Biology subjects

Domman, D.

Publications and source records attributed to Domman, D..

3 recordsLinked to original sources

bioRxiv2026

Global untreated wastewater hosts a vast reservoir of previously uncharacterized microbial lineages

Untreated wastewater are reservoirs of microbial communities originating from different sources within an urbanized human-populated area and is now regularly used for tracking and assessing levels of certain human pathogens like SARS-CoV-2, Salmonella, and Poliomyelitis. Wastewater microbial communities can exhibit high diversity, comprised of mostly non-pathogens alongside a smaller population of pathogens. Much of the research on wastewater has focused on either pathogens or microbiomes in the treatment plants, but not on the microbiome of untreated wastewater, which is perhaps more reflective of community health. Moreover, as wastewater usage expands to more known and unknown pathogen detection, a deeper understanding of both wastewaters overall genetic diversity and diversity over time is pivotal. Towards that goal, we characterized the observed microbial diversity of global untreated wastewater by analyzing 1,344 publicly available metagenomes, representing 6 continents, and created a global wastewater database hosted at https://doi.org/10.5281/zenodo.17794790. We elucidated the full spectrum of prokaryotic diversity by recovering and characterizing high quality bins, contigs, and reads from all the data. We provide the first comprehensive, publicly available database describing global wastewater by uncovering previously uncharacterized microbes, identifying geographically specific microbial populations, and creating a high-quality dataset to advance future microbiome, epidemiological, and biosurveillance research.

genomics↗

bioRxiv2025

Aeromonas: Genomic Insights into an Environmental Pathogen and Reservoir of Antimicrobial Resistance

Aeromonads are an ecologically versatile group of bacteria that cause infection in aquatic animals and are recognised as an emerging human pathogen. Despite this, our understanding of Aeromonas diversity, especially the relationship between clinical and environmental strains, remains limited. Here, we present a complete view of the Aeromonas genus, comprising 1,853 genomes, and a detailed comparison of clinical and environmental strains from South Asia, including 996 newly sequenced genomes from Bangladesh and India. Phylogenetic analyses revealed that Aeromonas is a highly diverse genus, with no distinct clade separating clinical and environmental isolates. We identified 28 Aeromonas species and 905 novel sequence types, comprising 72.5% of the genomes. Notably, we show a high incidence of AMR genes across all isolates, including against front and last-line antibiotics. Finally, we highlight frequent misidentification of Aeromonas as Vibrio cholerae, key to cholera-endemic regions where both genera co-exist and are associated with diarrhoeal disease. Our study underscores Aeromonas as an important environmental AMR reservoir and emerging multi-species pathogen capable of spilling over into human populations.

genomics↗

bioRxiv2019

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

Marine sponges represent one of the few eukaryotic groups that frequently harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. "Candidatus Nitrosospongia bastadiensis" is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbor nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals. Originality-Significance StatementMany marine sponges harbor symbiotic members of the Thaumarchaeota, but there is generally only indirect evidence available about their functional role within these filter-feeding animals. Furthermore, the specific adaptations of thaumarchaeal symbionts to their sponge hosts are incompletely understood. In this study, we thoroughly characterized a thaumarchaeal symbiont residing in the reef sponge Ianthella basta and demonstrate by using a combination of molecular tools and isotope techniques, that it is the only ammonia-oxidizer in its host. In contrast to other sponges, I. basta does not contain nitrite-oxidizing microbes and thus excretes considerable amounts of nitrite. Furthermore, using metagenomics and metaproteomics we reveal important adaptations of this symbiont, that represents a new genus within the Thaumarchaeota, and conclude that it most likely lives as a mixotroph in its sponge host.

microbiology↗