Submissions

Author Guidelines

Types of Publications

Microorganisms has no restrictions on the length of manuscripts, provided that the text is concise and comprehensive. Full experimental details must be provided so that the results can be reproduced. Microorganisms requires that authors publish all experimental controls and make full datasets available where possible.

Manuscripts submitted to Microorganisms should neither be published previously nor be under consideration for publication in another journal. The main article types are as follows:

• Articles: Original research manuscripts. The journal considers all original research manuscripts provided that the work reports scientifically sound experiments and provides a substantial amount of new information. Authors should not unnecessarily divide their work into several related manuscripts, although Short Communications of preliminary, but significant, results will be considered. The quality and impact of the study will be considered during peer review.
• Reviews: These provide concise and precise updates on the latest progress made in a given area of research.

Submission Process

Manuscripts for Microorganisms should be submitted online at susy.mdpi.com. The submitting author, who is generally the corresponding author, is responsible for the manuscript during the submission and peer-review process. The submitting author must ensure that all eligible co-authors have been included in the author list (read the criteria to qualify for authorship) and that they have all read and approved the submitted version of the manuscript. To submit your manuscript, register and log in to the submission website. Once you have registered, click here to go to the submission form for Microorganisms. All co-authors can see the manuscript details in the submission system, if they register and log in using the e-mail address provided during manuscript submission.

Accepted File Formats

Authors must use the Microsoft Word template to prepare their manuscripts. Using the template file will substantially shorten the time to complete copy-editing and publication of accepted manuscripts. The total amount of data for all files must not exceed 120 MB. If this is a problem, please contact the Editorial Office microbiology@scilip.com. Accepted file formats are:

• Microsoft Word: Manuscripts prepared in Microsoft Word must be converted into a single file before submission. When preparing manuscripts in Microsoft Word, the Microorganisms Microsoft Word template file must be used. Please insert your graphics (schemes, figures, etc.) in the main text after the paragraph of its first citation.

• LaTeX: Manuscripts prepared in LaTeX must be collated into one ZIP folder (including all source files and images, so that the Editorial Office can recompile the submitted PDF). When preparing manuscripts in LaTeX, please use the Microorganisms LaTeX template files. You can now also use the online application writeLaTeX to submit articles directly to Microorganisms. The MDPI LaTeX template file should be selected from the writeLaTeX template gallery.

• Supplementary files: May be any format, but it is recommended that you use common, non-proprietary formats where possible.

Disclaimer: Usage of these templates is exclusively intended for submission to the journal for peer-review, and strictly limited to this purpose and it cannot be used for posting online on preprint servers or other websites.

Free Format Submission

Microorganisms now accepts free format submission:

• We do not have strict formatting requirements, but all manuscripts must contain the required sections: Author Information, Abstract, Keywords, Introduction, Materials & Methods, Results, Conclusions, Figures and Tables with Captions, Funding Information, Author Contributions, Conflict of Interest and other Ethics Statements.
• Your references may be in any style, provided that you use the consistent formatting throughout. It is essential to include author(s) name(s), journal or book title, article or chapter title (where required), year of publication, volume and issue (where appropriate) and pagination. DOI numbers (Digital Object Identifier) are not mandatory but highly encouraged. The bibliography software package EndNote, Zotero, Mendeley, Reference Manager are recommended.
• When your manuscript reaches the revision stage, you will be requested to format the manuscript according to the journal guidelines.

Cover Letter

A cover letter must be included with each manuscript submission. It should be concise and explain why the content of the paper is significant, placing the findings in the context of existing work and why it fits the scope of the journal. Confirm that neither the manuscript nor any parts of its content are currently under consideration or published in another journal. Any prior submissions of the manuscript to MDPI journals must be acknowledged. The names of proposed and excluded reviewers should be provided in the submission system, not in the cover letter.

Author Biography

Authors are encouraged to add a biography (maximum 150 words) to the submission and publish it. This should be a single paragraph and should contain the following points:

1. Authors’ full names followed by current positions;
2. Education background including institution information and year of graduation (type and level of degree received);
3. Work experience;
4. Current and previous research interests;
5. Memberships of professional societies and awards received.

Manuscript Preparation

General Considerations

• Research manuscripts should comprise:
• Front matter: Title, Author list, Affiliations, Abstract, Keywords
• Research manuscript sections: Introduction, Materials and Methods, Results, Discussion, Conclusions (optional).
• Back matter: Supplementary Materials, Acknowledgments, Author Contributions, Conflicts of Interest, References.
• Review manuscripts should comprise the front matter, literature review sections and the back matter. The template file can also be used to prepare the front and back matter of your review manuscript. It is not necessary to follow the remaining structure. Structured reviews and meta-analyses should use the same structure as research articles and ensure they conform to the PRISMA guidelines.
• Graphical Abstract:

A graphical abstract (GA) is an image that appears alongside the text abstract in the Table of Contents. In addition to summarizing content, it should represent the topic of the article in an attention-grabbing way.

The GA should be a high-quality illustration or diagram in any of the following formats: PNG, JPEG, EPS, SVG, PSD or AI. Written text in a GA should be clear and easy to read, using one of the following fonts: Times, Arial, Courier, Helvetica, Ubuntu or Calibri.

The minimum required size for the GA is 560 × 1100 pixels (height × width). When submitting larger images, please make sure to keep to the same ratio.

• Abbreviations should be defined in parentheses the first time they appear in the abstract, main text, and in figure or table captions and used consistently thereafter.
• SI Units (International System of Units) should be used. Imperial, US customary and other units should be converted to SI units whenever possible.
• Accession numbers of RNA, DNA and protein sequences used in the manuscript should be provided in the Materials and Methods section.
• Equations: If you are using Word, please use either the Microsoft Equation Editor or the Math Type add-on. Equations should be editable by the editorial office and not appear in a picture format.
• Research Data and supplementary materials: Note that publication of your manuscript implies that you must make all materials, data, and protocols associated with the publication available to readers. Disclose at the submission stage any restrictions on the availability of materials or information.
• Preregistration: Where authors have preregistered studies or analysis plans, links to the preregistration must be provided in the manuscript.

Front Matter

These sections should appear in all manuscript types

• Title: The title of your manuscript should be concise, specific and relevant. It should identify if the study reports (human or animal) trial data, or is a systematic review, meta-analysis or replication study. When gene or protein names are included, the abbreviated name rather than full name should be used.
• Author List and Affiliations: Authors' full first and last names must be provided. The initials of any middle names can be added. The PubMed/MEDLINE standard format is used for affiliations: complete address information including city, zip code, state/province, and country. At least one author should be designated as corresponding author, and his or her email address and other details should be included at the end of the affiliation section.
• Abstract: The abstract should be a total of about 200 words maximum. The abstract should be a single paragraph and should follow the style of structured abstracts, but without headings: 1) Background: Place the question addressed in a broad context and highlight the purpose of the study; 2) Methods: Describe briefly the main methods or treatments applied. Include any relevant preregistration numbers, and species and strains of any animals used. 3) Results: Summarize the article's main findings; and 4) Conclusion: Indicate the main conclusions or interpretations. The abstract should be an objective representation of the article: it must not contain results which are not presented and substantiated in the main text and should not exaggerate the main conclusions.
• Keywords: Three to ten pertinent keywords need to be added after the abstract. We recommend that the keywords are specific to the article, yet reasonably common within the subject discipline.

Research Manuscript Sections

• Introduction: The introduction should briefly place the study in a broad context and highlight why it is important. It should define the purpose of the work and its significance, including specific hypotheses being tested. The current state of the research field should be reviewed carefully and key publications cited. Please highlight controversial and diverging hypotheses when necessary. Finally, briefly mention the main aim of the work and highlight the main conclusions. Keep the introduction comprehensible to scientists working outside the topic of the paper.
• Materials and Methods: They should be described with sufficient detail to allow others to replicate and build on published results. New methods and protocols should be described in detail while well-established methods can be briefly described and appropriately cited. Give the name and version of any software used and make clear whether computer code used is available. Include any pre-registration codes.
• Results: Provide a concise and precise description of the experimental results, their interpretation as well as the experimental conclusions that can be drawn.
• Discussion: Authors should discuss the results and how they can be interpreted in perspective of previous studies and of the working hypotheses. The findings and their implications should be discussed in the broadest context possible and limitations of the work highlighted. Future research directions may also be mentioned. This section may be combined with Results.
• Conclusions: This section is not mandatory, but can be added to the manuscript if the discussion is unusually long or complex.
• Patents: This section is not mandatory, but may be added if there are patents resulting from the work reported in this manuscript.

Back Matter

• Supplementary Materials: Describe any supplementary material published online alongside the manuscript (figure, tables, video, spreadsheets, etc.). Please indicate the name and title of each element as follows Figure S1: title, Table S1: title, etc.
• Funding: All sources of funding of the study should be disclosed. Clearly indicate grants that you have received in support of your research work and if you received funds to cover publication costs. Note that some funders will not refund article processing charges (APC) if the funder and grant number are not clearly and correctly identified in the paper. Funding information can be entered separately into the submission system by the authors during submission of their manuscript. Such funding information, if available, will be deposited to FundRef if the manuscript is finally published.
  Please add: “This research received no external funding” or “This research was funded by [name of funder] grant number [xxx]” and “The APC was funded by [XXX]” in this section. Check carefully that the details given are accurate and use the standard spelling of funding agency names at https://search.crossref.org/funding, any errors may affect your future funding.
• Acknowledgments: In this section you can acknowledge any support given which is not covered by the author contribution or funding sections. This may include administrative and technical support, or donations in kind (e.g., materials used for experiments).
• Author Contributions: Each author is expected to have made substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data; or the creation of new software used in the work; or have drafted the work or substantively revised it; AND has approved the submitted version (and version substantially edited by journal staff that involves the author’s contribution to the study); AND agrees to be personally accountable for the author’s own contributions and for ensuring that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and documented in the literature.
• For research articles with several authors, a short paragraph specifying their individual contributions must be provided. The following statements should be used "Conceptualization, X.X. and Y.Y.; Methodology, X.X.; Software, X.X.; Validation, X.X., Y.Y. and Z.Z.; Formal Analysis, X.X.; Investigation, X.X.; Resources, X.X.; Data Curation, X.X.; Writing – Original Draft Preparation, X.X.; Writing – Review & Editing, X.X.; Visualization, X.X.; Supervision, X.X.; Project Administration, X.X.; Funding Acquisition, Y.Y.”, please turn to the CRediT taxonomy for the term explanation. For more background on CRediT, "Authorship must include and be limited to those who have contributed substantially to the work. Please read the section concerning the criteria to qualify for authorship carefully".
• Data Availability Statement: In this section, please provide details regarding where data supporting reported results can be found, including links to publicly archived datasets analysed or generated during the study. Please refer to suggested Data Availability Statements in section “MDPI Research Data Policies”. You might choose to exclude this statement if the study did not report any data.
• Conflicts of Interest: Authors must identify and declare any personal circumstances or interest that may be perceived as influencing the representation or interpretation of reported research results. If there is no conflict of interest, please state "The authors declare no conflict of interest." Any role of the funding sponsors in the choice of research project; design of the study; in the collection, analyses or interpretation of data; in the writing of the manuscript; or in the decision to publish the results must be declared in this section. Microorganisms does not publish studies funded by the tobacco industry. Any projects funded by industry must pay special attention to the full declaration of funder involvement. If there is no role, please state “The sponsors had no role in the design, execution, interpretation, or writing of the study”.
• References: References must be numbered in order of appearance in the text (including table captions and figure legends) and listed individually at the end of the manuscript. We recommend preparing the references with a bibliography software package, such as EndNote, Reference Manager or Zotero to avoid typing mistakes and duplicated references. We encourage citations to data, computer code and other citable research material. If available online, you may use reference style 9. below.
• Citations and References in Supplementary files are permitted provided that they also appear in the main text and in the reference list.

In the text, reference numbers should be placed in square brackets [ ], and placed before the punctuation; for example [1], [1–3] or [1,3]. For embedded citations in the text with pagination, use both parentheses and brackets to indicate the reference number and page numbers; for example [5] (p. 10). or [6] (pp. 101–105).

The reference list should include the full title, as recommended by the ACS style guide. Style files for Endnote and Zotero are available.

References should be described as follows, depending on the type of work:

Journal Articles:
1. Author 1, A.B.; Author 2, C.D. Title of the article. Abbreviated Journal Name Year, Volume, page range.

Books and Book Chapters:
2. Author 1, A.; Author 2, B. Book Title, 3rd ed.; Publisher: Publisher Location, Country, Year; pp. 154–196.
3. Author 1, A.; Author 2, B. Title of the chapter. In Book Title, 2nd ed.; Editor 1, A., Editor 2, B., Eds.; Publisher: Publisher Location, Country, Year; Volume 3, pp. 154–196.

Unpublished work, submitted work, personal communication:
4. Author 1, A.B.; Author 2, C. Title of Unpublished Work. status (unpublished; manuscript in preparation).
5. Author 1, A.B.; Author 2, C. Title of Unpublished Work. Abbreviated Journal Name stage of publication (under review; accepted; in press).
6. Author 1, A.B. (University, City, State, Country); Author 2, C. (Institute, City, State, Country). Personal communication, Year.

Conference Proceedings:
7. Author 1, A.B.; Author 2, C.D.; Author 3, E.F. Title of Presentation. In Title of the Collected Work (if available), Proceedings of the Name of the Conference, Location of Conference, Country, Date of Conference; Editor 1, Editor 2, Eds. (if available); Publisher: City, Country, Year (if available); Abstract Number (optional), Pagination (optional).

Thesis:
8. Author 1, A.B. Title of Thesis. Level of Thesis, Degree-Granting University, Location of University, Date of Completion.

Websites:
9. Title of Site. Available online: URL (accessed on Day Month Year).
Unlike published works, websites may change over time or disappear, so we encourage you create an archive of the cited website using a service such as Website. Archived websites should be cited using the link provided as follows:

10. Title of Site. URL (archived on Day Month Year).

See the Reference List and Citations Guide for more detailed information.

Preparing Figures, Schemes and Tables

• File for Figures and Schemes must be provided during submission in a single zip archive and at a sufficiently high resolution (minimum 1000 pixels width/height, or a resolution of 300 dpi or higher). Common formats are accepted; however, TIFF, JPEG, EPS and PDF are preferred.
• Microorganisms can publish multimedia files in articles or as supplementary materials. Please contact the editorial office for further information.
• All Figures, Schemes and Tables should be inserted into the main text close to their first citation and must be numbered following their number of appearance (Figure 1, Scheme I, Figure 2, Scheme II, Table 1, etc.).
• All Figures, Schemes and Tables should have a short explanatory title and caption.
• All table columns should have an explanatory heading. To facilitate the copy-editing of larger tables, smaller fonts may be used, but no less than 8 pt. in size. Authors should use the Table option of Microsoft Word to create tables.
• Authors are encouraged to prepare figures and schemes in color (RGB at 8-bit per channel). There is no additional cost for publishing full color graphics.

Supplementary Materials, Data Deposit and Software Source Code

MDPI Research Data Policies

MDPI is committed to supporting open scientific exchange and enabling our authors to achieve best practices in sharing and archiving research data. We encourage all authors of articles published in MDPI journals to share their research data. Individual journal guidelines can be found at the journal ‘Instructions for Authors’ page. Data sharing policies concern the minimal dataset that supports the central findings of a published study. Generated data should be publicly available and cited in accordance with journal guidelines.

Where ethical, legal or privacy issues are present, data should not be shared. The authors should make any limitations clear in the Data Availability Statement upon submission. Authors should ensure that data shared are in accordance with consent provided by participants on the use of confidential data.

Data Availability Statements provide details regarding where data supporting reported results can be found, including links to publicly archived datasets analyzed or generated during the study.

Below are suggested Data Availability Statements:

• Data available in a publicly accessible repository
  The data presented in this study are openly available in [repository name e.g., FigShare] at [doi], reference number [reference number].
• Data available in a publicly accessible repository that does not issue DOIs
  Publicly available datasets were analysed in this study. This data can be found here: [link/accession number]
• Data available on request due to restrictions e.g., privacy or ethical
  The data presented in this study are available on request from the corresponding author. The data are not publicly available due to [insert reason here]
• 3rd Party Data
  Restrictions apply to the availability of these data. Data was obtained from [third party] and are available [from the authors / at URL] with the permission of [third party].
• Data sharing not applicable
  No new data were created or analyzed in this study. Data sharing is not applicable to this article.
• Data is contained within the article or supplementary material
  The data presented in this study are available in [insert article or supplementary material here]

Data citation:

• [dataset] Authors. Year. Dataset title; Data repository or archive; Version (if any); Persistent identifier (e.g., DOI).

Computer Code and Software

For work where novel computer code was developed, authors should release the code either by depositing in a recognized, public repository such as GitHub or uploading as supplementary information to the publication. The name, version, corporation and location information for all software used should be clearly indicated. Please include all the parameters used to run software/programs analyses.

Supplementary Material

Additional data and files can be uploaded as "Supplementary Files" during the manuscript submission process. The supplementary files will also be available to the referees as part of the peer-review process. Any file format is acceptable; however, we recommend that common, non-proprietary formats are used where possible.

References in Supplementary Files

Citations and References in Supplementary files are permitted provided that they also appear in the reference list of the main text.

Unpublished Data

Restrictions on data availability should be noted during submission and in the manuscript. "Data not shown" should be avoided: authors are encouraged to publish all observations related to the submitted manuscript as Supplementary Material. "Unpublished data" intended for publication in a manuscript that is either planned, "in preparation" or "submitted" but not yet accepted, should be cited in the text and a reference should be added in the References section. "Personal Communication" should also be cited in the text and reference added in the References section. (see also the MDPI reference list and citations style guide).

Remote Hosting and Large Data Sets

Data may be deposited with specialized service providers or institutional/subject repositories, preferably those that use the DataCite mechanism. Large data sets and files greater than 60 MB must be deposited in this way. For a list of other repositories specialized in scientific and experimental data, please consult databib.org or re3data.org. The data repository name, link to the data set (URL) and accession number, doi or handle number of the data set must be provided in the paper. The journal Data also accepts submissions of data set papers.

Deposition of Sequences and of Expression Data

New sequence information must be deposited to the appropriate database prior to submission of the manuscript. Accession numbers provided by the database should be included in the submitted manuscript. Manuscripts will not be published until the accession number is provided.

• New nucleic acid sequences must be deposited in one of the following databases: GenBank, EMBL, or DDBJ. Sequences should be submitted to only one database.
• New high throughput sequencing (HTS) datasets (RNA-seq, ChIP-Seq, degradome analysis, …) must be deposited either in the GEO database or in the NCBI’s Sequence Read Archive (SRA).
• New microarray data must be deposited either in the GEO or the ArrayExpress databases.The "Minimal Information About a Microarray Experiment" (MIAME) guidelines published by the Microarray Gene Expression Data Society must be followed.
• New protein sequences obtained by protein sequencing must be submitted to UniProt (submission tool SPIN). Annotated protein structure and its reference sequence must be submitted to RCSB of Protein Data Bank.

All sequence names and the accession numbers provided by the databases must be provided in the Materials and Methods section of the article.

Deposition of Proteomics Data

Methods used to generate the proteomics data should be described in detail and we encourage authors to adhere to the "Minimum Information About a Proteomics Experiment". All generated mass spectrometry raw data must be deposited in the appropriate public database such as ProteomeXchange, PRIDE or jPOST. At the time of submission, please include all relevant information in the materials and methods section, such as repository where the data was submitted and link, data set identifier, username and password needed to access the data.

Research and Publication Ethics

Research Ethics

Research Involving Human Subjects

When reporting on research that involves human subjects, human material, human tissues, or human data, authors must declare that the investigations were carried out following the rules of the Declaration of Helsinki of 1975 (https://www.wma.net/what-we-do/medical-ethics/declaration-of-helsinki/), revised in 2013. According to point 23 of this declaration, an approval from an ethics committee should have been obtained before undertaking the research. At a minimum, a statement including the project identification code, date of approval, and name of the ethics committee or institutional review board should be stated in Section ‘Institutional Review Board Statement’ of the article. Data relating to individual participants must be described in detail, but private information identifying participants need not be included unless the identifiable materials are of relevance to the research (for example, photographs of participants’ face that show a particular symptom). Editors reserve the right to reject any submission that does not meet these requirements.

Example of an ethical statement: "All subjects gave their informed consent for inclusion before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of XXX (Project identification code)."

A written informed consent for publication must be obtained from participating patients who can be identified (including by the patients themselves). Patients’ initials or other personal identifiers must not appear in any images. For manuscripts that include any case details, personal information, and/or images of patients, authors must obtain signed informed consent from patients (or their relatives/guardians) before submitting to an MDPI journal. Patient details must be anonymized as far as possible, e.g., do not mention specific age, ethnicity, or occupation where they are not relevant to the conclusions. A template permission form is available to download. A blank version of the form used to obtain permission (without the patient names or signature) must be uploaded with your submission.

You may refer to our sample form and provide an appropriate form after consulting with your affiliated institution. Alternatively, you may provide a detailed justification of why informed consent is not necessary. For the purposes of publishing in MDPI journals, a consent, permission, or release form should include unlimited permission for publication in all formats (including print, electronic, and online), in sublicensed and reprinted versions (including translations and derived works), and in other works and products under open access license. To respect patients’ and any other individual’s privacy, please do not send signed forms. The journal reserves the right to ask authors to provide signed forms if necessary.

Ethical Guidelines for the Use of Animals in Research

The editors will require that the benefits potentially derived from any research causing harm to animals are significant in relation to any cost endured by animals, and that procedures followed are unlikely to cause offense to the majority of readers. Authors should particularly ensure that their research complies with the commonly-accepted '3Rs':

• Replacement of animals by alternatives wherever possible,
• Reduction in number of animals used, and
• Refinement of experimental conditions and procedures to minimize the harm to animals.

Any experimental work must also have been conducted in accordance with relevant national legislation on the use of animals for research. For further guidance authors should refer to the Code of Practice for the Housing and Care of Animals Used in Scientific Procedures [1].

Manuscripts containing original descriptions of research conducted in experimental animals must contain details of approval by a properly constituted research ethics committee. As a minimum, the project identification code, date of approval and name of the ethics committee or institutional review board should be stated in Section ‘Institutional Review Board Statement’.

Microorganisms endorses the ARRIVE guidelines (www.nc3rs.org.uk/ARRIVE) for reporting experiments using live animals. Authors and reviewers can use the ARRIVE guidelines as a checklist, which can be found at www.nc3rs.org.uk/ARRIVEchecklist.

1. Home Office. Animals (Scientific Procedures) Act 1986. Code of Practice for the Housing and Care of Animals Used in Scientific Procedures.

Research Involving Cell Lines

Methods sections for submissions reporting on research with cell lines should state the origin of any cell lines. For established cell lines the provenance should be stated and references must also be given to either a published paper or to a commercial source. If previously unpublished de novo cell lines were used, including those gifted from another laboratory, details of institutional review board or ethics committee approval must be given, and confirmation of written informed consent must be provided if the line is of human origin.

An example of Ethical Statements:

The HCT116 cell line was obtained from XXXX. The MLH1⁺ cell line was provided by XXXXX, Ltd. The DLD-1 cell line was obtained from Dr. XXXX. The DR-GFP and SA-GFP reporter plasmids were obtained from Dr. XXX and the Rad51K133A expression vector was obtained from Dr. XXXX.

Research Involving Plants

Experimental research on plants (either cultivated or wild) including collection of plant material, must comply with institutional, national, or international guidelines. We recommend that authors comply with the Convention on Biological Diversity and the Convention on the Trade in Endangered Species of Wild Fauna and Flora.

For each submitted manuscript supporting genetic information and origin must be provided. For research manuscripts involving rare and non-model plants (other than, e.g., Arabidopsis thaliana, Nicotiana benthamiana, Oryza sativa, or many other typical model plants), voucher specimens must be deposited in an accessible herbarium or museum. Vouchers may be requested for review by future investigators to verify the identity of the material used in the study (especially if taxonomic rearrangements occur in the future). They should include details of the populations sampled on the site of collection (GPS coordinates), date of collection, and document the part(s) used in the study where appropriate. For rare, threatened or endangered species this can be waived but it is necessary for the author to describe this in the cover letter.