Journal of Applied Microbiology

Cover image for Vol. 122 Issue 6

Edited By: A. Gilmour

Impact Factor: 2.156

ISI Journal Citation Reports © Ranking: 2015: 76/123 (Microbiology); 79/161 (Biotechnology & Applied Microbiology)

Online ISSN: 1365-2672

Associated Title(s): Letters in Applied Microbiology

Author Guidelines

Journal of Applied Microbiology publishes high quality research and review papers on novel aspects of applied microbiology, including environmental, food, agricultural, medical, pharmaceutical, veterinary, soil, systematics, water and biodeterioration. Papers reporting work on all microorganisms, including viruses, are welcomed providing they demonstrate new findings of significance to the field as a whole.

In 2009, Journal of Applied Microbiology updated its Aims and Scope and will now publish only the top 25% of research. Click here to read the Editorial announcing the new Aims and Scope.


Author submission checklist

Contact the Editorial Office

Contact the Production Editor

Submit your manuscript now to Journal of Applied Microbiology

Click here to download the Colour Work Agreement Form

Guidelines for Electronic Graphics


Original Articles

Original Articles comprise most of the Journal and should have as their aim the development of concepts as well as the recording of facts. The manuscript should be prepared for a wide readership and as far as possible should present novel results of a substantial programme of research.

Review Articles

Review Articles will present a substantial survey with an adequate historical perspective of the literature on some facet of applied microbiology. We would prefer to see a distillation of early and present work within the field to show progress and explain the present interest and relevance. The manuscript should not be simply a review of past work or be concentrated largely on unpublished results.


New manuscripts sent to the Journal will be handled first by the Editorial Office who checks compliance with the guidelines to authors. The manuscript is assigned to a handling Editor by the Chief Editor, and goes through a rapid screening process at which stage a decision to reject or to go to full review is made. This step ensures a rapid rejection of unsuitable manuscripts for the journal. Manuscripts that go to full review are assigned a minimum of two reviewers. Following the return of two reports, the handling Editor provides a report to the Chief Editor, who takes the decision to accept, revise or reject the manuscript. Revised manuscripts are directly handled by the Chief Editor who decides whether or not the manuscript should go back to the handling Editor for additional comments from the reviewers. Following the return of a report from the handling Editor and reviewers, the Chief Editor makes the decision to accept, further revise or reject the manuscript.

Authors may be advised that short papers not exceeding four published pages would be better placed in Letters in Applied Microbiology. Sequential publication of numbered papers will not be permitted.


To ensure responsible publication practices, this Journal adheres to Wiley Blackwell’s publication ethics policies, which include guidelines on handling suspected publication misconduct and complaints about the Journal. This Journal is a member of, and subscribes to the principles of, the Committee on Publication Ethics.


Qualification for authorship should comprise (1) substantial contribution to conception and design or the acquisition and analysis of data, (2) drafting or critically revising the manuscript, and (3) approval of the final submitted version. All authors must satisfy all three criteria, and all those who do satisfy this criteria must be included in the list of authors when the paper is submitted to the Journal. By submission of a manuscript to the Journal, all authors warrant that they have the authority to publish the material and that the paper, or one substantially the same, has neither been published previously, nor is being considered for publication elsewhere. Submissions may be subject to testing for textual similarity to other published works via the CrossCheck software employed by the Journal.

Conflict of interest disclosure

Journal of Applied Microbiology requires that all authors disclose any potential sources of conflict of interest. Any interest or relationship, financial or otherwise, that might be perceived as influencing an author's objectivity is considered a potential source of conflict of interest. These must be disclosed when directly relevant or indirectly related to the work that the authors describe in their manuscript. Potential sources of conflict of interest include but are not limited to patent or stock ownership, membership of a company board of directors, membership of an advisory board or committee for a company, and consultancy for or receipt of speaker's fees from a company. The existence of a conflict of interest does not preclude publication in this journal.

If the authors have no conflict of interest to declare, they must also state this at submission. It is the responsibility of the corresponding author to review this policy with all authors and to collectively list in the cover letter to the Chief Editor, in the manuscript (in the Conflict of Interest section), and in the online submission system ALL pertinent commercial and other relationships.

Ethics of experimentation

The Journal will only accept manuscripts in which there is evidence of the ethical use of animals or harmful substances. The care and use of experimental animals must comply with all relevant local animal welfare laws, guidelines and policies, and a statement of such compliance should be provided upon submission. Where possible, alternative procedures that replace the use of animals, either partially or completely, for example in vitro biological systems, should be used. Where this is not possible, the minimum number of animals should be used and pain and suffering reduced, consistent with attaining the scientific objectives of the study. All reasonable steps must be taken to ensure the humane treatment of animals, so as to minimize discomfort, distress and pain. Animals in pain or moribund should be painlessly killed according to local euthanasia regulations. The Journal encourages corresponding authors of manuscripts involving animal research to refer to the ARRIVE guidelines before submission of a manuscript.

Potential threat to security

The Journal expects that all authors will conform to the National Science Advisory Board for Biosecurity (NSABB) guidelines for Dual Use Life Sciences Research. Where a reviewer is concerned that an article might include information that could be a threat to security then the Editor will treat the article as possible DURC (dual use research of concern) and may consult a specialist reviewer. Their advice will be taken into account by the Editor in making any final decision on publication.


The Journal asks authors of papers related to Schedule 5 biological agents to inform the Editor at the time of manuscript submission if their study has the potential for both benevolent and malevolent application. This is often referred to as “dual use research of concern”. The National Science Advisory Board for Biosecurity (NSABB) guidelines state that a “dual use research of concern” can arise in relation to “research that, based on current understanding, can be reasonably anticipated to provide knowledge, products, or technologies that could be directly misapplied by others to pose a threat to public health and safety, agricultural crops and other plants, animals, the environment, or material”.

Antibiotic antimicrobial testing and microbial resistance

A number of methods like disc diffusion, Etest, agar dilution, broth microdilution and broth macrodilution, are suitable for in vitro antimicrobial susceptibility testing. However, the test used must be performed in accordance with an internationally accepted procedure; for example tests published by the Clinical and Laboratory Standards Institute (CLSI), the British Society for Antimicrobial Chemotherepy (BSAC), the Deutsches Institut fur Normung e.V. (DIN) and the Comite de l'Antibiogramme de la Scoiete Francaise de Microbiologie (CA-SFM). Further guidence and interpretation of MIC 50 and MIC 90 values as well as guidence for the interpretation of multiresistance can be found in Schwarz et al. J. Antimicrobial Chemother 2010; 65: 601-604.

Data availability

Data that is integral to the paper must be made available in such a way as to enable readers to replicate, verify and build upon the conclusions published in the paper. Any restriction on the availability of this data must be disclosed at the time of submission. Data may be included as part of the main article where practical. We recommend that data for which public repositories are widely used, and are accessible to all, should be deposited in such a repository prior to publication. The appropriate linking details and identifier(s) should then be included in the publication and where possible the repository, to facilitate linking between the journal article and the data. If such a repository does not exist, data should be included as supporting information to the published paper or authors should agree to make their data available upon reasonable request.

  • Nucleotide sequence data should be deposited in the EMBL/GenBank/DDBJ Nucleotide Sequence Data Libraries and the accession number referenced in the manuscript text, e.g. “E. coli (GenBank accession no. EUXXXXXX.X)”. Sequence data should only be included if they are new (unpublished), complete (no unidentified nucleotides included) and if the sequence information itself provides important new biological insights of direct relevance to the question addressed in the manuscript. Generally sequences should not be submitted if the same gene has been reported in another species unless a comparison with related sequences contributes important new information.
  • Presentation of nucleotide sequences should include clear indications of nucleotide numbers and points of interest, e.g. promoter sequences, ribosome binding sites, mutations, insertions, probe sequences, etc. In the case of comparisons, nucleotides which differ between the sequences should be readily visible to the reader, e.g. by the use of bold face, shading, boxing or by the use of a dash to represent identical nucleotides. The font size used in the manuscript should facilitate appropriate reduction of the figure.

Copyright Transfer Agreement

If your paper is accepted, the author identified as the formal corresponding author for the paper will receive an email prompting them to login into Author Services; where via the Wiley Author Licensing Service (WALS) they will be able to complete the license agreement on behalf of all authors on the paper.

For authors signing the copyright transfer agreement

If the OnlineOpen option is not selected the corresponding author will be presented with the copyright transfer agreement (CTA) to sign. The terms and conditions of the CTA can be previewed in the samples associated with the Copyright FAQs below: CTA Terms and Conditions


For authors choosing OnlineOpen

If the OnlineOpen option is selected the corresponding author will have a choice of the following Creative Commons License Open Access Agreements (OAA):

Creative Commons Attribution License OAA

Creative Commons Attribution Non-Commercial License OAA

Creative Commons Attribution Non-Commercial -NoDerivs License OAA

To preview the terms and conditions of these open access agreements please visit the Copyright FAQs hosted on Wiley Author Services and visit

If you select the OnlineOpen option and your research is funded by The Wellcome Trust and members of the Research Councils UK (RCUK) you will be given the opportunity to publish your article under a CC-BY license supporting you in complying with Wellcome Trust and Research Councils UK requirements. For more information on this policy and the Journal’s compliant self-archiving policy please visit:

Referrals to the Open Access Journal MicrobiologyOpen and Food Science & Nutrition

This journal works together with two of Wiley's open access journals, MicrobiologyOpen and Food Science & Nutrition to enable rapid publication of good quality research that is unable to be accepted for publication by our journal. Authors may be offered the option of having the paper, along with any related peer reviews, automatically transferred for consideration by one of these two journals. MicrobiologyOpen and Food Science & Nutrition are Wiley open access journals and article publication fees apply. For more information, please go to and


Authors should submit their manuscripts online at The main text of a manuscript must be submitted as a Word document (.doc) or Rich Text Format (.rtf) file. For review purposes submitted papers (both original and revised articles) must be formatted with continuous line numbering and double spaced text throughout. All original files that you upload will be available for the Editorial Office to access.

Cover letter

The cover letter should contain answers to the following two questions, which will help the Editors in determining whether you manuscript should be sent for full peer review (~50 words per answer):
1. How does this work fits the Aims and Scope of the Journal?
2. In what way is this work novel?
The cover letter should also disclose any potential sources of conflict of interest that Editors may consider relevant to their manuscript.

Suggesting reviewers

Authors are invited to suggest at least two reviewers. It is not appropriate for reviewers to be members or former members of the authors' organization(s), or to have been associated with them. Conversely, authors may identify ‘non-preferred’ reviewers or institutions that they would rather were not approached. Authors should give justification for choosing non-preferred reviewers or institutions in their cover letter. Authors are advised that handling Editors reserve the right to select reviewers of their choice.


Manuscripts should be drafted as concisely as possible. As space in the Journal is at a premium, the Editors always reserve the right to require authors to reduce the length of their manuscripts. Manuscripts will not be reviewed unless the English is of a publishable standard.

It is strongly recommended that you use the author submission checklist to help you to prepare your submission to the Journal.

The main text of the manuscript should be prepared as a Word document (.doc) or Rich Text Format (.rtf) file. Text must be double-spaced, and the pages of the manuscript must be numbered consecutively.

The title page should show the title of the manuscript; the names of authors and place(s) where the work was done; an abbreviated running headline not exceeding 35 letters and spaces; and the complete contact details for the corresponding author.

Original Articles should not exceed 34 pages and should contain the following sections in this order:

  • ABSTRACT: A brief summary of about 150-200 words, should give the major findings of the investigation under the following four headings: Aims; Methods and Results; Conclusions; Significance and Impact of Study. A list of between five and eight keywords should be added;
  • INTRODUCTION: A balance must be struck between the pure and applied aspects of the subject;
  • MATERIALS AND METHODS: Ensure that the work can be repeated according to the details provided. By submission of a manuscript, the authors consent that biological material, including plasmids, viruses and microbial strains, unobtainable from national collections will be made available to members of the scientific community for non-commercial purposes subject to national and international regulations governing the supply of biological material. In the case of a new diagnostic PCR, you should consider the need for an internal amplification control (JAM 2004 96(2):221; available here).
  • RESULTS: Well-prepared tables and figures must be a cardinal feature of the 'Results' section because they convey the major observations to readers who scan a paper. Information provided in tables and figures should not be repeated in the text, but focus attention on the importance of the principal findings of the study. In general, journal papers will contain between one and seven figures and tables;
  • DISCUSSION: This must not recapitulate the results and authors must avoid the temptation of preparing a combined 'Results and Discussion' section;
  • ACKNOWLEDGEMENTS: Contributors who do not qualify as authors should be acknowledged and their particular contribution described. All sources of funding for the work reported, for all the authors, must be acknowledged. Both the research funder and the grant number (if applicable) should be given for each source of funds;
  • CONFLICT OF INTEREST: If no conflict of interest exists, then 'no conflict of interest declared' should appear within this section. Otherwise, authors should list all pertinent commercial and other relationships that may be perceived as a potential source of conflict of interest.
  • SUPPORTING INFORMATION (if applicable): Supporting Information can be a useful way for an author to include important but ancillary information with the online version of an article. Examples of Supporting Information include additional tables, data sets, figures, movie files, audio clips, 3D structures, and other related nonessential multimedia files. Supporting Information should be cited within the article text. The availability of supporting information should be indicated in the main manuscript by a section headed 'Supporting Information', under which should be appropriate legends for the material. It is published as supplied by the author, and a proof is not made available prior to publication; for these reasons, authors should provide any Supporting Information in the desired final format. For further information on recommended file types and requirements for submission, please visit:

Review Article manuscripts must normally not exceed 32 pages (A4) including references, figures and tables. As references can make a heavy demand on the pages available to you, it is suggested that you select key references only. The headings in Review Articles are of the author's choice, but the manuscript should begin with a short SUMMARY of 150-200 words. There is no requirement for review articles to have a ‘significance and impact’ section; this is at the discretion of the author.

Please check and confirm that your article is optimized for search engines. Keywords should appear in the title, abstract and throughout your article in order to increase your article's online visibility. For more information, please see Writing for SEO.


The Harvard system should be used. Citation of references having three or more names should be cited in the text as Jones et al. (1992) at the first and subsequent times of quoting the reference. A series of references should be given in ascending date order (Green and Smith 1946; Jones et al. 1956). Names with the prefixes de, do van, von, etc. will be placed in alphabetical order of the first letter of the prefix, e.g. von Braun would appear under 'V'. Different publications having the same author(s) and year will be distinguished by, for example, 1992a, 1992b. Papers or other publications having no obvious author(s) should usually be cited as 'Anon.' with the year in the text and bibliography. Web sites should be quoted in the text with an access date. Abbreviate journal titles according to Index Medicus ( Personal communications should be cited in the text with initials and family name of all individuals.

The following is an example of order and style to be used in the manuscript:

Fricker, C.R. (1995) Detection of Cryptosporidium and Giardia in water. In Protozoan Parasites in Water ed. Betts, W.B., Casemore, D., Fricker, C.R., Smith, H.V. and Watkins, J. pp.91-96. London: The Royal Society of Chemistry.

Garner, J.S. and Favero, M.S. (1985) Guidelines for Handwashing and Hospital Environment Control. US Public Health Service, Centers for Disease Control HHS No. 99-117. Washington DC: Government Printing Office.

Laverick, M.A., Wyn-Jones, A.P. and Carter, M.J. (2004) Quantitative RT-PCR for the enumeration of noroviruses (Norwalk-like viruses) in water and sewage. Lett Appl Microbiol 39, 127-135.


Tables must be prepared in the same format as the manuscript text, and should ideally appear at the end of the main manuscript file. Tables must not include ruled vertical or horizontal lines with the exception of headers and a footer (see example). The use of explanatory footnotes is permissible and they should be marked by the following (shown in order of preference): *, †, ‡, §, ¶, **, †† etc. For an example of table style, click here.


Figures should be uploaded to the online submission site as separate files. Authors are advised that poor quality figures may delay the publication of their paper. Symbols or keys representing data series in graphs and charts must not be shown on the figure itself but be included in the legend. For an example of figure style, click here.

Photographs must be of good quality and high contrast. The magnification must be indicated by adding a bar representing a stated length. Composite photographs can reduce the numbers that require publication. The Journal will not accept figures illustrating SDS-PAGE and agarose gels with multiple lanes, where lane order has been rearranged using digital imaging software. The figure should also show sufficient of the gel to reveal reference markers (e.g. the sample origin and a tracker dye, or a lane of molecular mass markers).

  • Save line art such as charts, graphs and illustrations in EPS or PDF format. Most programs have a ‘Save as...’ or ‘Export...’ feature to allow you to do this

  • Save photographic images in TIFF format. These should be at a resolution of at least 300 dpi at final size

  • Save figures containing a combination of photographic images and text (eg annotated photographic images with text labels) as EPS or PDF. Any photographic images embedded within these should be at least 300 dpi

  • Perform a visual check of the quality of the generated image. You should be able to zoom in to about 300% without the image becoming noticeably blurred or pixelated. If the image does appear pixelated at this zoom, then try going back to the original image and checking that it complies with the recommended format and settings

  • Detailed information on the submission of electronic artwork can be found at: http://media.wiley com/assets/7323/92/electronic_artwork_guidelines.pdf

Colour figures

Online-only colour in figures is free of charge, however it is essential in these cases that the figure legends apply equally well to both printed greyscale and online colour versions, and do not specifically refer to the colour. Alternatively you can opt to pay for colour in the print and online versions. If your paper is accepted and you have opted for printed colour, we will need a completed Colour Work Agreement Form. This form can be downloaded as a PDF from here and should be sent to the provided address on acceptance.

English usage, abbreviations and units

Use 'z' spelling where possible, except analyse, dialyse, hydrolyse, etc.; sulfur, sulfate, etc. When using numbers in the text, one to nine should be written in full and 10 and above should be written as numerals. The Journal uses SI units: g l-1 not g/l; d, h, min, s (time units) but week and year in full; mol l-1 (not M or N); probability is P; centrifugation conditions relative to gravity (g). Please refer to the Biochemical Journal 'Instructions to Authors'

Please click here for some examples of common abbreviations used in the Journal.

Microbial nomenclature

The Latin binomial name of micro-organisms, plants and animals (other than farm animals) must be given at first mention in the text; thereafter the generic name will be abbreviated in such a way that confusion is avoided when dealing with several genera all beginning with the same letter, viz. Pseudomonas, Proteus, Pediococcus, etc. (see list of abbreviations below). Subspecies are italized (Corynebacterium diphtheriae subsp. mitis); groups and types are printed in Roman and designated by capital letters or Arabic figures (e.g. Staphylococcus aureus group A). Common names will not have an initial capital letter nor will they be underlined in the manuscript, viz. pseudomonad, salmonellas. The specific name will be given in full in the captions to tables and figures. Major ranks are written in Roman with an initial capital (e.g. Enterobacteriaceae).

Please click here for a list of abbreviations currently in use for common generic names and for notes on referring to plant pathogenic bacteria.

Gnotobiotic animals

The terminology for describing the environmental status of animals in gnotobiotic experiments has established itself by usage. Germ-free implies freedom from any detectable microorganisms or viruses and it is limited by the tests used to detect contaminants. Conventional animals have a full complement of associated microbes. Open conventional animals are housed in a standard animal house. Isolator conventional animals are maintained in isolators and associated with full flora. Ex-germ-free animals are those with an associated flora which have become conventional.


Tests must be presented clearly to allow a reader with access to the data to repeat them. Statistical tests used in the study should be clearly indicated in the Materials and Methods section. It is not necessary to describe every statistical test fully, as long as it is clear from the context what was done. In particular, null hypotheses should be clearly stated.

Authors are urged to give consideration to the assumptions underlying any statistical tests used and to assure the reader that the assumptions are at least plausible. Authors should be prepared to use nonparametric tests if the assumptions do not seem to hold.


Not permitted other than on the first page of a manuscript where they are used to show the author's change of address and the address for correspondence.

Experimental hazards

Chemical or microbiological hazards that may be involved in the experiments must be explained. Authors should provide a description of the relevant safety precautions adopted or cite an accepted 'Code of Practice'.

English-language editing service

Authors for whom English is a second language may choose to have their manuscript professionally edited before submission to improve the English. A list of independent suppliers of editing services can be found here. All services are paid for and arranged by the author, and use of one of these services does not guarantee acceptance or preference for publication.



The corresponding author will receive an email alert containing a link to a web site. A working email address must therefore be provided for the corresponding author. The proof can be downloaded as a PDF file from this site and corrections made following the instructions sent with the proofs. Excessive changes made by the author in the proofs, excluding typesetter errors, may be charged separately.

Early View

Journal of Applied Microbiology is covered by Wiley Online Library's Early View service. Early View articles are complete full-text articles published online in advance of their publication in a printed issue. Articles are therefore available as soon as they are ready, rather than having to wait for the next scheduled print issue. Early View articles are complete and final. They have been fully reviewed, revised and edited for publication, and the authors' final corrections have been incorporated. Because they are in final form, no changes can be made after online publication. The nature of Early View articles means that they do not yet have volume, issue or page numbers, so Early View articles cannot be cited in the traditional way. They are therefore given a Digital Object Identifier (DOI), which allows the article to be cited and tracked before it is allocated to an issue. After print publication, the DOI remains valid and can continue to be used to cite and access the article. More information about DOIs can be found at:


A PDF offprint of the online published article will be provided free of charge to the corresponding author, and may be distributed subject to the Publisher's terms and conditions. Free access to the final PDF offprint or your article will be available via author services only. Please therefore sign up for author services if you would like to access your article PDF offprint and enjoy the many other benefits the service offers. Paper offprints of the printed published article may be purchased if ordered via the method stipulated on the instructions that will accompany the proofs. Printed offprints are posted to the correspondence address given for the paper unless a different address is specified when ordered. Note that it is not uncommon for printed offprints to take up to eight weeks to arrive after publication of the Journal.

Note to NIH Grantees

Pursuant to NIH mandate, Wiley Blackwell will post the accepted version of contributions authored by NIH grant-holders to PubMed Central upon acceptance. This accepted version will be made publicly available 12 months after publication. For further information, see

Author material archive policy

Please note that unless specifically requested, Wiley Blackwell will dispose of all hardcopy or electronic material submitted 2 months after publication. If you require the return of any material submitted, please inform the Managing Editor or Production Editor.


Whilst every effort is made by the Publishers and Editorial Board to see that no inaccurate or misleading data, opinion or statement appears in this Journal, they wish to make it clear that the data and opinions appearing in the articles and advertisements herein are the sole responsibility of the contributor or advertiser concerned. Accordingly, the Publishers and Editors and their respective employees, officers and agents accept no responsibility or liability whatsoever for the consequences of any such inaccurate or misleading data, opinion or statement.