The ISME Journal Template

Linus Pauling

Preparation of Articles

Please note that original articles must contain the following components.
Please see below for further details.
  • Cover letter
  • Title page (excluding acknowledgements)
  • Abstract
  • Introduction
  • Materials (or Subjects) and Methods
  • Results
  • Discussion
  • Acknowledgements
  • Conflict of Interest
  • References
  • Figure legends
  • Tables
  • Figures
Reports of clinical trials must adhere to the registration and reporting requirements listed in the Editorial Policies.

Cover Letter:
The uploaded covering letter must state the material is original research, has not been previously published and has not been submitted for publication elsewhere while under consideration. If the manuscript has been previously considered for publication in another journal, please include the previous reviewer comments, to help expedite the decision by the Editorial team. Please include a Conflict of Interest statement.
Title Page:
The title page should bear the title of the paper, the full names of all the authors and their affiliations, together with the name, full postal address, telephone and fax numbers and e-mail address of the author to whom correspondence and offprint requests are to be sent (this information is also asked for on the electronic submission form). The title page must also contain a Conflict of Interest statement (see Editorial Policy section).
  • The title should be brief, informative, of 150 characters or less and should not make a statement or conclusion.
  • The running title should consist of no more than 50 letters and spaces. It should be as brief as possible, convey the essential message of the paper and contain no abbreviations.
  • Authors should disclose the sources of any support for the work, received in the form of grants and/or equipment and drugs.
  • If authors regard it as essential to indicate that two or more co-authors are equal in status, they may be identified by an asterisk symbol with the caption ‘These authors contributed equally to this work’ immediately under the address list.

Subject Categories:
The Subject Categories are used to structure the current and archived online content of The ISME Journal, and to help readers interested in particular areas of microbial ecology find relevant information more easily. Subject Categories are also indicated in the table of contents and on the title page of the published article. Authors should suggest an appropriate Subject Category for the submitted manuscript. One category may be selected from the following list:
  • Microbial population and community ecology
  • Microbe-microbe and microbe-host interactions
  • Evolutionary genetics
  • Integrated genomics and post-genomics approaches in microbial ecology
  • Microbial engineering
  • Geomicrobiology and microbial contributions to geochemical cycles
  • Microbial ecology and functional diversity of natural habitats
  • Microbial ecosystem impacts

Original Articles must be prepared with an unstructured abstract designed to summarise the essential features of the paper in a logical and concise sequence.

Materials/Subjects and Methods:
This section should contain sufficient detail, so that all experimental procedures can be reproduced, and include references. Methods, however, that have been published in detail elsewhere should not be described in detail. Authors should provide the name of the manufacturer and their location for any specifically named medical equipment and instruments, and all drugs should be identified by their pharmaceutical names, and by their trade name if relevant.

Results and Discussion:
The Results section should briefly present the experimental data in text, tables or figures. Tables and figures should not be described extensively in the text, either. The discussion should focus on the interpretation and the significance of the findings with concise objective comments that describe their relation to other work in the area. It should not repeat information in the results. The final paragraph should highlight the main conclusion(s), and provide some indication of the direction future research should take.

These should be brief, and should include sources of support including sponsorship (e.g. university, charity, commercial organisation) and sources of material (e.g. novel drugs) not available commercially.

Conflict of Interest:
Authors must declare whether or not there are any competing financial interests in relation to the work described. This information must be included at this stage and will be published as part of the paper. Conflict of interest should be noted in the cover letter and also on the title page. Please see the Conflict of Interest documentation in the Editorial Policy section for detailed information.

Only papers directly related to the article should be cited. Exhaustive lists should be avoided. References should follow the Havard format. In the text of the manuscript, a reference should be cited by author and year of publication eg (Bailey & Kowalchuk, 2006) and (Heidelberg et al, 1994) and listed at the end of the paper in alphabetical order of first author. References should be listed and journal titles abbreviated according to the style used by Index Medicus, examples are given below.

All authors should be listed for papers with up to six authors; for papers with more than six authors, the first six only should be listed, followed by et al. Abbreviations for titles of medical periodicals should conform to those used in the latest edition of Index Medicus. The first and last page numbers for each reference should be provided. Abstracts and letters must be identified as such. Papers in press may be included in the list of references.

Personal communications must be allocated a number and included in the list of references in the usual way or simply referred to in the text; the authors may choose which method to use. In either case authors must obtain permission from the individual concerned to quote his/her unpublished work.

Journal article: Cho JC, Kim MW, Lee DH, Kim SJ. (1997). Response of bacterial communities to changes in composition of extracellular organic carbon from phytoplankton in Daechung reservoir (Korea). Arch Hydrobiol 138:559–576.

Journal article, e-pub ahead of print: Eng-Kiat L, Bowles DJ. A class of plant glycosyltransferases involved in cellular homeostasis. EMBO J 2004; e-pub ahead of print 8 July 2004, doi: 10.1038/sj.emboj.7600295.

Journal article, in press: Lim E-K, Ashford DA, Hou B, Jackson RG, Bowles DJ. (2004). Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides. Biotech Bioeng (in press).

Complete book: Sambrook J, Fritsch E, Maniatis T. (1989). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Press: New York. Chapter in book: Zinder, SH. (1998). Methanogens. In: Burlage, RS (ed). Techniques in Microbial Ecology. Oxford University Press: Oxford, pp 113– 136. 

Tables should only be used to present essential data; they should not duplicate what is written in the text. It is imperative that any tables used are editable, ideally presented in Excel. Each must be uploaded as a separate workbook with a title or caption and be clearly labelled, sequentially. Please make sure each table is cited within the text and in the correct order, e.g. (Table 3). Please save the files with extensions .xls / .xlsx / .ods / or .doc or .docx. Please ensure that you provide a 'flat' file, with single values in each cell with no macros or links to other workbooks or worksheets and no calculations or functions.

Figures and images should be labelled sequentially and cited in the text. Figures should not be embedded within the text but rather uploaded as separate files. Detailed guidelines for submitting artwork can be found by downloading our
Artwork Guidelines. The use of three-dimensional histograms is strongly discouraged when the addition of the third dimension gives no extra information.

Artwork Guidelines:
Detailed guidelines for submitting artwork can be found by downloading the guidelines PDF. Using the guidelines, please submit production quality artwork with your initial online submission. If you have followed the guidelines, we will not require the artwork to be resubmitted following the peerreview process, if your paper is accepted for publication.

Colour on the web:
Authors who wish their articles to have FREE colour figures on the web (only available in the HTML (full text) version of manuscripts) must supply separate files in the following format. These files should be submitted as supplementary information and authors are asked to mention they would like colour figures on the web in their submission letter.

Reuse of Display Items:
See the Editorial Policy section for information on using previously published tables or figures. Standard abbreviations: Because the majority of readers will have experience in microbial ecology, the journal will accept papers which use certain standard abbreviations, without definition in the summary or in the text. Non-standard abbreviations should be defined in full at their first usage in the Summary and again at the first usage in the text, in the conventional manner. If a term is used 1-4 times in the text, it should be defined in full throughout the text and not abbreviated.

Supplementary Information:
Supplementary information (SI) is peer-reviewed material directly relevant to the conclusion of an article that cannot be included in the printed version owing to space or format constraints. The article must be complete and selfexplanatory without the SI, which is posted on the journal's website and linked to the article. SI may consist of data files, graphics, movies or extensive tables. Please see our Artwork Guidelines for information on accepted file types. Authors should submit supplementary information files in the FINAL format as they are not edited, typeset or changed, and will appear online exactly as submitted. When submitting SI, authors are required to:
  • Include a text summary (no more than 50 words) to describe the contents of each file.
  • Identify the types of files (file formats) submitted.
  • Include the text “Supplementary information is available at (journal name)’s website” at the end of the article and before the references.


This section is only included in papers that rely on primary research. This section catalogues the results of the experiment. The results should be presented in a clear and unbiased way. Most results sections will contain links as well as citations Einstein 2006 and equations such as \(e^{i\pi}+1=0\)