personnel at the Study Department receives notification of the dissertation submission, verifies that the student has met all obligations (only publication requirements are checked directly by the programme Guarantor before the student even uploads the work to the SIS, see the previous paragraph) and confirms the submission in SIS. At this point, the student is formally registered for the defense.

At the medical faculties of Charles University the application for the dissertation defense is not submitted directly in the SIS, but must be delivered to the administrative department responsible for doctoral studies at the respective faculty as a printed, completed, and signed application form along with other required documents (links to the relevant websites for these forms are provided below).

Detailed information about the possible format of the Ph.D. thesis and the defense procedure can be found here.

Before the defense, the quality of the dissertation (its scientific content and formal aspects) is assessed by two reviewers (in necessary cases, the number of reviewers may be higher - e.g., in co-tutelle studies or in repeated defenses where the first attempt was unsuccessful). Reviewers cannot be any of the authors of the publications included as a part of the thesis and, of course, not any member of the research group of the supervisor. Proposals for reviewers are usually submitted by the supervisor to the relevant faculty coordinator or defense committee chair; these proposals may or may not be accepted.

In the case of an unsuccessful dissertation defense, the committee will determine whether it is necessary or possible to revise or supplement the work and specify concrete requirements. In such cases, the student cannot apply for a second defense attempt earlier than six months after the first attempt.

Recently defended Ph.D. theses can be found in the Charles University Digital Repository (use the Advanced Filters and set as Type of work "dizertační práce", then write "Obor mikrobiologie" string to the Search field, and sort by the Issue Date Descending)

Links to Faculty Websites Related to Doctoral Studies