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The PLOS Microbiome Channel – Meet the Editors

Zaid Abdo, Noelle Noyes, John Rawls, Jessica Metcalf and Pankaj Trivedi announce the launch of the PLOS Microbiome Channel.


Microorganisms including bacteria, viruses and fungi comprise a vast variety of microbiomes ranging from isolated streams in the Amazonian rainforest to the villi found in the human gastrointestinal tract. As ever-present communities, these microbiota are integrated into all aspects of both life and death, playing important roles that can influence the immunity of their hosts, affect environmental conditions and even introduce pressures in natural selection. The complexity of understanding how microbiomes function as well as their impact is studied in multiple research disciplines, utilising some of the most advanced technologies. With an appreciation of the broad diversity and importance of this field, PLOS is delighted today to launch the PLOS Microbiome Channel.

Channels are resources for research communities: a single “one-stop-shop” destination to discover and explore content from PLOS journals as well as the broader literature, supplemented by preprints, blogs, news, events, commentary and more to keep readers up to date with the latest research in their field.

The PLOS Microbiome Channel aims to curate the latest research into the microbiome in humans, animals, plants and the environment, and how it impacts and is impacted by these different systems, highlighting and providing access to tools and models used to improve our understanding of these systems.

The Channel Editors will highlight research that meets some or all of the following criteria:

  • Describes new discoveries and presents new cutting-edge microbiome science, with particular interests in the advancement of meta-omics (e.g. DNA, RNA, proteins, metabolites, etc.)
  • Describes new protocols, technologies and model systems used to generate data and discoveries within these areas
  • Describes new quantitative and computational methods applied in these areas  

The scope of the Microbiome Channel was developed with the Channel Editors distinguished scientific experts in their field who will be responsible for curating the content that goes into the Channel.

Meet the Editors

Zaid Abdo: 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)

Noelle Noyes: 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)

John Rawls: I am an Associate Professor in the Departments of Molecular Genetics and Microbiology, and Medicine at the Duke University School of Medicine. I also serve as director of the Duke Microbiome Center. After completing my undergraduate education at Emory University (1992-1996), I received a PhD in Developmental Biology from Washington University under the mentorship of Dr Stephen Johnson (1996-2001). I then trained as a postdoctoral fellow with Dr Jeffrey Gordon at the Center for Genome Sciences at Washington University (2001-2006). My interdisciplinary research program seeks to understand the molecular mechanisms underlying host-microbiome interactions. We use gnotobiotic, genetic, genomic, physiologic, and in vivo imaging approaches to determine how microbes interact with vertebrate hosts to regulate their metabolism and immunity, as well as the mechanisms underlying assembly of intestinal microbial communities. We pioneered the use of germ-free and gnotobiotic zebrafish to investigate the roles of microbiomes in vertebrate biology, and we currently use both zebrafish and mouse models to investigate the microbial signals and responsive host pathways that regulate host immunity, nutrition, and gene expression programs. Our studies in animal models are designed to address key gaps in knowledge about the role of the human microbiome in diseases such as the inflammatory bowel diseases, obesity, and diabetes. We also conduct primary research in humans to define microbial species and metabolites associated with these diseases which can then be tested and validated in our animal models. (Website & Twitter @RawlsLab)

Jessica Metcalf: I am a microbiome scientist who leads highly interdisciplinary, innovative research projects that span the fields of animal science, health, and forensics by combining experimental ecology, large genomic datasets, and bioinformatics tools. My group studies the microorganisms (bacteria, archaea, fungi, protists, etc) of the gastrointestinal tract of vertebrate animals with a focus on the effects of captivity and domestication on animal health. In a similar vein, we also study the loss of microbial diversity in the human gastrointestinal tract associated with the industrialization/urbanization of human populations. Finally, my lab is a leader in developing microbiome tools for forensic science. Our work on decomposition microbial ecology is currently being applied to better understand and predict meat shelf life and spoilage.
I earned a BS in chemistry from University of Georgia and a PhD in ecology and evolution from University of Colorado Boulder. I completed postdoctoral positions in ancient DNA at the University of Adelaide in South Australia and in microbiome science at UC San Diego. I joined Colorado State University in 2016 as part of the Microbiome Systems Cluster Hire Initiative, and I am currently an Associate Professor in the Department of Animal Sciences. (Website & Twitter @dirtysci)

Pankaj Trivedi: 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)


The Editors will regularly update the Channel to showcase the most up to date and impactful research and resources of interest to the microbiome community, and look forward to engaging with the community to build a useful resource for all. To nominate content for the Channel email channels@plos.org or tweet us @PLOSChannels with the hashtag #PLOSMicrobiome


Featured Image Credit: Eric Erbe, Wikimedia Commons, CC-0

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