Methodologies should present a new experimental or computational method, test or procedure. The method described may either be completely new, or may offer a better version of an existing method. The article must describe a demonstrable advance on what is currently available. The method needs to have been well tested and ideally, but not necessarily, used in a way that proves its value.
Availability of data, metadata and analytical scripts
At Microbiome we are striving to make reproducibility a priority. Data availability at time of submission is a key aspect to this process as it allows reviewers to fully evaluate your work.
Microbiome follows a strict data release policy (Research Data Policy Type 4). We require that all datasets on which the conclusions of the paper rely should be available to the reviewers and readers. We ask that authors make sure their datasets are either deposited in publicly available repositories (where available and appropriate) or presented in the main manuscript or additional supporting files whenever possible. Accompanying metadata must be available in the repository or as supporting files to the manuscript. Metadata should be formatted according to the MixS (Minimum Information about any (x) Sequence) standards developed by the Genome Standards Consortium (GSC). Template can be found here: http://gensc.org/mixs/). The sample identifiers in the repository must refer to the same sample identifiers used in the manuscript. Please see Springer Nature’s information on recommended repositories.
We are also requesting that authors make the code/scripts used for their analysis available as knitr files, iPython Notebooks, or any other formats they might find suitable. Again, this effort encourages transparency and complete reproducibility of your study. A good example is a paper published in Microbiome by Meadow et al.
Please include the live accession number, or similar, in a section entitled “Availability of data and materials”.
Use of experimental controls
As with reproducibility, at Microbiome we are striving to publish high quality study, and we believe that the use of experimental controls is critical to guarantee quality and credibility. We expect that studies include controls, especially when analyzing samples believed to carry a very low bacterial/fungal/viral biomass. Materials and reagent, experimental sampling and processing can introduce contamination (DNA or cells) that if not controlled would jeopardize the integrity and quality of a study. Thus, we expect that studies submitted to Microbiome include sampling controls, extraction controls, PCR amplification controls as negative controls, but also positive controls (mock communities or others). These controls should be sequenced, and the sequence data reported in the paper and made available along with the sample sequence data in a public repository.
Nomenclature of organisms
Bacterial names should be written according to the guidelines of the American Society for Microbiology and the Journal of Bacteriology. Essentially, the names of all microbial taxa (kingdom, phyla, class, order, family, genus, species, and subspecies) should be italicized in the manuscript and the figures. Do not italicize strain designations or numbers.
Terminology to describe Microbiome studies
At Microbiome we have decided to follow the recommendations of Marchesi et al. with regards to vocabulary used to describe different aspects of microbial communities and their environments.
A common example is the use of the term 16S,16S rDNA, 16S rDNA gene, 16S gene which are not appropriate. These should be replaced with 16S rRNA gene.
Please make sure that you comply with all these criteria.
Preparing your Manuscript
The information below details the section headings that you should include in your manuscript and what information should be within each section.
Please note that your manuscript must include a 'Declarations' section including all of the subheadings (please see below for more information).
The title page should:
- present a title that includes, if appropriate, the study design
- list the full names, institutional addresses and email addresses for all authors
- if a collaboration group should be listed as an author, please list the Group name as an author. If you would like the names of the individual members of the Group to be searchable through their individual PubMed records, please include this information in the “Acknowledgements” section in accordance with the instructions below
- indicate the corresponding author
The Abstract should not exceed 350 words. Please minimize the use of abbreviations and do not cite references in the abstract. The abstract must include the following separate sections:
- Background: the context and purpose of the study
- Results: the main findings
- Conclusions: a brief summary and potential implications
Three to ten keywords representing the main content of the article.
The Background section should explain the background to the study, its aims, a summary of the existing literature and why this study was necessary.
This should include the findings of the study including, if appropriate, results of statistical analysis which must be included either in the text or as tables and figures.
For research articles this section should discuss the implications of the findings in context of existing research and highlight limitations of the study. For study protocols and methodology manuscripts this section should include a discussion of any practical or operational issues involved in performing the study and any issues not covered in other sections.
This should state clearly the main conclusions and provide an explanation of the importance and relevance of the study to the field.
The methods section should include:
- the aim, design and setting of the study
- the characteristics of participants or description of materials
- a clear description of all processes, interventions and comparisons. Generic names should generally be used. When proprietary brands are used in research, include the brand names in parentheses
- the type of statistical analysis used, including a power calculation if appropriate
List of abbreviations
If abbreviations are used in the text they should be defined in the text at first use, and a list of abbreviations can be provided.
All manuscripts must contain the following sections under the heading 'Declarations':
- Ethics approval and consent to participate
- Consent for publication
- Availability of data and material
- Competing interests
- Authors' contributions
- Authors' information (optional)
Please see below for details on the information to be included in these sections.
If any of the sections are not relevant to your manuscript, please include the heading and write 'Not applicable' for that section.
Ethics approval and consent to participate
Manuscripts reporting studies involving human participants, human data or human tissue must:
- include a statement on ethics approval and consent (even where the need for approval was waived)
- include the name of the ethics committee that approved the study and the committee’s reference number if appropriate
Studies involving animals must include a statement on ethics approval.
See our editorial policies for more information.
If your manuscript does not report on or involve the use of any animal or human data or tissue, please state “Not applicable” in this section.
Consent for publication
If your manuscript contains any individual person’s data in any form (including any individual details, images or videos), consent for publication must be obtained from that person, or in the case of children, their parent or legal guardian. All presentations of case reports must have consent for publication.
You can use your institutional consent form or our consent form if you prefer. You should not send the form to us on submission, but we may request to see a copy at any stage (including after publication).
See our editorial policies for more information on consent for publication.
If your manuscript does not contain data from any individual person, please state “Not applicable” in this section.
Availability of data and materials
All manuscripts must include an ‘Availability of data and materials’ statement. Data availability statements should include information on where data supporting the results reported in the article can be found including, where applicable, hyperlinks to publicly archived datasets analysed or generated during the study. By data we mean the minimal dataset that would be necessary to interpret, replicate and build upon the findings reported in the article. We recognise it is not always possible to share research data publicly, for instance when individual privacy could be compromised, and in such instances data availability should still be stated in the manuscript along with any conditions for access.
Data availability statements can take one of the following forms (or a combination of more than one if required for multiple datasets):
- The datasets generated and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS]
- The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
- All data generated or analysed during this study are included in this published article [and its supplementary information files].
- Data sharing is not applicable to this article as no datasets were generated or analysed during the current study.
- Not applicable. If your manuscript does not contain any data, please state 'Not applicable' in this section.
More examples of template data availability statements, which include examples of openly available and restricted access datasets, are available here.
BioMed Central also requires that authors cite any publicly available data on which the conclusions of the paper rely in the manuscript. Data citations should include a persistent identifier (such as a DOI) and should ideally be included in the reference list. Citations of datasets, when they appear in the reference list, should include the minimum information recommended by DataCite and follow journal style. Dataset identifiers including DOIs should be expressed as full URLs. For example:
Hao Z, AghaKouchak A, Nakhjiri N, Farahmand A. Global integrated drought monitoring and prediction system (GIDMaPS) data sets. figshare. 2014. http://dx.doi.org/10.6084/m9.figshare.853801
With the corresponding text in the Availability of data and materials statement:
The datasets generated during and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS].[Reference number]
All financial and non-financial competing interests must be declared in this section.
See our editorial policies for a full explanation of competing interests. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.
Please use the authors initials to refer to each authors' competing interests int his section.
If you do not have any competing interests, please state "The authors declare that they have no competing interests" in this section.
All sources of funding for the research reported should be declared. The role of the funding body in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript should be declared.
The individual contributions of authors to the manuscript should be specified in this section. Guidance and criteria for authorship can be found in our editorial policies.
Please use initials to refer to each author's contribution in this section, for example: "FC analyzed and interpreted the patient data regarding the hematological disease and the transplant. RH performed the histological examination of the kidney, and was a major contributor in writing the manuscript. All authors read and approved the final manuscript."
Please acknowledge anyone who contributed towards the article who does not meet the criteria for authorship including anyone who provided professional writing services or materials.
Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section.
See our editorial policies for a full explanation of acknowledgements and authorship criteria.
If you do not have anyone to acknowledge, please write "Not applicable" in this section.
Group authorship (for manuscripts involving a collaboration group): if you would like the names of the individual members of a collaboration Group to be searchable through their individual PubMed records, please ensure that the title of the collaboration Group is included on the title page and in the submission system and also include collaborating author names as the last paragraph of the “Acknowledgements” section. Please add authors in the format First Name, Middle initial(s) (optional), Last Name. You can add institution or country information for each author if you wish, but this should be consistent across all authors.
Please note that individual names may not be present in the PubMed record at the time a published article is initially included in PubMed as it takes PubMed additional time to code this information.
This section is optional.
You may choose to use this section to include any relevant information about the author(s) that may aid the reader's interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.
Endnotes should be designated within the text using a superscript lowercase letter and all notes (along with their corresponding letter) should be included in the Endnotes section. Please format this section in a paragraph rather than a list.
All references, including URLs, must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. The reference numbers must be finalized and the reference list fully formatted before submission.
Examples of the BioMed Central reference style are shown below. Please ensure that the reference style is followed precisely.
See our editorial policies for author guidance on good citation practice.
Web links and URLs: All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: The Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link (e.g. for blogs) they should be included in the reference.
Example reference style:
Article within a journal
Smith JJ. The world of science. Am J Sci. 1999;36:234-5.
Article within a journal (no page numbers)
Rohrmann S, Overvad K, Bueno-de-Mesquita HB, Jakobsen MU, Egeberg R, Tjønneland A, et al. Meat consumption and mortality - results from the European Prospective Investigation into Cancer and Nutrition. BMC Med. 2013;11:63.
Article within a journal by DOI
Slifka MK, Whitton JL. Clinical implications of dysregulated cytokine production. Dig J Mol Med. 2000; doi:10.1007/s801090000086.
Article within a journal supplement
Frumin AM, Nussbaum J, Esposito M. Functional asplenia: demonstration of splenic activity by bone marrow scan. Blood 1979;59 Suppl 1:26-32.
Book chapter, or an article within a book
Wyllie AH, Kerr JFR, Currie AR. Cell death: the significance of apoptosis. In: Bourne GH, Danielli JF, Jeon KW, editors. International review of cytology. London: Academic; 1980. p. 251-306.
OnlineFirst chapter in a series (without a volume designation but with a DOI)
Saito Y, Hyuga H. Rate equation approaches to amplification of enantiomeric excess and chiral symmetry breaking. Top Curr Chem. 2007. doi:10.1007/128_2006_108.
Complete book, authored
Blenkinsopp A, Paxton P. Symptoms in the pharmacy: a guide to the management of common illness. 3rd ed. Oxford: Blackwell Science; 1998.
Doe J. Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. 1999. http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999.
Healthwise Knowledgebase. US Pharmacopeia, Rockville. 1998. http://www.healthwise.org. Accessed 21 Sept 1998.
Supplementary material/private homepage
Doe J. Title of supplementary material. 2000. http://www.privatehomepage.com. Accessed 22 Feb 2000.
Doe, J: Title of preprint. http://www.uni-heidelberg.de/mydata.html (1999). Accessed 25 Dec 1999.
Doe, J: Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt (1999). Accessed 12 Nov 1999.
ISSN International Centre: The ISSN register. http://www.issn.org (2006). Accessed 20 Feb 2007.
Dataset with persistent identifier
Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S-S, et al. Genome data from sweet and grain sorghum (Sorghum bicolor). GigaScience Database. 2011. http://dx.doi.org/10.5524/100012.
Figures, tables additional files
See General formatting guidelines for information on how to format figures, tables and additional files.