How to format your references using the The ISME Journal citation style

This is a short guide how to format citations and the bibliography in a manuscript for The ISME Journal. For a complete guide how to prepare your manuscript refer to the journal's instructions to authors.

Using reference management software

Typically you don't format your citations and bibliography by hand. The easiest way is to use a reference manager:

PaperpileThe citation style is built in and you can choose it in Settings > Citation Style or Paperpile > Citation Style in Google Docs.
EndNoteDownload the output style file
Mendeley, Zotero, Papers, and othersThe style is either built in or you can download a CSL file that is supported by most references management programs.
BibTeXBibTeX syles are usually part of a LaTeX template. Check the instructions to authors if the publisher offers a LaTeX template for this journal.

Journal articles

Those examples are references to articles in scholarly journals and how they are supposed to appear in your bibliography.

Not all journals organize their published articles in volumes and issues, so these fields are optional. Some electronic journals do not provide a page range, but instead list an article identifier. In a case like this it's safe to use the article identifier instead of the page range.

A journal article with 1 author
Ballschmiter K. Atmospheric chemistry. A marine source for alkyl nitrates. Science 2002; 297: 1127–1128.
A journal article with 2 authors
Hu EM, Cowie LL. High-redshift galaxy populations. Nature 2006; 440: 1145–1150.
A journal article with 3 authors
Debruyne R, Schwarz C, Poinar H. Comment on ‘Whole-genome shotgun sequencing of mitochondria from ancient hair shafts’. Science 2008; 322: 857; author reply 857.
A journal article with 7 or more authors
Shakya R, Reid LJ, Reczek CR, Cole F, Egli D, Lin C-S, et al. BRCA1 tumor suppression depends on BRCT phosphoprotein binding, but not its E3 ligase activity. Science 2011; 334: 525–528.

Books and book chapters

Here are examples of references for authored and edited books as well as book chapters.

An authored book
Juhnke GA, Granello DH, Granello PF. Suicide, Self-Injury, and Violence in the Schools. 2010. John Wiley & Sons, Inc., Hoboken, NJ.
An edited book
Margaria T, Steffen B (eds). Leveraging Applications of Formal Methods, Verification and Validation: Third International Symposium, ISoLA 2008, Porto Sani, Greece, October 13-15, 2008. Proceedings. 2008. Springer, Berlin, Heidelberg.
A chapter in an edited book
Ma H-T, Beaven MA. Regulators of Ca2+ Signaling in Mast Cells: Potential Targets for Treatment of Mast Cell-Related Diseases? In: Gilfillan AM, Metcalfe DD (eds). Mast Cell Biology: Contemporary and Emerging Topics. 2011. Springer US, Boston, MA, pp 62–90.

Web sites

Sometimes references to web sites should appear directly in the text rather than in the bibliography. Refer to the Instructions to authors for The ISME Journal.

Blog post
Hale T. Spider Carries A Mouse Up A Refrigerator Like It’s No Big Deal. IFLScience. Accessed 30 Oct 2018.


This example shows the general structure used for government reports, technical reports, and scientific reports. If you can't locate the report number then it might be better to cite the report as a book. For reports it is usually not individual people that are credited as authors, but a governmental department or agency like "U. S. Food and Drug Administration" or "National Cancer Institute".

Government report
Government Accountability Office. Railroad Financing: Stakeholders’ Views on Recent Changes to the Railroad Rehabilitation and Improvement Financing Program. 2016. U.S. Government Printing Office, Washington, DC.

Theses and dissertations

Theses including Ph.D. dissertations, Master's theses or Bachelor theses follow the basic format outlined below.

Doctoral dissertation
Caprile JA. The geochemical influence of trace element concentrations from marine sedimentary bedrock on freshwater streams in the western Transverse Mountain Ranges. 2016. Doctoral dissertation, California State University, Long Beach.

News paper articles

Unlike scholarly journals, news papers do not usually have a volume and issue number. Instead, the full date and page number is required for a correct reference.

New York Times article
Photographs by GEORGE ETHEREDGE for THE NEW YORK TIMES. New York City’s Sconces. New York Times . 2016. , RE10

In-text citations

References should be cited in the text by sequential numbers in square brackets:

This sentence cites one reference [1].
This sentence cites two references [1, 2].
This sentence cites four references [1–4].

About the journal

Full journal titleThe ISME Journal
AbbreviationISME J.
ISSN (print)1751-7362
ISSN (online)1751-7370
ScopeEcology, Evolution, Behavior and Systematics

Other styles