Researchers from Bishop Barham University College in Uganda and Aix Marseille University in France set out to map the fungal communities living in the topsoil of fifteen different dumpsites in Kabale. Their findings, published in Frontiers in Fungal Biology, reveal a surprisingly rich and medically relevant fungal world, including opportunistic pathogens and species with worrying antifungal profiles. The work is among the first detailed investigations of dumpsite fungi in Uganda, where waste management remains a perennial challenge with no clearly safe solution in sight.

The team chose a technique called culturomics, a high-throughput culturing method designed to capture as many viable microorganisms as possible. It is a deliberate alternative to metagenomics, the current darling of environmental microbiology. Metagenomics reads genetic material directly from soil, but it struggles with fungi: fungal species are genetically heterogeneous, many fungal sequences are absent from reference databases, and the method detects DNA from dead organisms that may never have been alive in that soil at all. Culturomics, by contrast, grows the living fungi, allowing researchers to isolate, purify, and identify them one by one.

The technical execution was meticulous. Soil was collected with a soil auger from the top ten centimeters, the biologically active zone, at each of the fifteen dumpsites, using a composite sampling approach. Back in the lab, five grams of soil from each duplicate were suspended in phosphate-buffered saline, serially diluted, and plated onto five different culture media: Sabouraud Dextrose Agar, Potato Dextrose Agar, Malt Extract Agar, ChromAgar, and a relatively new medium called FastFung. Chloramphenicol was added to suppress bacterial growth, and plates were incubated at thirty degrees Celsius. Purified fungal colonies were then identified by sequencing the ITS region of the ribosomal RNA gene, the standard barcode for fungi, with additional beta-tubulin and Tef gene amplification used to confirm Penicillium and Fusarium isolates.

The results were striking. Fifty-four different fungal species were recovered, and FastFung emerged as the clear champion, yielding the highest number of isolates and supporting growth in almost all species. It outperformed the conventional workhorses Sabouraud and Potato Dextrose Agar, followed by Malt Extract Agar and ChromAgar. FastFung is based on Schaedler agar, enriched with essential elements for fastidious fungi and containing specific antibacterial ingredients to inhibit contaminant bacteria. Its superior performance here supports emerging evidence that media composition significantly influences fungal recovery, and that enriched media can coax out slow-growing or fastidious taxa that conventional media miss entirely.

Who lives in these dumpsite soils? The most prevalent genera were Trichoderma, Fusarium, and Aspergillus, three names that carry serious weight in both ecology and medicine. Phylogenetic analysis showed that the families Aspergillaceae, Hypocreaceae, and Nectriaceae were the most represented across all media types. Network analysis revealed that some Aspergillus species, including A. clavatus, A. flavipes, A. flavus, and A. niger, were generalists capable of growing on every medium tested, while others like A. parasiticus showed far more specialized growth requirements. The minimal overlap among media in the Venn analysis demonstrated strong selectivity, underscoring the importance of using multiple media to capture the full diversity of fungi in any environment.

The medical relevance of the findings is hard to ignore. Alongside the dominant genera, the researchers isolated pathogenic and opportunistic fungi such as Simplicillium lamellicola, Mortierella multispora, and Torulaspora delbrueckii. Aspergillus species are well-recognized opportunistic pathogens associated with respiratory infections and allergic responses, particularly in immunocompromised individuals. Fusarium species are known producers of mycotoxins, including trichothecenes, fumonisins, and zearalenones, which are toxic and carcinogenic to animals and have been associated with human esophageal cancer and birth defects. Even Trichoderma, often celebrated as a beneficial biocontrol agent, contains species that can cause lethal infections in patients with leukemia, HIV, or transplants, and infections caused by these fungi are typically diagnosed late and exhibit low sensitivity to commonly applied antifungal drugs.

To probe the clinical dimension further, the team screened all Aspergillus isolates for susceptibility to common antifungal agents using E-test strips, following Clinical and Laboratory Standards Institute guidelines. The good news: no resistance was detected, with all minimum inhibitory concentration values below established resistance thresholds. The more nuanced news: A. clavatus stood out as the least susceptible isolate, showing the highest MICs for several drugs, including caspofungin at 1.5 micrograms per milliliter and voriconazole at 0.75 micrograms per milliliter. By contrast, A. flavus and A. niger appeared highly susceptible to caspofungin, with extraordinarily low MICs of 0.0094 and 0.016 micrograms per milliliter respectively. The authors note that the broader problem of environmental antifungal resistance is growing, with widespread agricultural azole fungicides increasingly implicated in cross-resistance in clinically relevant fungi such as Aspergillus fumigatus.

Beyond the pathogens, the dumpsites also harbor fungi with genuine promise. Trichoderma species can detoxify toxic compounds and accelerate the degradation of organic material, making them candidates for bioremediation, a far better alternative than burning refuse and polluting the air. Ascomycota, the dominant phylum in these soils, are essential for cycling soil nutrients and breaking down organic materials. The isolation of Uromyces vignae, a rust fungus that infects beans, quietly reflects the centrality of beans as a staple food in Uganda. The dumpsites, in other words, are not just hazards; they are complex fungal communities with both ecological and biotechnological value waiting to be understood.

The researchers emphasize that dumpsites can serve as reservoirs of medically important fungi, and that leachate from waste sites can transport microbial contaminants into surrounding water bodies, potentially causing health hazards to local populations. When contaminated water is used for drinking, cooking, and washing, it becomes an exposure pathway for at-risk infections, especially among vulnerable groups. The study provides baseline data on the diversity, distribution, and potential functional roles of culturable fungal communities in Kabale’s dumpsite soils, and the authors call for regular mycological monitoring of dumpsites, better waste management strategies, and frequent water quality testing in surrounding areas. Future studies integrating culture-independent methods will be essential to fully characterize these communities, but the message is already clear: the fungi beneath our feet in the world’s dumpsites deserve far more attention than they have ever received.

Subject of Research: Unravelling soil fungal communities in dumpsites in Kabale, Western Uganda using culturomics

Article Title: Unravelling soil fungal communities in dumpsites in Kabale, Western Uganda using culturomics

Article References: Odebode, A., & Ranque, S. (2026). Unravelling soil fungal communities in dumpsites in Kabale, Western Uganda using culturomics. Frontiers in Fungal Biology, 7, Article 1823753. https://doi.org/10.3389/ffunb.2026.1823753

Image Credits: AI Generated

DOI: 10.3389/ffunb.2026.1823753

Keywords: Unravelling, soil, fungal, communities, dumpsites, Kabale, Western, Uganda, culturomics, scientific research

Endophytic bacteria are microorganisms that colonize the interior tissues of plants without causing disease. Far from being passive squatters, these bacteria often engage in intimate metabolic exchanges with their hosts, supplying nutrients, modulating hormone signaling, priming immune responses and helping the plant withstand environmental stress. In medicinal plants, endophytes have attracted particular interest because some strains can influence the production of secondary metabolites, the very compounds that give medicinal plants their pharmacological value. For A. lappa, which thrives at high elevations where cold temperatures and intense ultraviolet radiation impose constant physiological challenges, the endophytic community could be especially important in underpinning the plant’s resilience. Until this study, however, no one had characterized the diversity or the functional potential of the bacteria living within its roots.

The research team took a dual approach that combined culturomics, the systematic isolation and identification of living microorganisms, with high-throughput microbiomic sequencing of the total root-associated bacterial DNA. This two-pronged strategy matters because each method captures a different slice of microbial reality. Cultivation recovers living strains that can be stored, tested and deployed, but many environmental bacteria resist growth on artificial media. Sequencing, by contrast, surveys the genetic signatures of the entire community, including species that have never been cultured in a laboratory, but it yields no living isolates. By running both approaches in parallel, the researchers could cross-validate their results and build a far more complete picture of who lives inside the roots of A. lappa and what those residents might be doing.

The culturing effort was remarkably productive. From the roots of A. lappa plants, the team isolated a total of 473 endophytic bacterial strains. To make this collection manageable for identification, they selected 157 representative strains and characterized them taxonomically. These representatives turned out to span three bacterial phyla, eighteen genera and fifty-five distinct species, a striking level of diversity for a single plant organ. Among the cultured representatives, certain taxa stood out as dominant, and notably the genera Serratia and Pseudomonas emerged as prominent members of the culturable community. The collection of 473 living strains now constitutes a preserved microbial resource bank that can be drawn upon for future experiments, breeding programs and product development aimed at this medicinal crop.

High-throughput sequencing of the root samples revealed an even broader hidden diversity. The sequencing data identified 35 bacterial phyla, 825 genera and 4,755 amplicon sequence variants, or ASVs, which are precise genetic operational units used to distinguish closely related bacterial populations. The dominant phyla detected were Pseudomonadota, Actinobacteriota and Bacillota, three of the most widespread and ecologically versatile bacterial lineages in plant-associated environments. At the genus level, Serratia and Pseudomonas again topped the abundance rankings, an important point of agreement with the culture-based results. When two independent methods converge on the same dominant taxa, confidence in the biological signal rises substantially, because the biases inherent in each technique are unlikely to produce identical artifacts. The convergence suggests that these genera are genuinely central players in the root endophytic community of A. lappa.

Identifying the residents of a microbial community is only the first step; understanding what they can do is the deeper question. To probe functional potential, the researchers applied three complementary computational prediction frameworks: PICRUSt2, FAPROTAX and BugBase. Each tool infers community functions from taxonomic composition by drawing on reference genomes and curated functional databases. PICRUSt2 predicts the metabolic pathways encoded by the community’s genes, FAPROTAX maps taxa onto known ecological functions such as degradation of specific compound classes, and BugBase assesses phenotype-level traits such as stress tolerance. The three methods together painted a coherent picture of a community equipped for plant growth promotion, the degradation of aromatic compounds and hydrocarbons, and adaptation to low temperatures.

Each of these predicted functions carries practical significance. Plant growth promotion by endophytes typically involves mechanisms such as nitrogen fixation, phosphate solubilization, siderophore production and synthesis of plant hormones, capabilities that can reduce the need for chemical fertilizers. The predicted capacity to degrade aromatic compounds and hydrocarbons points toward bioremediation potential, meaning the bacteria might help break down organic pollutants in soils where the medicinal plant is grown, a valuable trait for maintaining the purity of herbal medicine raw materials. The low-temperature adaptation signal is particularly intriguing given that A. lappa is a high-altitude species whose cultivation zones experience cold stress. Endophytes that help their host tolerate chilling could directly improve yields and quality in mountain agriculture, and the authors suggest the community may contribute to the plant’s resistance to low temperatures.

The authors are careful to note an important caveat: the functional predictions are based on in silico analyses, meaning they are computational inferences rather than experimentally demonstrated activities. Prediction tools extrapolate from what is known about related bacteria, and actual functions in the specific context of the A. lappa root environment must be confirmed through laboratory and greenhouse testing. This is a standard and appropriate limitation for a first survey of an unstudied microbiome. Nevertheless, the predicted functional landscape provides a concrete roadmap for follow-up work. Researchers can now prioritize specific strains, for example dominant Pseudomonas and Serratia isolates, for assays of growth promotion, pollutant degradation and cold tolerance, rather than screening blindly through hundreds of candidates.

The broader implications extend beyond a single medicinal species. Microbial fertilizers, biopesticides and bioremediation agents are all growth areas in sustainable agriculture, and native endophytes isolated from the crop they are meant to support are often ideal candidates for such products because they are already adapted to the host and its environment. The strain collection assembled in this study, with its 473 isolates representing 55 species across three phyla, constitutes exactly the kind of raw material from which such applications can be developed. For A. lappa specifically, whose status as a major Yunnan medicine makes it economically significant to regional agriculture, the prospect of microbiome-informed cultivation practices could improve both the sustainability and the quality of production in high-altitude farming systems.

This study also demonstrates the value of pairing culturomics with sequencing as a template for exploring the microbiomes of other understudied medicinal plants. Many traditional medicinal species grow in extreme environments, and their endophytic communities remain largely unmapped despite their potential to influence both plant health and metabolite profiles. By documenting 35 phyla, 825 genera and 4,755 ASVs in the roots of A. lappa, and by showing that culture-dependent and culture-independent methods agree on the dominant taxa, the researchers have established a baseline against which future studies can measure seasonal change, geographic variation and the effects of cultivation practices. The work, funded by the National Natural Science Foundation of China and the National Key R&D Program of China, marks the beginning rather than the end of the story, as the predicted functions await experimental validation and the isolated strains await deployment. What is already clear, however, is that inside the roots of this ancient medicinal plant lives a rich bacterial world whose secrets are only now coming to light.

Subject of Research: Diversity and functional potential of root endophytic bacterial communities in the high-altitude medicinal plant Aucklandia lappa Decne.

Article Title: Diversity and functional prediction of endophytic bacterial communities in Aucklandia lappa Decne.

Article References: Li, Y., Yang, Y., Wang, M., Wang, P., Xu, W., Liu, F., Li, Q., & Hu, X. (2026). Diversity and functional prediction of endophytic bacterial communities in Aucklandia lappa Decne.. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09915-7

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09915-7

Keywords: Aucklandia lappa, endophytic bacteria, microbiome, culturomics, high-throughput sequencing, Pseudomonas, Serratia, plant growth promotion, bioremediation, cold tolerance, medicinal plants, Yunnan

The genus Pseudomonas is one of the most versatile groups of bacteria known to science. First defined in 1894 by the German mycologist Walter Migula, it comprises Gram-negative, aerobic, rod-shaped bacteria equipped with flagella. Over more than a century of microbiological discovery, the genus has grown to encompass 381 validly published species, according to the List of Prokaryotic names with Standing in Nomenclature, with Pseudomonas aeruginosa serving as the type species. Members of the genus colonize soil, rivers, plants and animal hosts, and their roles range from promoting plant growth and cleaning contaminated environments to causing serious opportunistic infections in vulnerable patients. Among the many niches these bacteria occupy is human milk, a biological fluid whose microbial community helps seed the newborn gut and shapes early immune and metabolic development.

Despite the growing interest in the milk microbiome, African populations remain markedly under-studied, and most surveys of milk bacteria rely on culture-independent methods that detect genetic signatures without ever yielding a living isolate. Motivated by this gap, the research team turned to a culture-based, genome-resolved strategy. Breast milk samples were collected from mothers of both malnourished and healthy children in Niakhar, Senegal, with informed consent and approval from the Ethical and Scientific Committee of the Senegalese Ministry of Health and Public Hygiene. Ten to fifteen milliliters of milk from each participant were transported at four degrees Celsius to a laboratory in Dakar, aliquoted, frozen at minus eighty degrees Celsius, and later shipped on dry ice to Marseille for culturing, sequencing and analysis.

Two strains, designated Marseille-QA0332 and Marseille-QA0892, emerged from this effort. The first was obtained by direct plating of milk onto Columbia blood agar during routine colony counting, before any enrichment step. The second was recovered through a culturomics protocol, in which milk was inoculated into a series of liquid enrichment media and subcultured at scheduled intervals over thirty days; strain QA0892 appeared at the day-fifteen subculture from an aerobic blood-culture bottle containing MacConkey broth. Rigorous sterility controls, in which every batch of medium was tested for contamination before use, ensured that any bacterial growth traced back to the milk samples themselves rather than to laboratory reagents.

Initial identification attempts using MALDI-TOF mass spectrometry failed to match either isolate to a known species, prompting whole-genome sequencing. Comparison of 16S ribosomal RNA gene sequences showed that strain QA0332 shared its highest similarity, 97.98 percent, with Pseudomonas ceruminis, while strain QA0892 was 99 percent similar to Pseudomonas matsuisoli. Those figures alone might have suggested close relatives, but whole-genome comparisons told a different story. Average nucleotide identity values, which should exceed roughly 95 to 96 percent between strains of the same species, came in at just 81.1 to 81.4 percent for QA0332 against its nearest neighbors and 75.0 percent for QA0892 against P. matsuisoli. Digital DNA-DNA hybridization values, with a species threshold of 70 percent, were even lower, at 26.7 percent and 21.1 percent respectively. By every genomic yardstick, the two isolates represented lineages distinct from any previously described species.

The phenotypic portraits of the two bacteria are strikingly different. Pseudomonas senegalensis grows optimally at 37 degrees Celsius under aerobic conditions and forms circular, convex, yellowish, mucoid colonies. It is motile, non-spore-forming, oxidase- and catalase-positive, and capable of fermenting a broad range of sugars including glucose, xylose, arabinose and trehalose. It also produces urease and arginine dihydrolase, traits that help distinguish it from close relatives. Pseudomonas millioni, by contrast, prefers cooler temperatures, growing best at room temperature and 28 degrees Celsius in alkaline media, and its colonies mature from translucent punctiform dots into dry, filamentous, opaque mats. Uniquely among its comparisons, it reduces nitrate to nitrite and hydrolyzes esculin. Fatty acid profiling by gas chromatography further separated the two: the cell membranes of P. senegalensis are dominated by hexadecanoic acid and cis-9,10-methylene-hexadecanoic acid, while those of P. millioni feature a more balanced mixture of unsaturated and saturated fatty acids.

Genome architecture reinforced the case for two new species. Pseudomonas senegalensis carries a single circular chromosome of 4,577,173 base pairs with a GC content of 63.65 percent, encoding 4,173 genes, of which 4,079 are protein-coding. Pseudomonas millioni has a slightly larger chromosome of 4,658,126 base pairs, a GC content of 60.22 percent, and 4,327 genes. Neither genome contains plasmids, and functional annotation revealed repertoires dominated by amino acid transport, transcription, energy production and inorganic ion metabolism, consistent with metabolically versatile, free-living organisms. Mining of secondary metabolite biosynthetic gene clusters uncovered eleven candidate regions in P. senegalensis and eight in P. millioni, including a pseudomonine-like metallophore cluster in the former, suggesting a siderophore-based iron-scavenging system well suited to the iron-limited environment of milk. Both genomes also harbor carotenoid, hydrogen cyanide and N-acetylglutaminylglutamine amide clusters, although the researchers caution that these remain computational predictions rather than chemically validated products.

From a clinical standpoint, the news is reassuring. Screening against virulence factor databases found none of the hallmark weapons of Pseudomonas aeruginosa: no type III secretion system, no exotoxin A, no elastase or phospholipases, and no high-risk pathogenicity islands. No acquired resistance genes, such as extended-spectrum beta-lactamases or carbapenemases, were detected in either genome. The only resistance determinants identified were intrinsic chromosomal efflux pumps and regulators typical of the genus. One notable exception emerged in Pseudomonas millioni, which proved resistant to the antibiotic ceftazidime. A targeted search revealed a chromosomal class C beta-lactamase, bearing the three canonical catalytic motifs of Ambler class C enzymes, that accounts for this phenotype. Because the enzyme is intrinsic and not transmissible, the researchers conclude that both species pose a low biosafety risk, though they note that pathogenic potential cannot be formally excluded without infection models.

Perhaps the most intriguing evidence for the ecological identity of these bacteria comes from mining public metagenomic archives through the IMNGS platform. Both species were detected predominantly in human-associated ecosystems rather than environmental ones. Pseudomonas senegalensis appeared in 0.95 percent of human gut metagenomes and 0.69 percent of skin metagenomes, while Pseudomonas millioni was found in 1.53 percent of gut metagenomes and 0.50 percent of blood metagenomes. This pattern of low prevalence but consistent human association supports the idea that the two organisms are genuine members of the human microbiome rather than transient contaminants. The researchers argue that the combination of viable cultured isolates, verified sterile media and expected recovery of Pseudomonas from milk makes a laboratory origin for the strains implausible.

The discovery also carries a cautionary lesson about genome-based inference. Both genomes encode a carotenoid biosynthetic cluster, yet only Pseudomonas senegalensis forms visibly yellow colonies. This dissociation between genotype and phenotype demonstrates that the mere presence of a biosynthetic gene cluster does not guarantee its expression, tempering the functional conclusions that can be drawn from genome mining alone. With type strains deposited in the Collection de Souches de l’Unité des Rickettsies in Marseille and the Colección Española de Cultivos Tipo in Spain, and genome sequences available in GenBank, Pseudomonas senegalensis and Pseudomonas millioni now stand as formally recognized members of the bacterial tree of life, and as reminders of how much microbial diversity still hides in ordinary human fluids waiting to be cultured.

Subject of Research: Discovery and taxonomic description of two novel Pseudomonas species isolated from human breast milk in Senegal

Article Title: Pseudomonas senegalensis sp. nov. and Pseudomonas millioni sp. nov., two novel species isolated from the breast milk of Senegalese women

Article References: Sarr, S., Ndour, O., Seck, E. H., Abdoulaye, A. I., Beye, M., Diatta, G., Bassene, H., Diop, M., Bellali, S., Semmar, R., Alibar, S., Boukili, M., Kacel, I., Armstrong, N., Couderc, C., Thiakane, C., Alou, M. T., Sokhna, C., & Camara, M. (2026). Pseudomonas senegalensis sp. nov. and Pseudomonas millioni sp. nov., two novel species isolated from the breast milk of Senegalese women. New Microbes and New Infections, 73, Article 101846. https://doi.org/10.1016/j.nmni.2026.101846

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101846

Keywords: Pseudomonas senegalensis, Pseudomonas millioni, breast milk microbiota, new bacterial species, taxonogenomics, Senegal, culturomics, whole-genome sequencing, antimicrobial resistance, human microbiome, MALDI-TOF, New Microbes and New Infections