Welcome to the Microbiome Across Biological Systems Call for Papers!

A Cross-Journal Call for Papers by PLOS ONEPLOS Biology, and PLOS Pathogens

– The submission deadline for this Collection has been extended to August 23, 2019 –


PLOS ONE Guest Editors –

Zaid Abdo

Sanjay Chotirmall

Thomas Dawson

Suzanne Ishaq

Noelle Noyes

Pankaj Trivedi

– The Microbiome Across Biological Systems: A PLOS ONE and PLOS BIOLOGY Call for Papers –  

Microbiomes are complex communities of bacteria, fungi, archaea, viruses, and microscopic eukaryotic organisms that can inhabit diverse environments, from the human gut, to soil, to even the atmosphere. These communities can impact an equally wide range of processes, including human brain development, pathogen virulence, and ecosystem nutrient cycling. New technologies and methods for studying microbiomes—their composition, formation, and how they influence their surroundings—are constantly emerging and researchers are only just starting to untangle these complex interactions. PLOS ONE and PLOS Biology are committed to highlighting this important area of emerging research.


We invite you to submit interdisciplinary research exploring environmental, urban, or host associated microbiomes. We welcome studies involving microbial communities, their function, composition, and health implications as well as any factors influencing these communities. Areas of particular interest include:


Microbiomes in Human Health and Disease

Microbial cells in and on the human body vastly outnumber host eukaryotic cells. As we consider human health and disease, it is essential to understand the composition and function of the human microbiome. Suggested topics in this area include but are not limited to:

  • Microbiome transplants
  • Gut-brain axis
  • Microbial metabolites and health
  • Personalized medicine
  • Microbiome dynamics and stability
  • Microbiomes and immunotherapy
  • The microbiome and drug interactions
  • Age related microbiomes
  • Microbiomes and disease


Microbiomes in the Environment

Microbial communities are ubiquitous and can be found in all environments whether they are host related or host independent, urban or natural, terrestrial or aquatic or atmospheric. Understanding microbial communities and their interactions can have far reaching impacts. Suggested topics in the area include but are not limited to:  

  • Microbiomes and agriculture
  • Plant and soil related microbial interactions
  • Urban or built environment microbial communities
  • Microbiomes and the natural environment
  • Wildlife microbial communities
  • Marine microbiomes


New Frontiers in Microbiome Research

Microbiome experiments and community profiling can result in massive amounts of information and innovative products. New techniques are needed to both analyse and identify meaningful patterns from these large datasets as well as to develop new ways of utilizing microbiomes. Suggested topics in this area include but are not limited to:  

  • Engineering of microbial communities
  • Novel methods for genetic, genomic, metabolomic, and other molecular analyses of microbiomes
  • Computational methods
  • Probiotic therapeutics


PLOS Pathogens Microbiome Research: A Call for Papers –

PLOS Pathogens invites microbiome research which includes substantive mechanistic advances about how the microbiome directly or indirectly influences host-pathogen or pathogen-pathogen interaction and how these interact in novel ways. Research can deal directly with the interaction between microbiome and infectious diseases or indirectly with the development of the immune system by the microbiota.


Topics include, but are not limited to:

  • Microbiota influence on immunity: changes to the immune system and susceptibility to infection caused by microbiota, colonization resistance
  • Microbiota influence on pathogens: microbiota impact on the selection or evolution of pathogens, horizontal gene transfer, influence on the expression of certain known pathogenic loci within infectious organisms, microbiota influence on infection
  • Pathogenic influence on microbiota: changes to the structure of resident communities and immunity after pathogenic infection, inter-kingdom interactions
  • The immune system’s interaction with microbiota: how the immune system discriminates pathogens from commensals


PLOS ONE accepts scientifically rigorous research, regardless of perceived impact. PLOS ONE’s broad scope provides a platform to publish primary research, including interdisciplinary and replication studies, as well as negative results. The journal’s publication criteria are based on high ethical standards and the rigor of the methodology and conclusions reported.


PLOS Biology features works of exceptional significance, originality, and relevance in all areas of biological science, from molecules to ecosystems, including works at the interface of other disciplines, such as chemistry, medicine, and mathematics. In addition to outstanding Research Articles, we also publish provocative Short Reports, which can be based on a more limited number of experiments, and exceptional Methods and Resources. Our audience is the international scientific community as well as educators, policy makers, patient advocacy groups, and interested members of the public around the world.


PLOS Pathogens publishes outstanding original research and commentary that significantly advance the understanding of pathogen-host interactions and their consequences for health, showcasing the breadth of research on bacteria, fungi, parasites, prions, viruses, and the microbiome.


Please submit your manuscripts by August 23, 2019 to be considered by a panel of Guest Editors for this Call for Papers. When submitting, please specify in your cover letter that you are submitting to “The Microbiome Across Biological Systems” Call for Papers. Final collection to be published in early 2020.


Meet the PLOS ONE Editors

Zaid Abdo

Guest Editor, PLOS ONE 

I am an Associate Professor in the Department of Microbiology, Immunology and Pathology at Colorado State University. A main research objective of my lab is to understand the microbial community structure, its interactions and function, and how this microbial community interacts with as well as affects its hosts’ health and as its surrounding environment.

Much of my work for over a decade and a half has been mainly focused on the human microbiome, studying the vaginal microbiome, the semen microbiome, the human milk microbiome, and the relationship between the microbiome of the GI tract and disease. This is in addition to a focus on utilizing metagenomic tools to study the evolution and spread of plasmid carriers of antimicrobial resistance within the microbiome.

My research also involves developing and applying computational tools for processing and analysis of the resulting high throughput metagenomics sequence data, and the associated metadata, in addition to developing inferential and predictive models to facilitate understanding of these complex biological systems. (Website & Twitter @ZaidAbd51024700)


Sanjay Haresh Chotirmall

Guest Editor, PLOS ONE 

Assistant Professor Sanjay Haresh Chotirmall graduated from the Royal College of Surgeons in Ireland (RCSI) with an honours degree and the colleges’ gold medal in Microbiology. He completed his early clinical training at Beaumont Hospital Dublin, while attaining memberships of the Royal College of Physicians of Ireland (MRCPI) and the United Kingdom (MRCP UK). Following this, he completed higher specialist training in Respiratory and Critical Care Medicine across multiple hospital sites in the Republic of Ireland.

As a recognized clinician-scientist, Asst Prof Chotirmall is now at the Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore and has established a Translational Respiratory Research Group, with focus on infection, inflammation, and immunity, in the context of chronic inflammatory respiratory diseases that affect Asian populations. Research in the Chotirmall lab shares a core translational respiratory focus with a common goal to improve patient care through advancing the understanding of disease from a scientific basis. The group pursues research in a number of areas with significant clinical importance that impact Singaporeans and other Asian populations including chronic inflammatory lung disease, infectious lung disease and the pulmonary microbiome.


Thomas Dawson

Guest Editor, PLOS ONE 

Tom Dawson earned his Bachelor’s in Chemistry from West Virginia University in 1986, a Ph.D. in Pharmacology from the University of North Carolina in 1994 and was a Clinical Medical Genetics Fellow in Pediatrics at the Duke University Medical Center 1994-96.  While at UNC Tom identified and patented a novel proto-oncogene, merTK, which is involved in normal retinal function and myloid development.  At Duke, Tom worked with Dr. Y-T Chen on metabolic disease, and was a member of the team that developed Myozyme, a treatment for Glycogen Storage Disease Type II, Pompe Disease. From 1998-2015 Tom worked in Procter & Gamble’s Beauty Technology Division, understanding and intervening in hair and scalp disorders including dandruff, male pattern baldness, and age-related hair thinning.

The dandruff investigations led to Malassezia fungi and included identification of the dandruff causal species (M. globosa and M. restricta), an undiscovered pathogenic mechanism, novel intervention strategies, multiple publications and patents, and a technology currently in market in H&S.  Tom leads a global consortium on Malassezia phylogeny, physiology, and pathogenesis. In 2013 Tom relocated from Cincinnati to Singapore to lead development of P&G’s life sciences in the new Singapore Technical Center, SgIC.

In April of 2015 Tom joined the Skin Research Institute, Singapore to develop and lead a translational program in hair and scalp biology, including research focused on the cutaneous eukaryotic microbiome and its effects on normal and abnormal skin, with an emphasis on Malassezia and their interaction with the human host.

Suzanne L. Ishaq

Guest Editor, PLOS ONE 

Dr. Suzanne L. Ishaq is a Research Assistant Professor of Microbial Ecology in the Biology and the Built Environment Center at the University of Oregon, where she is part of a collaborative research team working to understand how building design influences the indoor microbiome and human health.  Her research background melds host-associated, soil-associated, and building-associated microbial ecology to understand microbial communities, the dynamics that shift them, and how they might alter host or occupant health.  Previously, she completed two post-doctoral researcher projects at Montana State University.  The most recent was with the Department of Land Resources and Environmental Sciences, where she focused on the effect of farming system and climate change on soil bacterial ecosystems. The first was with the Department of Animal and Range Sciences working on the bioinformatic analysis of soil, water, and host-associated microbes.

She received her Doctorate in Animal, Nutrition and Food Science from the University of Vermont, Dept. of Animal Science.  Her graduate study focused on the rumen microbiology of the moose (Alces alces), including identification using high throughput sequencing and DNA analysis, isolation of bacteria using anaerobic culturing techniques, and investigation/application of economically and environmentally important species. Her philosophy is that researchers have an obligation to share and disseminate the results of their work, and to engage both the general public and the specific groups that may benefit from those findings.  

Noelle Noyes

Guest Editor, PLOS ONE 

My current research focuses on epidemiology as a vehicle for integrating diverse methods to better understand complex, multi-faceted issues at the intersection of agriculture and public health. One such issue is antimicrobial resistance, but we also investigate how microbial ecology is linked to animal health and disease and food safety. My overall goal is to use scientific discovery as a vehicle to help solve challenging problems in a win-win-win manner, for the benefit of animals, people and the environment. I place high value on transdisciplinary and collaborative research, and my background reflects this.

I received my BA in European Studies from Amherst College, with a concentration in Asian Languages and Civilizations. I received my MA from Osnabrück Universität, Germany while conducting independent research on an Alexander von Humboldt Fellowship and bartending at the local kneipe. I then worked as a consultant for Mercator Partners in Boston, specializing in innovation strategy and mergers/acquisitions for high-tech companies.

After deciding that corporate America wasn’t for me, I decided to pursue veterinary school. While waitressing and wrangling cows, dogs and cats (not at the same time), I took all of the science pre-reqs for vet school and was accepted into the DVM-PhD program at Colorado State University, where I received my doctorate in epidemiology, a USDA NIFA post-doctoral fellowship, and a veterinary degree (large animal medicine). I am now Assistant Professor in the College of Veterinary Medicine at University of Minnesota. (Website & Twitter @noelle_noyes)


Pankaj Trivedi

Guest Editor, PLOS ONE 

I am an Assistant Professor in the Department of Bioagricultural Sciences and Pest Management at Colorado State University. My research goal is to elucidate and exploit the multitrophic interactions among and between microbiome and the plant environment that influence the health and productivity of managed and natural systems, especially in response to environmental change. Areas of my research interest are broad and include (1) microbial ecology; (2) “omics” technologies; (3) plant-microbe-insect interactions; (4) predictive computational modeling; and (5) microbiome engineering.

Research projects in my lab will address the assembly, fitness and roles of plant, insect, and soil-associated microbiomes; how these are influenced by various biotic and abiotic factors; and what are their consequences on plant productivity, agro- ecosystems sustainability, and local and global level ecological processes. By providing systems-level understanding of plant microbiomes the research will develop new computational tools and host/microbiome models that enable plant breeders and plant ecologists to predict beneficial interactions to achieve improved yields and plant resilience in changing environments. (Website & Twitter @pankajtri29)

PLOS ONE Handling Editors

Clement Adebamowo Polak Aich Pankaj Arora Annamaria Bevivino
Luigimaria Borruso Franck Carbonero Luca Cocolin Andrew Dalby
Karen Davison Guido Favia Omri Finkel Jonathan Jacobs
Paul Jensen Peggy Lai Alan Landay John Lee
Hari Misra Jose Montoya Nikhil Pai Si Hong Park
Brandt Pence Krista Power Namita Rout Joy Scaria
Jae-Ho Shin Hauke Smidt Davida Smyth Palanisami Thavamani
Ryan Thomas Holger Till Guangming Zhong Erwin Zoetendal

Submission Instructions

Articles must be submitted by August 23, 2019

Are you ready to submit or want to learn more about how the submission process works? To make it as easy as possible for our communities, we have all of our PLOS ONE submission instructions posted online. If there are any details you can’t find, please email us at

Submission instructions for PLOS Biology are posted here and questions can be directed to 

PLOS Pathogens has submission instructions posted here, and questions can be sent to

When submitting a manuscript, please specify that you are submitting to the Collection “The Microbiome Across Biological Systems” in your cover letter. In addition, for  PLOS ONE, please enter “The Microbiome Across Biological Systems” in the “Collections and Calls for Papers” field in the Additional Information section of the submission form. 

Publishing Process

We aim to be as transparent as possible about our publishing and peer review processes. Papers submitted to PLOS ONE and under consideration for the Microbiome Across Biological Systems will be specially handled by hand-selected active researchers from our Editorial Board working in Microbiome research, in partnership with PLOS ONE Staff Editor Anna Simonin. Papers submitted to PLOS Biology will be handled with our standard process, with additional input and curation from the Guest Editors. 

For more information please see the PLOS ONE Editorial and Peer Review Information page or the PLOS Biology Editor and Peer Review Information page, as relevant. 

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