That's when a citation of your work suggests a way to close a "blind spot" — a problem in the data that you couldn't solve yourself.

The working group of ESCORIAL study, a Spanish study of HIV-infected patients with HCV-related cirrhosis published a paper in Journal of Infection and Public Health [1] citing our paper on bacterial lipoxygenases from 2020 [2]. Earlier, this group successfully published other articles on the same project [3, 4]. 

The context of the citation is interesting primarily because lipoxygenases are not the focus of the paper at all. The authors studied differences in the blood microbiome in hepatitis C patients having compensated and decompensated cirrhosis. In addition to a depleted microbiome composition and a predominance of Proteobacteria, patients with cirrhosis showed an increased DNA content of bacteria of the order Sphingomonadales in the blood [1].

The catch is that there is not much “compromising material” on sphingomonads from a medical point of view. They have been believed to be just hanging around, not bothering anyone and decomposing oil. Their role in pathogenesis and symbiosis is still poorly elucidated with the exception of one species, Sphingomonas paucimobilis [5]. In search of the explanation of the higher abundance of Sphingomonadales, the authors of the new paper found our article, where we had written about the role of lipoxygenases in the ‘’host-microbe‘’ relationship and drew attention to a whole bunch of lipoxygenases of sphingomonads with unclear functional attribution [2]. The authors have referred to these considerations of ours.

It should be noted that there is no assurance that our sample and that of our colleagues included the same sphingomonads. According to our in-house “lipoxygenase occurrence index” we have implemented in the cited work, sphingomonadales were not among the leaders. This fact  keeps the matter open: a lot of sphingomonads could stay lipoxygenase-negative in our analysis. On the other hand, metagenomic studies usually allow us to explore the microbial composition down to the order or a family level, and the exact listing of species might be impossible. Thus, we cannot be sure that the lipoxygenase-positive set of sphingomonads in our research and the blood-recovered set in the new ESCORIAL paper are the same or even intersect. This suspected link needs careful verification. 

However, in our trees and networks, sphingomonads’ lipoxygenases form a suspiciously large cluster which is located close to the clusters pathogen-related and symbiont-related lipoxygenases. I have elaborated the symbiont-related and pathogen-related clusters in my recent bioRxiv preprint [6] and found additional evidence that these bacteria lipoxygenases could play a role in multiple medical conditions, but we still could not find any explanation of presence of lipoxygenases in sphingomonads.    

With the new paper of the ESCORIAL study group, the puzzle seems to start fitting together. It shows the possible explanation and the direction of further scientific search in the field of sphingomonadal lipoxygenases. Moreover, this discussion of our findings in a medicine-related paper stresses the importance of my recent preprint [6] where our conclusions regarding lipoxygenases in pathogenic bacteria are corrected and refined. Soon, I will post an additional explainer regarding this research.

Stay tuned! 

UPD on 22.09.2024: The discussed paper [1] has been formally published in Journal of Infection and Public Health. I have updated all references to it accordingly.

References

1. Brochado-Kith, O., Marta, R. A. V. A., Berenguer, J., González-García, J., David, R. O. J. O., Cristina, D. Í. E. Z., ... & ESCORIAL Study Group. (2024). Altered blood microbiome in patients with HCV-related Child-Pugh Class B cirrhosis. Journal of Infection and Public Health, 102524. https://doi.org/10.1016/j.jiph.2024.102524
2. Kurakin, G. F., Samoukina, A. M., & Potapova, N. A. (2020). Bacterial and protozoan lipoxygenases could be involved in cell-to-cell signaling and immune response suppression. Biochemistry (Moscow), 85, 1048-1063. https://doi.org/10.1134/S0006297920090059
3. Salgüero, S., Brochado-Kith, Ó., Verdices, A. V., Berenguer, J., González-García, J., Martínez, I., ... & Resino, S. (2023). PBMCs gene expression signature of advanced cirrhosis with high risk for clinically significant portal hypertension in HIV/HCV coinfected patients: A cross-control study. Biomedicine & Pharmacotherapy, 159, 114220. https://doi.org/10.1016/j.biopha.2023.114220
4. Medrano, L. M., Berenguer, J., Salgüero, S., González-García, J., Díez, C., Hontañón, V., ... & Resino, S. (2021). Successful HCV therapy reduces liver disease severity and inflammation biomarkers in HIV/HCV-coinfected patients with advanced cirrhosis: a cohort study. Frontiers in Medicine, 8, 615342. https://doi.org/10.3389/fmed.2021.615342
5. Rohilla, R., Raina, D., Singh, M., Pandita, A. K., & Patwal, S. (2021). Evaluation of Sphingomonas paucimobilis as an emerging nosocomial pathogen in a teaching hospital in Uttarakhand. Iranian Journal of Microbiology, 13(5), 617. https://doi.org/10.18502/ijm.v13i5.7425
6. Kurakin, G. (2022). Bacterial lipoxygenases are associated with host-microbe interactions and may provide cross-kingdom host jumps. bioRxiv, 2022-06. https://doi.org/10.1101/2022.06.21.497025