Biology subjects

Kalinski, J.-C. J.

Publications and source records attributed to Kalinski, J.-C. J..

3 recordsLinked to original sources

bioRxiv2026

A Functional Metabolomics Framework to Track Microbiome Drug Metabolism

Understanding how gut microbes transform drugs, and how this influences microbiome composition and function, remains a key question to better understand the efficacy and side effects of pharmaceuticals. To accelerate the discovery of microbiome-derived drug metabolites, we developed a functional metabolomics workflow that combines the use of synthetic microbial communities (SynComs) with a time-series resolved molecular networking approach and advanced computational metabolite annotation. We demonstrate how this framework can be used to illuminate chemical transformation dynamics in a gut SynCom (Com20) with 50 clinical drugs. Our results highlight a multitude of drug metabolites, including multi-step metabolic cascades, some of which correlated to shifts in microbial taxa, suggesting functional links between microbiome composition and biochemical transformations. Our computational data analysis workflow is publicly available through the GNPS2 ecosystem at chemprop.gnps2.org, which can be used to prioritize biotransformations and other (bio)chemical reactions in various biological and abiotic systems.

systems biology↗

bioRxiv2024

Shaping chemodiversity: A unique spirochete symbiont of pyrroloiminoquinone-producing marine sponges

Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions. IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.

microbiology↗

bioRxiv2020

Family matters: The genomes of conserved bacterial symbionts provide insight into specialized metabolic relationships with their sponge host

As the oldest extant metazoans, sponges (Phylum Porifera) have been forming symbiotic relationships with microbes that may date back as far as 700 million years. Most symbionts are conserved within a narrow host range and perform specialized functions. However, there are widely distributed bacterial taxa such as Poribacteria, SAUL and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added eleven new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these broad-host range, sponge-associated bacteria likely perform distinct functions within their hosts and that their respective phylogenies are incongruent with their host phylogenies. These results suggests that ancestors of these bacteria may have undergone multiple association events, rather than a single association event followed by co-evolution. IMPORTANCEMarine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three know bacterial taxa (Entoporibacteria, SAUL and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. Understanding what distinguishes these broad-host range symbionts from specialized symbionts will provide insight into the mechanisms by which sponges form these symbioses. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. This contrasts with specialized symbionts, where function is often a strain-specific trait and have co-evolved with their host following a single association event.

microbiology↗