Journal of Oral Microbiology

Oral Dark Matter – Finding Paths into the Unknown Unknowns

Already in 1894, Willoughby Miller first observed that not all bacteria from infected root canals, as seen under the microscope in Robert Koch's laboratory at the Charité, could be cultured on agar plates. Since then, our knowledge on the genetic diversity of the oral microbiome has exploded with the development of PCR, cloning techniques, fluorescent in situ hybridization, and, most importantly, high-throughput sequencing (NGS). As a result, a huge number of microorganisms has been characterized genetically without being cultured. Hence, the term 'microbial dark matter' was coined to describe microorganisms that have been found in sequencing data, but have not been cultured. However, the term “dark matter” does not only encompass the functional and taxonomic identity of individual species. With its highly diverse niches, the oral cavity represents a complex interwoven web of ecosystems whose interdependencies and biological principles are still mostly unknown, yet not only important to oral health and disease, but of fundamental interest to microbial ecology.

Mounting evidence points towards the role of the oral microbes in human systemic health in a wide range of conditions from colorectal cancer over metabolic diseases to neurodegeneration. However, the mapping, functional characterization, and ecological understanding of oral microbes lags the epidemiological insights that demonstrate the crucial role of the oral microbiome in human health and disease. Many insights into oral microbiology have been won using a relatively small collection of model organisms that do not reflect the biological diversity within the oral cavity, indicating that many biological mechanisms important to human health, also beyond oral health, are still in the dark. Culturing these unculturables will be important to get information about their characteristics and virulence traits which may lead to a better understanding of oral disease etiology and in turn may also result in new treatment options for oral diseases.

Thus, we invited original research, perspectives, reviews that shine a light into the realms of the oral microbiome that are still in the dark. In particular, we invite studies targeting:

1. Research into culturing the un-culturable – that means research that develop, validate and demonstrate paradigms of culturomics, the integration of modern multi-omics approaches into classical microbiological culturing efforts. Also, research describing failed approaches are invited.
2. Research mapping the functionalities of oral microbes via both computational as well as empirical tools
3. Research into the theoretical ecology, spatial biology and host-microbiome interplay within the oral cavity, explicitly also inviting in silico approaches and AI applications
4. Experimental and epidemiological research into domains of oral microbiology such as fungi, bacteriophages, archaea, and protozoa that provide crucial insights beyond the bacterial domain
5. Metagenomic sequencing research at scale that deliver insights into the taxonomic and functional diversity across the world, explicitly inviting efforts from non-Western countries

Not fitting for this Article Collection in contrast are studies that deepen our understanding of culturable model organisms, 16S-based studies highlighting epidemiological associations of oral genera with human diseases, and studies looking at individual pathogen-host relations of single taxa.

Keywords

• Culturomics
• Meta-genomics
• Computational ecology
• Culture technique
• Oral ecology

­­All manuscripts submitted to this Article Collection will undergo a full peer-review; the Guest Advisor for this Collection will not be handling the manuscripts (unless they are an Editorial Board member).

Please review the journal scope and author submission instructions prior to submitting a manuscript.

The deadline for submitting manuscripts is 31 August 2027.

Please contact Zhiyuan Zhang at zhiyuan.zhang@taylorandfrancis.com with any queries and discount codes regarding this Article Collection.

Please be sure to select the appropriate Article Collection from the drop-down menu in the submission system.

Guest Advisors

Johannes Hertel is Professor for Systems Biology and Translation in Psychiatry at the University Medicine Greifswald, with a background in biomathematics and psychology. Fascinated by the intrinsic diversity of microbes, his main research focus is on mapping microbial ecology and functionalities, generating new paradigms for the personalized functional characterization of human microbiomes.

Fabian Cieplik is Professor and Head of the Department of Operative Dentistry and Periodontology at the Medical Center – University of Freiburg. He is a trained dentist but has been working in the field of oral microbiology for his whole career, with recent research focusing on oral biofilms and oral microbial ecology, antimicrobial approaches, and resistance ecology.

Ali Al-Ahmad is an associate professor and head of the laboratories in the Department of Operative Dentistry and Periodontology at the University Medical Centre Freiburg. He has a background in general and applied microbiology and has worked in the field of oral microbiology for over 22 years. His recent research has focused on oral microbial ecology, including oral microbial adhesion and biofilms, biomaterial-associated infections, and resistance ecology.