Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria

Reviewer #1 (Public review):

Summary:

This study experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate. Multiple, independent molecular, animal, and in vitro experimental models were introduced into this research. The authors found that microbiome composition influenced multiple oxalate-microbe-host interfaces. Oxalobacter formigenes were only effective against a poor oxalate-degrading microbiota background and give critical new insights into why clinical intervention trials with this species exhibit variable outcomes. Data suggest that, while heterogeneity in the microbiome impacts multiple diet-host-microbe interfaces, metabolic redundancy among diverse microorganisms in specific diet-microbe axes is a critical variable that may impact the efficacy of bacteriotherapies, which can help guide patient and probiotic selection criteria in probiotic clinical trials.

Strengths:

The paper has made significant progress in both the depth and breadth of scientific research by systematically comparing multiple experimental methods across multiple dimensions. Particularly through in-depth analysis from the enzymatic perspective, it has not only successfully identified several key strains and redundant genes, which is of great significance for understanding the functions of enzymes, the characteristics of strains, and the mechanisms of genes in microbial communities, but also provided a valuable reference for subsequent experimental design and theoretical research.

More importantly, the establishment of a novel research approach to probiotics and gut microbiota in this paper represents a major contribution to the current research field. The proposal of this new approach not only breaks through the limitations of traditional research but also offers new perspectives and strategies for the screening, optimization of probiotics, and the regulation of gut microbiota balance. This holds potential significant value for improving human health and the prevention and treatment of related diseases.

Weaknesses:

While the study has excellently examined the overall changes in microbial community structure and the functions of individual bacteria, it lacks a focused investigation on the metabolic cross-feeding relationships between oxalate-degrading bacteria and related microorganisms, failing to provide a foundational microbial community or model for future research. Although this paper conducts a detailed study on oxalate metabolism, it would be beneficial to visually present the enrichment of different microbial community structures in metabolic pathways using graphical models.

Furthermore, the authors have done a commendable job in studying the roles of key bacteria. If the interactions and effects of upstream and downstream metabolically related bacteria could be integrated, it would provide readers with even more meaningful information. By illustrating how these bacteria interact within the metabolic network, readers can gain a deeper understanding of the complex ecological and functional relationships within microbial communities. Such an integrated approach would not only enhance the scientific value of the study but also facilitate future research in this area.

Reviewer #2 (Public review):

Summary:

Using the well-studied oxalate-microbiome-host system, the authors propose a novel conceptual and experimental framework for developing targeted bacteriotherapies using a three-phase pre-clinical workflow. The third phase is based on a 'complex system theoretical approach' in which multi-omics technologies are combined in independent in vivo and in vitro models to successfully identify the most pertinent variables that influence specific phenotypes in diet-host-microbe systems. The innovation relies on the third phase since phase I and phase II are the dominant approaches everyone in the microbiome field uses.

Strengths:

The authors used a multidisciplinary approach which included:

(1) fecal transplant of two distinct microbial communities into Swiss-Webster mice (SWM) to characterize the host response (hepatic response-transcriptomics) and microbial activity (untargeted metabolomics of the stool samples) to different oxalate concentrations;

(2) longitudinal analysis of the N. albigulia gut microbiome composition in response to varying concentrations of oxalate by shotgun metagenomics, with deep bioinformatic analyses of the genomes assembled; and

(3) development of synthetic microbial communities around oxalate metabolisms and evaluation of these communities' activity in oxalate degradation in vivo.

Weaknesses:

However, I have concerns about the frame the authors tried to provide for a 'complex system theoretical approach' and how the data are interpreted within this frame. Several of the conclusions the authors provide do not seem to have sufficient data to support them.