Call for papers - Genomics of microbiomes

Guest Editors

Alessio Mengoni, PhD, University of Florence, Italy
Konstantinos Papadimitriou, PhD, Agricultural University of Athens, Greece

Submission Status: Open | Submission Deadline: 7 January 2026

BMC Genomics invites researchers to contribute their findings on the genomics of microbiomes, highlighting their roles in ecology, health, disease, and environmental systems. We welcome submissions that explore the genetic diversity, functional capabilities, and ecological significance of microbiomes across various environments, utilizing cutting-edge genomic techniques and multi-omics approaches to deepen our understanding of these vital communities.

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Meet the Guest Editors

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Alessio Mengoni, PhD, University of Florence, Italy

Alessio Mengoni is a professor of genetics in the Department of Biology at the University of Florence, Italy (lab website: www.dblage.unifi.it). He graduated in biology and obtained a PhD in genetics from the University of Pavia, Italy, in 2000. During his PhD, he worked on the evolutionary genetics of plants, then shifted his focus to studying microbial communities. He also conducted research at SCK-CEN in Belgium and at the Vrije Universiteit in Amsterdam. He has been a visiting professor at the universities of Gdansk in Poland and Guangzhou (Sun Yay-sen University) in China, where he taught courses in genomics and systems biology. His main research interests revolve around studying bacterial genome evolution, especially concerning plant-microorganism interactions and symbiosis, for designing applications in agricultural and environmental biotechnology. He is the author of over 200 scientific articles and a founding associate of a spin-off company from the University of Florence (EcolGene S.r.l.) specializing in microbiological and genetic analysis.

Konstantinos Papadimitriou, PhD, Agricultural University of Athens, Greece

Konstantinos has a BSc/MSc in Food Science and Technology from the Agricultural University of Athens (1998). He then pursued an MSc in Genetic Manipulation and Molecular Biology from Sussex University (2000). He was awarded the PhD in Food Microbiology with distinction from AUA (2006). His research interests include the microbiology of dairy products, the physiology, the genetics and the genomics of lactic acid bacteria, the metagenomics of traditional fermented foods, single cell microbiology, plasmid biology, and applied bioinformatics. He is also interested in probiotics research and the application of probiotics in human health. Konstantinos is currently an Assistant Professor of Food Quality Control in the Department of Food Science and Human Nutrition at the Agricultural University of Athens (Greece).

About the Collection

The study of microbiomes has emerged as a dynamic field at the intersection of genomics, ecology, and health sciences. Microbiomes encompass the diverse communities of microorganisms, including bacteria, viruses, and unicellular eukaryotes, residing in various environments, such as the human body, food, soil, and aquatic systems. Understanding the genomic makeup of these microbiomes is crucial for unraveling their complex interactions with hosts and the environment. As advances in sequencing technologies, including single molecule sequencing, metagenomics and single cell omics, continue to evolve, researchers are better equipped to explore the rich genetic diversity (including pangenomes and epigenomes) and functional capacities of microbiomes across different ecosystems.

Investigating the genomics of microbiomes is pivotal for addressing critical questions in ecology, health, disease, and environmental sustainability. For instance, recent breakthroughs in the field have illustrated how microbiomes influence human health, from their roles in metabolism and immune function to their impact on mental health. Furthermore, understanding the genomics of environmental microbiomes can provide insights into biogeochemical processes and ecological resilience. As we deepen our knowledge of these microbial communities and develop computational biology methods to model their functionality, we stand to enhance our ability to harness their potential for applications in medicine, agriculture, and environmental management.

Future research in this area holds the promise of transformative advances in our understanding of microbiomes. The integration of multi-omics approaches, combining genomics with transcriptomics, proteomics, and metabolomics, may lead to a holistic view of microbial community dynamics and their functional implications. Additionally, developments in artificial intelligence and machine learning could further accelerate discoveries, enabling the identification of novel microbial functions and their roles in health and disease. As we continue to explore these intricate relationships, we can anticipate innovative strategies for harnessing microbiomes for therapeutic and environmental applications.

Topics of interest include, but are not limited to:

Genomics and epigenomics of host-microbe interactions
X-omics studies in environmental and host-microbiomes
Advances in genomics of unculturable microorganisms
Genome-guided development of synthetic microbiomes and consortia
Microbiomes and environmental resilience: a genomic perspective
The human microbiome: genetic diversity and functional potential
Microbial adaptation and evolution in changing environments
The role of microbiomes in antibiotic resistance and pathogenesis
Computational and AI-driven methods for microbiome genomics
Microbiome applications in sustainable agriculture and environmental management

All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.

There are currently no articles in this collection.

Submission Guidelines

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This Collection welcomes submission of original Research Articles. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Genomics of microbiomes" from the dropdown menu.

All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.