Biology subjects

Cho, J.-C.

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

5 recordsLinked to original sources

bioRxiv2026

Cultivation and genomic characterization of the first representative of the globally distributed marine UBA868 group

Members of the UBA868 group within the order Arenicellales are globally distributed marine Gammaproteobacteria predicted to participate in sulfur and carbon cycling, yet their physiology and ecological roles remain unknown due to the absence of cultured representatives. Here, we report the isolation and characterization of the first heterotrophic representative of the previously uncultured UBA868 group. Using dilution-to-extinction cultivation, we obtained four isolates from the Yellow Sea whose high-quality genomes represent a single UBA868 species. One strain, IMCC57338, maintained in axenic culture, exhibited small coccoid morphology and slow growth (doubling time [~]2.9 days), consistent with an oligotrophic lifestyle. Genome analysis revealed a predominantly aerobic chemoorganoheterotrophic lifestyle with a streamlined central carbon metabolism, including a complete glyoxylate shunt and limited carbohydrate utilization capacity, suggesting adaptation to low-nutrient conditions. The genome also encodes pathways for methylated amine oxidation coupled to formaldehyde assimilation via the serine cycle, indicating a capacity for methylotrophy. Genes encoding sulfur oxidation (Sox) and reverse dissimilatory sulfite reductase (rDsr) pathways further suggest a capacity for sulfur-based chemolithoheterotrophy. Global metagenomic and metatranscriptomic read recruitment showed that the species represented by IMCC57338 is widely distributed across ocean basins and pelagic depth layers, with higher abundance and transcriptional activity in mesopelagic waters. Our findings provide the first physiological and genomic insights into the UBA868 group and suggest that members of this lineage contribute to the cycling of organic carbon, C1 compounds, and sulfur in marine ecosystems.

microbiology↗

bioRxiv2026

Cross-cohort analysis reveals conserved gut virome signatures and phage-encoded auxiliary functions in ulcerative colitis

While gut bacteriome dysbiosis is a well-established hallmark of ulcerative colitis (UC), the ecological and functional remodeling of the gut virome conserved across diverse populations remains unclear. Here, by constructing a cross-cohort atlas of the UC-associated fecal virome, we show that viral reorganization closely parallels bacterial dysbiosis, with enrichment of phages targeting disease-associated bacterial taxa. We identified a conserved set of UC-associated viral signatures that robustly distinguished UC from healthy controls using machine-learning-based classification across independent cohorts. Functional profiling further revealed that phages enriched in UC carried higher densities of auxiliary metabolic genes (AMGs) related to virulence and antibiotic resistance than phages depleted in UC, with immune evasion and glycopeptide resistance genes particularly overrepresented. Together, our cross-cohort approach highlights the value of the gut virome-based diagnostic framework for UC and suggests that phage-encoded AMGs may contribute to shaping the gut ecosystem under inflammatory conditions.

microbiology↗

bioRxiv2023

Cultivation of SAR202 Bacteria from the Ocean

Here we report the first successful cultivation of SAR202 bacteria, a superorder in the phylum Chloroflexota, which have long been at the top of "most wanted" lists of uncultivated microbial life. It has been proposed that ancient expansions of catabolic enzyme paralogs in SAR202 broadened the spectrum of organic compounds they could oxidize, leading to transformations of the Earths carbon cycle. We cultured the cells from surface seawater using dilution-to-extinction culturing. Their growth was very slow (0.18-0.24 day-1) and was inhibited by exposure to light. The genomes, of ca. 3.08 Mbp, encoded archaella, archaeal motility structures, and multiple sets of paralogs, including 80 genes in enolase superfamily and 44 genes in NAD(P)-dependent dehydrogenase family. We propose that these paralogs participate in multiple parallel pathways of non-phosphorylative sugar and sugar acid catabolism, and demonstrate that, as predicted by this scheme, the sugars -fucose and -rhamnose and their lactone and acid forms are utilized by these cells.

microbiology↗

bioRxiv2021

Heme auxotrophy in abundant aquatic microbial lineages

Heme, a porphyrin ring complexed with iron, is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms1,2. Several microbial groups are known to lack the de novo heme biosynthetic pathway and therefore require exogenous heme from the environment3. These heme auxotroph groups are largely limited to pathogens4,5, symbionts6,7, or microorganisms living in nutrient-replete conditions8, whereas the complete absence of heme biosynthesis is extremely rare in free-living organisms9. Here, we show that the acI lineage, a predominant and ubiquitous free-living bacterial group in freshwater habitats, is auxotrophic for heme. We found that two recently cultivated acI isolates10 require exogenous heme for their growth. According to whole-genome analyses, all (n=20) isolated acI strains lacked essential enzymes necessary for heme biosynthesis, indicating that heme auxotrophy is a conserved trait in this lineage. Analyses of >24,000 representative genomes for species clusters of the Genome Taxonomy Database (GTDB) revealed that heme auxotrophy is widespread across abundant but not-yet-cultivated microbial groups, including Patescibacteria, Marinisomatota (SAR406), Actinomarinales (OM1), and marine group III Euryarchaeota. Our findings indicate that heme auxotrophy is a more common phenomenon than previously thought, and may lead to use of heme as a growth factor to increase the cultured microbial diversity.

microbiology↗

bioRxiv2018

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase

Unlike the ocean from which abundant microorganisms with streamlined genomes such as Prochlorococcus, Pelagibacter, and Nitrosopumilus have been isolated, no stable axenic bacterial cultures are available for the ubiquitous freshwater actinobacterial acI lineage. The acI lineage is among the most successful limnic bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. Dilution-to-extinction culturing followed by whole-genome amplification recently yielded 20 complete acI genomes from lakes in Asia and Europe. However, stably growing pure cultures have not been established despite various efforts at cultivation using growth factors predicted from genome information. Here, we report two pure cultures of the acI lineage successfully maintained by supplementing the growth media with catalase. Catalase was critical for stabilizing growth by degrading hydrogen peroxide, irrespective of the genomic presence of the catalase-peroxidase (katG) gene, making the acI strains the first example of the Black Queen hypothesis reported for freshwater bacteria. The two strains, representing two novel species, displayed differential phenotypes and distinct preferences for reduced sulfurs and carbohydrates, some of which were difficult to predict based on genomic information. Our results suggest that culture of previously uncultured freshwater bacteria can be facilitated by a simple catalase-supplement method and indicate that genome-based metabolic prediction can be complemented by physiological analyses.

microbiology↗