Special Interview with Frontiers in Bioscience-Landmark Author Dr. Gabriel Žoldák: Exploring Microbial Load and New Directions in Gut Microbiome Research

2 February 2026

 

Recently, Dr. Gabriel Žoldák and his team published a commentary article in Frontiers in Bioscience-Landmark entitled “Gut Microbial Load as a Hidden Driver of Microbiome Diversity and Function” (Volume 30, Issue 8, 2025). In this article, the authors provide an in-depth analysis of the study by Nishijima et al. published in Cell, highlighting the critical importance of absolute microbial abundance in microbiome research and its potential implications for clinical translation. To further explore the story behind this research, its innovative significance, and future directions, we interviewed Dr. Gabriel Žoldák's team.

 

Part 1: The Story and Journey Behind the Article

1. Could you briefly introduce the core members of your team? What first drew your attention to this article, and what motivated you to write this commentary?

This commentary came from our ProteoForce project team, which integrates expertise in biophysics and microbiology to explore new out-of-the-box applications in single-molecule research. Project members include MSc. Ondrej Ragač, Dr. Simona Sovová, Dr. Natália Chomová, MSc. Kristína Papayová, Ing. Patrik Varga, Prof. Pavol Miškovský, Dr. Jonatan Göran Johannesson, Dr. Shubhashis Datta, and Assoc. Prof. Gabriel Žoldák as the PI. We were drawn to the original article because it systematically quantified “microbial load”—a parameter largely overlooked in microbiome research. We wrote the commentary to underline why absolute microbial abundance matters and to encourage its integration into both experimental and clinical studies.

2. In your opinion, what is the most groundbreaking or unconventional aspect of Nishijima et al.’s study?

The Nishijima et al. study introduces an innovative approach by using microbial load as a key indicator of microbiota composition and function in relation to host factors. This perspective enhances our understanding of microbial communities in health and disease. The use of a machine-learning model to predict microbial load from relative abundance is particularly notable for processing and handling extensive metagenomic datasets that require precise absolute measurements. Given the links between microbial load and various diseases, establishing experimental frameworks for confirming causality through controlled studies is essential. It is also important to address frequency-dependent phenotypes and the scalability of this parameter in future research. These advancements could significantly enhance our understanding of microbiota-related health issues.

3. Could you give us a brief overview of the main points you elaborated on in your commentary?

The main focus is on the relationship between the absolute numbers of bacteria and their relative abundance, which is identified using Pearson correlations. By classifying bacterial species into functional groups, we can better understand their correlations and interactions. For instance, an increase in the pathobiont Clostridium bolteae is negatively correlated with Roseburia intestinalis but positively correlated with another pathobiont. These correlations often stem from phylogenetic relationships, as related species tend to support one another. In addition, there is a direct link between bacterial load and diversity. Higher bacterial loads often lead to greater metabolic potential due to increased synergy among bacteria. In contrast, lower bacterial loads are associated with opportunistic oral taxa and may be linked to diseases such as inflammatory bowel disease.

 

Part 2: Article Content and Innovative Value

1. Of the four future directions you mentioned (mechanisms, thresholds, generalizability, and multi-omics), which one do you feel is the most pressing or has the greatest impact?

Among the four directions we highlighted—mechanisms, thresholds, generalizability, and multi-omics— thresholds are the most pressing. Without establishing clinically meaningful cut-offs for microbial load, it is difficult to translate microbiome research into diagnostics or interventions.

2. In your commentary, you pointed out that “microbial load” is an often-overlooked but important factor. Could you share, in simple words, why it matters so much?

In simple words, knowing the total number of microbes is like knowing how many “workers” are in a factory. Relative abundance only tells you the percentages of each worker type, but not whether there are 100 or 10,000 workers. The total number determines overall capacity and output, and also how well these workers can interact with each other. In ecology, this mirrors an Allee effect (or “network effect” in human society, or how individual fitness depends on the population size): just as a large town supports more professions, stronger economic output,      and richer collaboration networks than a small village with the same proportions of professions. A high microbial load enables more cooperation, more specialized functions, and a more resilient “community.” In the gut, a higher microbial load not only boosts metabolite production but also strengthens inter-microbial cooperation, host interactions, and colonization resistance—essentially creating a more resilient and functional ecosystem.

3. You also brought up some technical challenges, such as the limitations of current measurement methods. From your perspective, what area do you think needs the most improvement going forward?

From our perspective, the primary methods for absolute quantification of microbial load, like flow cytometry and qPCR, present both technical variability and practical limitations, particularly in large clinical studies. In addition, there are challenges with current methods that make it difficult to examine and influence just a single parameter, since the available techniques lack the necessary information. When it comes to sequencing techniques, we see cost and accessibility as significant barriers. These issues ultimately lead to a reduction in available data, limiting the ability to compare results across different studies.

4. Looking ahead, how do you see the new perspective of “total microbial load” shaping future disease research or even clinical diagnosis?

Incorporating “total microbial load” will likely refine risk stratification for diseases like inflammatory bowel disease, metabolic disorders, and infections. It could become a routine measurement, much like cell counts in blood tests. This parameter can also help to more objectively assess the effects of treatments, probiotics, or diet interventions.

5. What is your next research plan?

We are currently focusing on expanding our single-molecule biophysics approaches to new systems. In addition, we are developing techniques to study specific cell types within complex microbial communities and to monitor how their behavior and responses change when the total microbial load varies. We also plan to use laser optical tweezers to investigate bacterial vitality and resilience, including their response to laser-induced stress and potential killing, which will help us understand survival mechanisms at the single-cell level. We are simultaneously building collaborations to apply these measurements in clinical cohorts.

 

Part 3: Interaction with the Journal

1. What made you decide to submit this work to our journal? In your view, what aspects of our journal were most attractive to you?

We chose your journal because it reaches a wide international audience and publishes timely, interdisciplinary articles. It’s well indexed and visible to both basic scientists and clinicians, which is exactly the readership we wanted for our commentary.

2. How would you describe your experience with the submission in our journal? Were there any parts of the process that left a strong impression on you?

Our experience was very positive. The submission system was simple, communication with editors was quick, and the review process was constructive. The efficient handling and helpful feedback stood out and left a strong, positive impression on us.

3. Looking ahead, what kinds of topics or research directions would you like to see more of in our journal?

Our team is particularly interested in publications that focus on developing new methodologies and standardizing procedures in specific areas, such as bacteriophages. We also encourage studies that connect laboratory results with clinical research or practical applications in the field.

 

Through this interview, Dr. Žoldák and his team shared their in-depth reflections on microbial load as a research perspective, while also highlighting the value of interdisciplinary collaboration in advancing frontier science. Their emphasis on methodological innovation, mentorship of young researchers, and open scientific exchange resonates strongly with the mission of our journal.

We sincerely thank Dr. Žoldák and his team for their time and thoughtful insights. Our journal remains committed to serving as a platform for such meaningful scientific exchange.

 

Article Details: Gut Microbial Load As a Hidden Driver of Microbiome Diversity and Function

Journal homepage: Frontiers in Bioscience-Landmark