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Aims and scope

Gut Pathogens is a fast publishing, inclusive and prominent international journal which recognizes the need for a publishing platform uniquely tailored to reflect the full breadth of research in the biology and medicine of pathogens, commensals and functional microbiota of the gut, in the context of infections caused by gastric/enteric bacteria, viruses and other causative agents. The journal publishes basic, clinical and cutting-edge research on all aspects of the above mentioned organisms including probiotic bacteria and yeasts and their products. The scope also covers the related ecology, molecular genetics, physiology and epidemiology of these pathogens. The journal actively invites timely reports on the novel aspects of genomics, metagenomics, microbiota profiling and systems biology in the context of the infections caused by E. coli, Salmonella, Shigella, Campylobacters, Helicobacters, Vibrio and other important enteropathogens.

Gut Pathogens will also consider, at the discretion of the editors, descriptive studies identifying a new genome sequence of a gut pathogen or a series of related microbial pathogens or commensals (such as those obtained from new hosts, niches, settings, outbreaks and epidemics) and those obtained from single or multiple hosts at one or different time points (chronological evolution).

Short articles that briefly and concisely describe the isolation and characterization of new pathogenic species or variants thereof, or a new strain or type based on sequence analysis or association studies of host and pathogen genetic repertoires or polymorphisms (functional molecular infection epidemiology) are also welcome.

Topical areas include, but are not limited to:

  • Microbial etiology of gut ailments
  • Gut invasion mechanisms
  • Microbial toxins and virulence factors in infections of the gut and associated glands - liver, pancreas
  • Bacterial adaptation to gut niches and evolution of pathogenicity
  • Biology and ecology of gut commensals and microbiota in health and disease, in the context of infection and immunity
  • Biology and ecology of probiotic organisms in the context of infections
  • Host susceptibility or resistance to gut pathogens
  • Immune mechanisms of gut infections
  • Etiology of inflammatory bowel diseases and the underlying pathogen triggers
  • Molecular and serological diagnosis of gut infections
  • Treatment and drug resistance mechanisms
  • Molecular epidemiology, transmission dynamics and evolutionary genetics of gut pathogens
  • Vaccines for gut pathogens
  • Comparative and veterinary infectious diseases of the gut
  • Pathogenesis of bacterial, parasitic and viral infections of the gut
  • Genome sequencing, comparative genomics and systems biology in the context of gastric-enteric pathogens
  • Microbiota analysis, metagenomics and gut microbiomes in the context of infections of the gut

Society affiliation

Gut Pathogens is a network partner of The International Society for Genomic and Evolutionary Microbiology (ISOGEM).

The International Society for Genomic and Evolutionary Microbiology is a non-profit, non-political, scientific society committed to the development of post genomic research, publication and education in the context of better public health and the environment with a special emphasis on genomics, metagenomics, evolution and stratification of microbial traits, functions and systems.

Open access

All articles published by Gut Pathogens are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers. Further information about open access can be found here.

As authors of articles published in Gut Pathogens you are the copyright holders of your article and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate your article, according to the BMC license agreement.

For those of you who are US government employees or are prevented from being copyright holders for similar reasons, BMC can accommodate non-standard copyright lines. Please contact us if further information is needed.

Article processing charges (APC)

Authors who publish open access in Gut Pathogens are required to pay an article processing charge (APC). The APC price will be determined from the date on which the article is accepted for publication.

The current APC, subject to VAT or local taxes where applicable, is: £2290.00/$3190.00/€2690.00

Visit our open access support portal and our Journal Pricing FAQs for further information.

Open access funding

Visit Springer Nature’s open access funding & support services for information about research funders and institutions that provide funding for APCs.

Springer Nature offers agreements that enable institutions to cover open access publishing costs. Learn more about our open access agreements to check your eligibility and discover whether this journal is included.

Springer Nature offers APC waivers and discounts for articles published in our fully open access journals whose corresponding authors are based in the world’s lowest income countries (see our APC waivers and discounts policy for further information). Requests for APC waivers and discounts from other authors will be considered on a case-by-case basis, and may be granted in cases of financial need (see our open access policies for journals for more information). All applications for discretionary APC waivers and discounts should be made at the point of manuscript submission; requests made during the review process or after acceptance are unable to be considered.

Indexing services

All articles published in Gut Pathogens are included in:

  • CAS
  • Citebase
  • DOAJ
  • Google Scholar
  • Journal Citation Reports/Science Edition
  • OAIster
  • PubMed
  • PubMed Central
  • Science Citation Index Expanded
  • Scopus
  • ​Zetoc

The full text of all articles is deposited in digital archives around the world to guarantee long-term digital preservation. You can also access all articles published by BioMed Central on SpringerLink.

Peer-review policy

Peer-review is the system used to assess the quality of a manuscript before it is published. Independent researchers in the relevant research area assess submitted manuscripts for originality, validity and significance to help editors determine whether the manuscript should be published in their journal. You can read more about the peer-review process here.

Gut Pathogens operates a single-blind peer-review system, where the reviewers are aware of the names and affiliations of the authors, but the reviewer reports provided to authors are anonymous.
The benefit of single-blind peer review is that it is the traditional model of peer review that many reviewers are comfortable with, and it facilitates a dispassionate critique of a manuscript.

Manuscripts submitted to Gut Pathogens will be examined by the Editor-in-Chief before being sent for peer review. Manuscripts will be sent to two reviewers, one of which may be a member of the Gut Pathogens Editorial Board with specialist knowledge in the area of the submitted manuscript. If conflicting recommendations arise from the peer-review, the manuscript will be sent for further review. Statisticians will be consulted where needed, and final decisions will be made by the Editor-in-Chief with consultation of the Editorial Board.

Edited by Niyaz Ahmed and Leonardo Sechi, Gut Pathogens is supported by an expert Editorial Board.

Editorial policies

All manuscripts submitted to Gut Pathogens should adhere to BioMed Central's editorial policies.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Citing articles in Gut Pathogens

Articles in Gut Pathogens  should be cited in the same way as articles in a traditional journal. Because articles are not printed, they do not have page numbers; instead, they are given a unique article number.

Article citations follow this format:

Authors: Title. Gut Pathog [year], [volume number]:[article number].

e.g. Roberts LD, Hassall DG, Winegar DA, Haselden JN, Nicholls AW, Griffin JL: Increased hepatic oxidative metabolism distinguishes the action of Peroxisome Proliferator-Activated Receptor delta from Peroxisome Proliferator-Activated Receptor gamma in the Ob/Ob mouse. Gut Pathog 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Appeals and complaints

Authors who wish to appeal a rejection or make a complaint should follow the procedure outlined in the BMC Editorial Policies.

Benefits of publishing with BMC

High visibility

Gut Pathogens's open access policy allows maximum visibility of articles published in the journal as they are available to a wide, global audience. 

Speed of publication

Gut Pathogens offers a fast publication schedule whilst maintaining rigorous peer review; all articles must be submitted online, and peer review is managed fully electronically (articles are distributed in PDF form, which is automatically generated from the submitted files). Articles will be published with their final citation after acceptance, in both fully browsable web form, and as a formatted PDF.


Online publication in Gut Pathogens gives you the opportunity to publish large datasets, large numbers of color illustrations and moving pictures, to display data in a form that can be read directly by other software packages so as to allow readers to manipulate the data for themselves, and to create all relevant links (for example, to PubMed, to sequence and other databases, and to other articles).

Promotion and press coverage

Articles published in Gut Pathogens are included in article alerts and regular email updates. Some may be highlighted on Gut Pathogens’s pages and on the BMC homepage.

In addition, articles published in Gut Pathogens may be promoted by press releases to the general or scientific press. These activities increase the exposure and number of accesses for articles published in Gut Pathogens. A list of articles recently press-released by journals published by BMC is available here.


As an author of an article published in Gut Pathogens you retain the copyright of your article and you are free to reproduce and disseminate your work (for further details, see the BMC license agreement).

For further information about the advantages of publishing in a journal from BMC, please click here.