Guide to Authors


Article Type Specifications

Article: An Article is a substantial, in-depth, novel research study of interest to the readership of the journal. The structure an Article should follow is detailed below. Although ISME J emphasizes discovery-based research, we are willing to consider breakthrough method papers that represent major advances for the field of microbial ecology. We recommend our partner journal, ISME Communications, for most methods-oriented manuscripts.
Specifications: Unstructured abstract max. 250 words; Main body of text (excluding abstract, tables/figures, and references) not to exceed 5,000 words; Max 8 tables or figures; Max 100 references

Review Article: Reviews are comprehensive analyses of specific topics that are typically solicited by the Reviews Editor; however we also welcome independent proposals.
Specifications: Unstructured abstract max. 250 words; Main body of text (excluding abstract, tables/figures, and references) not to exceed 3,000 words; Figures and tables are encouraged; Max 100 references

Brief Communication: These are studies that fall short of the criteria for full research papers (e.g., exciting new results with a relatively simple experimental design, without confirmatory follow-up work expected for an Article).
Specifications: Unstructured abstract, one paragraph, max. 250 words; Main body of text (excluding abstract, tables/figures, and references) not to exceed 1,000 words; Max 2 tables or figures; Max 20 references

Comment: Comments discuss issues of particular importance for the field of microbial ecology. Comments may include highlights of significant papers, in the current issue or elsewhere, or comprise poignant opinions, responses to previously published items, or other timely information. Comments may be either solicited by the Reviews Editor or offered as an unsolicited submission. If you wish to offer an unsolicited contribution, we ask you to first contact the Reviews Editor with your request, including a short description of the content and implications of your comment.
Specifications: No abstract required; Main body of text (excluding tables/figures, and references) not to exceed 1,500 words; Max 3 tables or figures; Max 10 references

Perspective: Hybrid between a commentary and a review, providing an opinion-driven perspective on a particular research topic or field of interest to The ISME Journal readership. Authors should present a provocative view that can be supported by data and literature with the goal of sparking debate and stimulating future research directions. Perspective articles are usually by invitation of the Reviews Editor, but authors wishing to contribute a perspective article are free to submit an unsolicited request to the Reviews Editor with an outline of the intended article. If the subject and content are deemed of interest, an invitation letter will then be extended by the editorial office.
Specifications: No abstract required; Main body of text (excluding tables/figures, and references) not to exceed 3,000 words; Max 3 tables or figures; Max 20 references

Winogradsky Review (by invitation only): Comprehensive analysis of specific topics in microbial ecology that are solicited by the Reviews Editor. Proposals for a Winogradsky Review may be submitted; however, in this case authors should only send an outline of the proposed paper for initial consideration. 
Specifications: Unstructured abstract, one paragraph, max. 250 words; Main body of text (excluding abstract, tables/figures, and references) not to exceed 5,000 words; Max 6 tables or figures; Max 100 references

Pre-submission enquiries

Although our Editors-in-Chief do not offer a formal process for pre-submission enquiries, we would like to share the following comments to help authors when contemplating submission to The ISME Journal:

  • Is the research novel and does it represent a major advance?
  • Does the work clearly fit within the scope of our journal? 
  • Has the research been conducted with state-of-the-art approaches? 

If the answer to all three of these questions is yes, the study may well be appropriate for The ISME Journal, regardless of the system being studied. In this case, please feel free to submit the full manuscript via the online submission system

Publication charges

Colour Charges
There is a charge if authors choose to publish their figures in colour in print publication (which includes the online PDF). VAT or local taxes will be added where applicable.
Colour charges will not apply to authors who choose to pay an article processing charge to make their paper Open Access - for further information on open access publication see our Author Services page.

  Number of colour illustrations








Cost:     Rest of world







per figure

Page Charges
In addition to existing colour charges all papers accepted to The ISME Journal that have a final publication layout exceeding 12 pages will be subject to a moderate page charge. After final layout for publication, each page of an article (over the initial 12 pages) will incur a fixed charge of £132/ $205 per page. Page charges will not apply to authors who choose to pay an article processing charge to make their paper open access. For further information on open access publication, see our Author Services page.

Preparation of Articles

House Style: Authors should adhere to the following formatting guidelines

  • Text should be double spaced with a wide margin.
  • All pages and lines should be numbered.
  • Do not make lines thinner than 1pt (0.36 mm).
  • Use a solid colour fill for graphs rather than patterns.
  • Colour should be distinct when being used as an identifying tool.
  • Commas, not spaces, should be used to separate thousands.
  • At first mention of a manufacturer, the town (and state if USA) and country should be provided.
  • Statistical methods: For normally distributed data, mean (SD) is the preferred summary statistic. Relative risks should be expressed as odds ratios with 95% confidence intervals. To compare two methods for measuring a variable the method of Bland & Altman (1986, Lancet 1, 307–310) should be used; for this, calculation of a p value only is not appropriate.
  • Units: Use metric units (SI units) as fully as possible. Preferably give measurements of energy in kiloJoules or megaJoules with kilocalories in parentheses (1 kcal = 4.186kJ). Use % throughout.
  • Abbreviations: On first using an abbreviation place it in parentheses after the full item. Very common abbreviations such as PCR or RNA need not be defined. Note these abbreviations: gram g; litre l; milligram mg; kilogram kg; kilojoule kJ; megajoule MJ; weight wt; seconds s; minutes min; hours h. Do not add ‘s’ for plural units. Terms used only once should not be abbreviated.

Cover Letter: Authors should provide a cover letter that includes the affiliation and contact information for the corresponding author. Authors should briefly discuss the importance of the work and explain why it is considered appropriate for the diverse readership of The ISME Journal. The cover letter should confirm 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.

Title Page: The title page should contain:

  • Title of the paper - brief, informative, of 150 characters or less. Good titles should state the main discovery of the research without overly emphasizing methodology.
  • Full names of all the authors and their affiliations, together with e-mail address of the corresponding author. 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.
  • Competing Interests statement (see Editorial Policy section). Authors should disclose the sources of any support for the work received in the form of grants and/or equipment and drugs

Large Language Models (LLMs), such as ChatGPT, do not currently satisfy our authorship criteria. Notably an attribution of authorship carries with it accountability for the work, which cannot be effectively applied to LLMs. Use of an LLM should be properly documented in the Methods section (and if a Methods section is not available, in a suitable alternative part) of the manuscript.

Abstract: Abstracts must be prepared as an unstructured paragraph designed to summarise the essential features of the paper in a logical and concise sequence.

Graphical Abstracts (optional): A graphical abstract, which summarizes the manuscript in a visual way, is designed to attract the attention of readers in the table of contents of the journal. Files should be uploaded as a ‘Figure’ and be labelled ‘Graphical abstract’.  A standard file format (.tiff, .eps, .jpg, .bmp, .doc, or .pdf.) should be used, and the graphic should be 9 cm wide x 5 cm high when printed at full scale and a minimum of 300 dpi. All graphical abstracts should be submitted with a white background and imagery should fill the available width, whenever possible. Colour graphical abstracts are encouraged and will be published at no additional charge. Textual statements should be kept to a minimum.

Introduction: The Introduction should assume that the reader is knowledgeable in the field and should therefore be as brief as possible but can include a short historical review where desirable.

Materials/Subjects and Methods: This section should contain sufficient detail, so that all experimental procedures can be reproduced and include references. Methods that have been published elsewhere should not be described in detail - please do not copy/paste method text from other publications, even if your own work. 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: 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.

Discussion: 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 found in the results. The final paragraph should highlight the main conclusion, and describe the direction that future research should take.

Acknowledgements: 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.

Competing Interests: 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, but should also be noted on the title page. Please see the Competing Interests definition in the Editorial Policies section for detailed information.

Data Availability Statement: An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. The ISME Journal adheres to Springer Nature’s Data Policy Type 3. This means that a submission to the journal implies that materials described in the manuscript, including all relevant raw data, will be freely available to any researcher wishing to use them for non-commercial purposes, without breaching participant confidentiality. It also means that a Data Availability Statement (see here for more details) must be included as part of your manuscript.

References: Only papers directly related to the article should be cited. Exhaustive lists should be avoided. References should follow the Vancouver format. In the text they should appear as numbers starting at one and at the end of the paper they should be listed (double-spaced) in numerical order corresponding to the order of citation in the text. Where a reference is to appear next to a number in the text, for example following an equation, chemical formula or biological acronym, citations should be written as (ref. X). Example “detectable levels of endogenous Bcl-2 (ref. 3), as confirmed by western blot”.
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 can 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:  Neidlein S, Wirth R, Pourhassan M. Iron deficiency, fatigue and muscle strength and function in older hospitalized patients. Eur J Clin Nutr. 2020; 75:456–463.
Journal article, in press:  Gallardo RL, Juneja HS, Gardner FH. Normal human marrow stromal cells induce clonal growth of human malignant T-lymphoblasts. Int J Cell Cloning (in press).
Complete book:  Atkinson K, Champlin R, Ritz J, Fibbe W, Ljungman P, Brenner MK (eds). Clinical Bone Marrow and Blood Stem Cell Transplantation. 3rd ed. Cambridge University Press, Cambridge, 2004.
Chapter in book:  Coccia PF. Hematopoietic cell transplantation for osteopetrosis. In: Blume KG, Forman SJ, Appelbaum FR (eds). Thomas' Hematopoietic Cell Transplantation. 3rd ed. Blackwell Publishing Ltd, Malden, 2004. pp 1443–1454.
Abstract:  Abstracts from the 2020 Annual Scientific Meeting of the British and Irish Hypertension Society (BIHS). J Hum Hypertens 34; 2020; 1–20
Website:  Kassambara A. rstatix: pipe-friendly framework for basic statistical tests. 2020.
Online Document:  Doe J. Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. 1999. of subordinate document. Accessed 15 Jan 1999.  

Tables: Tables should only be used to present essential data; they should not duplicate what is written in the text. All tables must be 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. 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.

Figure Legends: These should be brief, specific, and appear on a separate manuscript page after the References section.

Figures: 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. The use of three-dimensional histograms is strongly discouraged unless the addition of the third dimension is important for conveying the results. Composite figures containing more than three individual figures will count as two figures. All parts of a figure should be grouped together. Where possible large figures and tables should be included as supplementary material.
Detailed guidelines for submitting artwork can be found by downloading our Artwork Guidelines. 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 peer-review process, if your paper is accepted for publication.

Graphs, Histograms, and Statistics
Plotting individual data points is preferred to just showing means, especially where N<10
If error bars are shown, they must be described in the figure legend
Axes on graphs should extend to zero, except for log axes
Statistical analyses (including error bars and p values) should only be shown for independently repeated experiments, and must not be shown for replicates of a single experiment
The number of times an experiment was repeated (N) must be stated in the legend

Supplementary Information: Supplementary information is 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 self-explanatory without the Supplementary Information, which is posted on the journal's website and linked to the article. Supplementary Information may consist of data files, graphics, movies or extensive tables.

Please submit supplementary figures, small tables and text as a single combined PDF document. Tables longer than one page should be provided as an Excel or similar file type. Please refer to the journal’s Data Policies, outlined in the Editorial Policies section of these guidelines for additional options for such files, and which provides guidance on alternatives to supplementary files for data deposition, linking, preservation, and storage.

For optimal quality video files, please use H.264 encoding, the standard aspect ratio of 16:9 (4:3 is second best) and do not compress the video. Important: Supplementary information is not copyedited, so please ensure that it is clearly and succinctly presented, that the style and terminology conform to the rest of the manuscript, and that any tracked-changes or review mark-ups are removed.

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 Supplementary Information, 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.

Please note: We do not allow the resupplying of Supplementary Information files for style reasons after a paper has been exported in production, unless there is a serious error that affects the science and, if by not replacing, it would lead to a formal correction once the paper has been published. In these cases we would make an exception and replace the file; however, there are very few instances where a Supplementary Information file would be corrected post publication.

Subject Ontology 
Upon submission authors will be asked to select a series of subject terms relevant to the topic of their manuscript from our subject ontology. Providing these terms will ensure your article is more discoverable and will appear on appropriate subject specific pages on, in addition to the journal’s own pages. Your article should be indexed with at least one, and up to four unique subject terms that describe the key subjects and concepts in your manuscript. Click here for help with this.