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The Doctoral Study Programme Microbiology

This web page offers information aimed at applicants, students and supervisors of the doctoral study programme Microbiology, relevant for all three faculties the programme is co-accredited at. This information concerns:

Characterization of the Programme (the postgraduate profile and career options)
Institutions Guaranteeing and Supervising the Programme (faculties and other institutions the programme is co-accredited at; laboratories of main supervisors; currently open PhD. and postdoc positions)
Supervisors and Co-supervisors (their duties, documents necessary for the approval by the Subject Area Board)
The Guarantor of the Programme, the Subject Area Board and the Faculty Co-ordinators (contact information)
The Admission Procedure (requirements and recommendations for the applicants, the current admission conditions and schedule, how to enroll in the study after acceptance into the programme)
Doctoral Bursaries and Scholarships

Study Duties and the Individual Curriculum / Study Plan

The State Doctoral Examination, the Doctoral Thesis and Its Defence (their dates and how to apply for the SDE or the defence of the doctoral thesis)

Links to Useful Web Pages (main web pages for the doctoral study at the individual faculties, links to various forms, instruction manuals, contact information for the responsible administrative personnel)

Characterization of the Programme, the Postgraduate Profile and Career Options

The purpose of the programme is to provide its students with advanced theoretical and practical knowledge in various areas of microbiology, that should enable them to formulate scientific problems, to propose methodical and experimental approaches necessary for their solutions,  to interpret their results and to present them in appropriate form at various professional and non-professional venues.

The postgraduate is able to work independently and creatively on research projects, to propose different variants of solution of some scientific problem, and to correctly and critically evaluate and interpret the obtained data. He/she is able to employ current microbiological, molecular biology, biochemical, analytical and biophysical methods, as well as to present the results of scientific experiments to both professional and non-professional public at national/international levels. The postgraduate is also able to independently both write and review scientific publications and project proposals. He/she is fully competent to be a member of international and interdisciplinary scientific teams and to cooperate with other researchers.

The utilisation of various methods of functional genomics and proteomics has revealed a unique genetic potential of microorganisms and remarkable variability of their life processes. Thus, microbiology is currently a very rapidly advancing scientific field concerning both fundamental and applied research, which offers various opportunities for its graduates and postgraduates in the academic domain as well as in the industrial sector. The postgraduates of the Microbiology programme should easily be able to find an employment as researchers/lecturers at universities and various scientific institutions and technological centers engaged in basic and applied microbiology (or related biology/biochemistry/medicine) research. Other career options can be found in the non-academic domain (both public and private sectors): biotechnology and pharmaceutic industry, clinical microbiology - molecular and biochemical diagnostics of infectious diseases, food microbiology, bioremediation, water service and management, etc.

Institutions Guaranteeing and Supervising the Programme

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

Besides the above-mentioned faculties and institutes, other supervisors of our students work also at other institutions that carry out microbiological research, e.g., the Crop Research Institute, etc.

More detailed information on the laboratories of main supervisors of our students can be found here. The currently open Ph.D. and/or postdoc positions together with the offerred topics of doctoral projects can be found on the same web page (unfortunately, some are only in Czech language). However, if the applicant is interested in some scientific subject researched in the respective laboratory, it is possible (and recommended) to contact the head of the laboratory even in case when there is no currently advertised open position – it is often possible to come to some agreement.

Requirements for Supervisors

The supervisor is responsible for the research supervision of the student. He/she should teach the student how to publicly present the results of his/her research to the scientific community and to convey his/her scientific skills and knowledge to other students, as well as how to make international contacts with other scientists and how to acquire financial means to fund his projects. The duty of the supervisor is also to recommend literature sources relevant for the doctoral project and (together with the supervising institution/faculty) to provide the student with the necessary operational and technological support. The supervisor is required to monitor the fulfillment of the student’s duties, to regularly discuss the obtained results of doctoral project and to facilitate and supervise the necessary publication activity of the student as set by the Study Area Board. He/she must, together with the student, prepare and submit the Individual Curriculum / Study Plan, to regularly (at least once a year) assess the student´s work and to submit this assessment in the Study Information System to the Subject Area Board (see Article 4, Consolidated Rector's Directive No. 19/2018 as amended by Rector's Directive No. 5/2020).

The supervisor of a doctoral student can be a member of the academic staff of the Charles University or another scientist whose area of research lies in the main scientific fields of our programme. He/she must guarantee the high quality of the doctoral project and the proper supervision of the doctoral student (this means that he/she should have enough time to do this). The supervisor is appointed and removed by the dean of the respective faculty upon the proposal of the Subject Area Board. In case the potential supervisor does not hold an academic degree of either Associate Professor or Full Professor, he/she must be first approved by the Subject Area Board of the programme and by the Scientific Council of the respective faculty (according to the current rules, this approval must be done separately for each doctoral study programme and each faculty, i.e., even if the future supervisor is already approved for some doctoral study programme at the respective faculty and now applies for a supervising role in another study programme at the same faculty, or is already approved at one co-accredited faculty of some doctoral study programme and now applies for a supervising role at another faculty of the same programme, it is always necessary to apply anew!). For this approval, it is necessary to furnish following documents:

1) the curriculum vitae (besides standard entries, it is recommended to supply an information on the experience with supervising B.Sc., M.Sc. and/or Ph.D. students in any study programme at any university) - required

2) the list of publications - required

2) the annotation(s) of project(s) which the potential supervisor wants to offer to our postgraduate students (one or more, it is also recommended to also supply an information on the financial backing of the respective project(s)) - recommended but optional

In case of the Faculty of Science, it is sufficient to send these documents by e-mail to the Head of the Subject Area Board. The Faculties of Medicine may require other additional supplements (besides the above stated requirements set by our Study Area Board) and have specific directives for supervisor applications including whether the electronic application is sufficient or whether a written and signed form is necessary. In these cases, the applications have to be sent not directly to the Head of the Subject Area Board, but to the respective administrative department that supervises the organization of the doctoral studies. See the web pages of the First or Second Faculties of Medicine for more information or contact the relevant employes of these departments (the First or Second Faculties of Medicine). Note: the approval procedure can be rather lengthy and depends on the frequency of meetings of the Study Area Board and the respective Scientific Councils. Only after the approval procedure is successfully finished, the supervisor is oficially appointed by the dean of the respective faculty and gets a Letter of Appointment (this is administered by the personnel at the department that deals with the doctoral study at the respective faculty).

Regarding potential co-supervisors (also called advisors), the situation is similar. The advisor should be a specialist in some area that the facilities of the supervisor and/or his/her laboratory cannot sufficiently guarantee on theoretical or technological level (see Article 5 of the Consolidated Rector's Directive No. 19/2018 as amended by Rector's Directive No. 5/2020). The appointment of the advisor to the respective student should be always suggested by the supervisor and the requirements for these applications are similar to those stated above for the supervisor (with the exception that no annotation of the project is necessary; on the other hand, it should be stated which student the respective person should be advisor of and why)

In case the supervisor does not correctly fulfill his/her duties (i.e., if there are serious problems with his/her supervision of the student) the doctoral student should firstly contact the Guarantor of the Programme, who decides on the best approach and further solution (depending on the respective situation).

The Guarantor of the Programme, the Subject Area Board and the Faculty Co-ordinators

The Guarantor of the Study Programme and the Head of the Subject Area Board: Ivo Konopásek, CSc., Assistant Professor at the Faculty of Science, Charles University

The Subject Area Board: the current composition of the Subject Area Board can be found here. The Subject Area Board of the doctoral study programme Microbiology is a part of the Coordination Board of Doctoral Study Programmes in Natural Sciences and also a part of the Coordination Group of the Doctoral Study Programmes in Biology and Medicine.

The Co-ordinators of the Study Programme at the Respective Faculties:

Faculty Co-ordinator E-mail  Phone Where to Find Us 
Faculty of Science RNDr. Ivo Konopásek, CSc., Assistant Professor konop@natur.cuni.cz +420 221 951 711 Department of Genetics and Microbiology, Viničná 5, Praha 2 - Nové Město,

50.0717261N, 14.4240942E

First Faculty of Medicine RNDr. Jaroslav Julák, CSc., Assistant Professor jaroslav.julak@lf1.cuni.cz +420 224 968 466 Institute of Immunology and Microbiology, Studničkova 2028/7, Praha 2 - Nové Město,

50.0698708N, 14.4245094E

Second Faculty of Medicine MUDr. Pavel Dřevínek, Ph.D., Full Professor pavel.drevinek@lfmotol.cuni.cz

+420 224 435 350

Department of Medical Microbiology, V úvalu 84/1, Praha 5 - Motol,

50.0741847N, 14.3408656E

The Admission Procedure

Prior to submitting the formal application for the study, the applicants are strongly recommended to contact some potential supervisor from one of our faculties or other co-operating institutions (see above) and to come to a preliminary agreement regarding the possibility of work on some doctoral project in the respective laboratory. In such case it is also strongly recommended to submit as a supplement to the application form (and other necessary requirements) a short but cogent annotation of the proposed doctoral research project (including its preliminary title, name/surname of the supervisor and his/her place of work). A potential supervisor is then more than welcome (even required by our Faculties of Medicine) to be present at the official admission interview. 

The official admission interview takes place once a year. The deadline for applications is usually at the end of April and the admission interviews then take place usually at the end of June. The details of the admission procedure can slightly change between years; the current admission conditions and other information on the admission procedure can be always found at the web pages of the Charles University and the respective faculties (the Faculty of Science, the First or Second Faculties of Medicine).

Applicants for the doctoral study at the Faculty of Science can also apply for the STARS programme scholarship which is aimed to attract the excellent students. STARS students get an additional financial supplement to their regular doctoral bursary each month.

The admission interview is in oral form. After the necessary formalities, the applicant must briefly (5 min at maximum) talk about his/her proposed doctoral project or at least to present a general idea which scientific field he/she would want to be engaged in during the doctoral study. It is also possible to briefly mention the topic and purpose of the M.Sc. thesis or other scientific experience. The questions of the members of the admission committee will follow this talk and will be mostly related to the proposed project. The applicant should be able to independently think about the project and to come with ideas how the relevant scientific problem could be studied, what difficulties could various proposed solutions be met with, etc. The general knowledge of the applicant in the field of microbiology, can be also examined by the members of the admission committee.

Some of our co-operating institutions (mostly the research institutes of the Czech Academy of Sciences) also hold their own preliminary round of interviews (usually in January or February) – the respective information on this can be found on their web pages.

The successful applicants will be informed about their acceptance into the programme officially either by a letter or by e-mail by the administrative personnel dealing with the doctoral study at the respective faculty of the Charles University. Prior to start of the academic year (usually by the end of September), the students have to oficially enroll/register in the study programme. Information about this enrollment/registration (its time and place, the necessary documents that have to be submitted, etc.) can be found at the web pages of the respective faculties (the Faculty of Science, the First or Second Faculties of Medicine) or it is possible to contact the respective administrative personnel for further details (see the end of this page).

Doctoral Bursaries and Scholarships

All doctoral students enrolled in a full-time version (not in the combined version) of the doctoral programme are awarded a monthly doctoral bursary during the standard length of the study (i.e., four years). This bursary is not awarded to the students that were previously enrolled in a Ph.D. programme at some Czech public higher education institution and their previous study was not successfully concluded (see Scholarship and Bursary Rules of the Charles University). Students also do not get this bursary during the official period(s) of interruption of their study. The specific amount of the bursary is determined by the dean of the respective faculty (see the respective Dean´s Provisions/Measures: the Faculty of Science (currently in Czech only); the First or Second Faculties of Medicine). After successful passing of the state doctoral examination by the student, the doctoral bursary is usually increased. However, it is also possible for the dean of the faculty to reduce the bursary based on the evaluation of the student by the Subject Area Board (mostly in cases where the student significantly fails to fulfill the individual curriculum / study plan).

Doctoral students can be also awarded other scholarships/bursaries in accordance with the Scholarship and Bursary Rules of the Charles University and the rules of the respective faculties (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.). The Faculty of Science also offers its excellent Ph.D. students an opportunity to take a part of the STARS programme. They can be also nominated for various awards. More detailed information on this aspect of the doctoral study can be found at the web pages of the individual faculties (the Faculty of Science, the First or Second Faculties of Medicine) or will be provided by the respective administrative personnel dealing with doctoral students (see below for the contact information). Doctoral students can be also employed by their supervising institution in accordance with the current employment legislation; however, this possibility always depends on the decision of the respective institution where their supervisor is employed and is not in any way guaranteed! (please, contact your potential supervisor regarding this possibility if you want to know more).

Study Duties and the Individual Curriculum / Study Plan

Preparation and Regular Assessment of the Fulfillment of the Individual Curriculum

The Individual Curriculum / Study Plan (ISP) has to be prepared and carried out in accordance with the requirements of the Subject Area Board (see below). Regarding the technical side of its preparation and yearly filling out, a detailed instructions can be found at the web pages of the Study Department of the Faculty of Science (these instructions can be mostly followed by the students of the Faculties of Medicine as well; however they should be adjusted to the respective demands of these faculties; other instructions can be found, e.g., at the web pages of the Second Faculty of Medicine for students registered there).

The recommendations of the Head of the Subject Area Board regarding the factual side of the Individual Curriculum / Study Plan can be found here:

Study Duties

During their first and second year of the study, our doctoral students must complete two compulsory lectures/courses:

In case student could not complete one (or more) of these required courses for serious reasons (e.g., Co-tutelle study), it is possible to replace it/them with other lecture/course(s) of similar character; however, the Study Area Board must agree with suggested solution

Further two additional lectures/courses that must be also part of the Individual Curriculum / Study Plan are selected by the doctoral student together with his/her supervisor depending on the scientific/technical needs of the student. However, a lecture/course with some truly scientific subject must be always chosen (so called soft skills lectures/courses cannot be accepted as the required study duty, although they can be also included in the ISP and completed if it is a wish of the student or a requirement of the faculty he/she is registered in). There is an extensive list of lectures/courses that can be selected; student can choose from various options offered, e.g., to graduate students of the Department of Genetics and Microbiology, Faculty of Science, Charles University (in Czech Only; however, with links to the respective lectures/courses in the Study Information System), from the list of lectures/courses that are of interest for the doctoral students of the Molecular and Cellular Biology, Genetics and Virology programme, the lectures/courses offered by other departments of the Biological or Chemical Sections of the Faculty of Science with similar research focus, as well as the Faculty of Mathematics and Physics or Faculties of Medicine. It is, of course, possible to select and successfully pass more lectures/courses according to the needs and interests of the student and the recommendations of his/her supervisor.

The third study duty that must be completed is a certified English language exam (FCE, CAE, TOEFL) or an exam organized by Institute of Language and Preparatory Studies, Charles University.

Additional courses that are currently opened and could be of interest for our doctoral students can be also found at the web pages of the Doctoral Study Programmes in Biology and Medicine, or at the Doctoral Study Hub of the Charles University.

Besides the above-stated requirements set by the Subject Area Board, some additional study duties can be stipulated by the internal rules of the respective faculty the student is registered in. In case when it is explicitely stated in these rules, the successful completion of such study duties can be an additional condition necessary to be included in the ISP (please contact the respective faculty co-ordinator or administrative personnel for further information on this).

Participation in Conferences

During the standard length of their study, the students must present the results of their research (in English) two times at the Conference of Doctoral Students of the Microbiology Programme. The first presentation usually takes place during the 2nd year of the study (the introduction to the respective project) and the second presentation is realized during the 4th year of the study (the results and  a general readines for the thesis defence).

The Subject Area Board also strongly recommends an active participation (i.e., the student should present his/her own lecture or poster) of doctoral students in national and particularly international conferences; this will enable them to acquire necessary and useful experience for their further scientific work. Our students should also participate in various types of regular conferences for doctoral students organized by their respective faculty / supervising institution; participation in this type of conference can even be an obligatory component of the ISP in case when it is explicitely stated in the internal rules of the respective faculty (strictly required for the students of the First and Second Faculties of Medicine; as regards the Faculty of Science, it can be required for students who work on their doctoral projects at some institute of the Czech Academy of Sciences or other institution that regularly organizes such conferences).

Participation in Preparation of Grant Proposals

The students should particularly endeavour to prepare and submit their own grant application to the Charles University Grant Agency (GA UK) in the yearly competition for grant allocation. The active involvement of students in preparation of grant proposals of the supervising laboratory is also recommended by the Subject Area Board.

Participation in International Cooperation

Doctoral students are strongly recommended to complete a research internship abroad during their study (total length at least 1 month). The decision on the inclusion of such internship in the ISP rests mainly with the supervisor and its realization depends on the options and resources of the supervising laboratory. In case such internship is not possible, the doctoral students must participate in international scientific cooperation by some other way in compliance with the Standards of the Study Programmes of Charles University.

Information on various opportunities for international mobility and its financing, the open positions for short-term or long-term internships abroad, etc., can be found at the Doctoral Study Hub of the Charles University or the web pages of the individual faculties (the Faculty of Science,  the First or Second Faculties of Medicine). For further information, please contact the administrative personnel at the appropriate departments of the respective faculties.

Creative Work and the Publication Activity

The core of the doctoral study lies in the original, high-quality research independently carried out by the doctoral student. This research must result in at least two original scientific publications relevant to the topic of the doctoral thesis and published during the course of the doctoral study. At least at one of these “original research articles” the doctoral student must be its first author and must significantly participate in its creation. The two required papers must be published in peer-reviewed journals indexed in reputable databases acknowledged by the general scientific community (Web of Science, journals with the impact factor, IF). If the paper is not yet published/assigned DOI, the students must present a record of confirmation of its acceptance by the respective scientific journal, otherwise such publication cannot be counted among the required number. The shared first-authorship can be accepted as the first-authorship only after the agreement of the Guarantor of the Programme and the Subject Area Board; this applies also in case when the second required publication is another type than an “original research article”. 

The necessary information on the correct wording and the rules for the use of the official institutional affiliation(s) can be find in the Appendix 1 to the Constitution of Charles University (Article 5) or in the Appendix to the Rector´s Directive 24/2018. It is also always necessary to abide by the rules of the respective faculty in this respect. The students must always include the respective university/faculty affiliation in any publication that was financially supported by the Charles University Grant Agency or other university agencies that support research (otherwise such publication would not be accepted at the end of the respective project as the fulfillment of grant conditions). All publications (with the exception of conference abstracts) with the university/faculty affiliation must be also registered in the university database OBD (see the Rector´s Directive 24/2018, Article 11). Further information on these aspects of the publication activity can be given by the Head of the Subject Area Board.

All doctoral students should also set up their Personal Identifiers for Researchers, i.e., 1) ORCID/Publons ID, 2) Researcher ID for Web of Science and 3) Scopus ID (see the Rector´s Directive 24/2018, Article 5).

The State Doctoral Examination (SDE) and the Defence of the Doctoral Thesis

State doctoral examinations and thesis defences are organized individually. It is possible to apply for them any time during the whole academic year. The application for the SDE or the defence of the doctoral thesis must be submitted as a printed, filled and signed form (together with other documents as required) directly to the respective administrative department dealing with the doctoral study, i.e., NOT electronically! (the links to the web pages with the application forms and the instructions regarding the other documents that must be submitted at the same time as the application form can be found below).

The State Doctoral Examination

Our doctoral students must apply for the SDE during the third year of their study at the latest. In case their first attempt to pass this examination is not successful, the second attempt must be made during the academic year following the first SDE attempt at the latest. 

The State Doctoral Examination (SDE) checks whether the student´s general theoretical knowledge of microbiology is of a sufficient depth and width regarding the current state of knowledge in this scientific field. The purpose of the examination is also to test the student´s scientific abilities, i.e., to comprehend the essence of any scientific problem and to propose their own creative solutions.

A short (maximum 10 min) presentation by the student, which introduces the topic of the respective doctoral project to the the members of the committee is a necessary part of the SDE (the SDE begins with this presentation).

The SDE further consists of an oral examination focused on the student´s knowledge on two subjects:

1) the obligatory subject:

  • Physiology of Microorganisms
  • Genetics of Microorganisms

2) the elective subject (the student selects one option among these stated below, in accordance to his/her doctoral project):

  • Molecular Biology
  • Medical Microbiology

The SDE focuses on three levels of student´s knowledge: 1) good general theoretical background and orientation in the whole field of microbiology; 2) knowledge on various methodical approaches utilized in microbiology, particularly these related specifically to his/her own research (their principles, various advantages and disadvantages); 3) advanced and detailed knowledge on the current state of scientific topics directly related to his/her doctoral project.

More detailed information on the SDE procedure and relevant requirements for the doctoral students associated with this examination (particularly the detailed summaries of required knowledge on the above mentioned obligatory and elective subjects) can be found here.

The Doctoral Thesis and Its Defence

The doctoral thesis is a culmination and the main result of the whole doctoral study. It must be an original work of the doctoral student. It should provide sufficient information necessary for the assessment whether the student is qualified for an independent research work in his/her respective scientific field. The doctoral student should be able to comprehensively describe and adequately cover the topic of the doctoral thesis, as well as to independently formulate opinions and questions based on the results of his/her doctoral project.

Prior to the submission of the doctoral thesis for its defence, all study duties stated in the Individual Study Curriculum must be successfully completed and the same applies for the SDE. In addition to this, the publication requirements for the so-called "long" or "short" form of the doctoral thesis (see below) must be fulfilled; these publications must be relevant to the topic of the doctoral thesis and published during the course of the doctoral study in IF journals (see Creative Work and Publication Activity Requirements). 

More detailed information on the allowed form of the doctoral thesis and the procedure of its defence can be found here.

Prior to the defence, the quality and originality of the thesis (as well as its various formal aspects) is assessed independently by two reviewers (in some cases, e.g., in the co-tutelle form of the study, there can be more reviewers). No person that is a co-author of any publication the doctoral thesis is based on can fulfill the role of the reviewer of the respective thesis.

If the first attempt at the thesis defence fails, the Committee for the Defence of Doctoral Thesis determines whether it is possible to re-write or in some way supplement the thesis. Also, the Committee specifically states what is necessary to do before the second attempt. This second attempt at the defence of the doctoral thesis cannot be realized before at least six months passed after the first attempt.

Doctoral theses of past students of the Microbiology programme, that were (recently) defended, can be found in the Charles University Digital Repository.

Links to Web Pages of the Respective Faculties Relevant to the Doctoral Study

Faculty Main Web Pages for the Doctoral Study Forms for Doctoral Students and Their Supervisors  Administrative Personnel Dealing with the Doctoral Students and Applicants 
Faculty of Science https://www.natur.cuni.cz/eng/study/student/doctoral https://www.natur.cuni.cz/eng/study/student/doctoral/forms https://www.natur.cuni.cz/eng/study/department-of-student-affairs
First Faculty of Medicine https://en.lf1.cuni.cz/doctoral-studies- https://en.lf1.cuni.cz/forms-for-phd-students https://en.lf1.cuni.cz/contacts?sWorkPlaceID=LF1354#contacts
Second Faculty of Medicine https://www.lf2.cuni.cz/en/phd/doctoral-studies https://www.lf2.cuni.cz/en/phd/phd-study/forms-and-patterns

https://www.lf2.cuni.cz/en/phd/phd

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