Fermented foods represent complex microbial ecosystems that contribute to food quality, functionality, and potential health benefits, yet many traditional fermented foods remain poorly characterized. The aim of this study was to study microbial diversity, and functional potential of underexplored traditional Indonesian fermented food. The fermented products displayed substantial variation in bacterial richness, ranging from 65 to 614 bacterial amplicon sequence variants across samples. The microbial communities were dominated by bacterial taxa affiliated with the orders Bacillales and Lactobacillales, alongside fungal taxa from the order Mucorales. The plant-based products i.e. tape ketan and tape singkong had a higher bacterial abundance but lower diversity than animal-based terasi. We found significant correlations between bacterial and fungal communities dominated by positive cooccurrence patterns and highly complex networks especially in terasi. Each food product was characterized by a unique functional profile of genes linked to beneficial metabolic functions (biosynthesis of bacteriocins, short-chain fatty acids, and vitamins) but tape ketan samples demonstrated the highest diversity and abundance of them. Metagenome assembled genomes reflect a high diversity of health beneficial properties as well as substrate-specific degradation capabilities. Traditional Indonesian fermented foods harbour functionally redundant but phylogenetically diverse taxa offering a potential source for probiotic traits and functional food development.

Clostridioides difficile infection (CDI) is a toxin-mediated gastro-intestinal disease. Yet, C. difficile is a phylogenetically diverse species that includes many non-toxigenic strains. In general, these are understudied, despite having significant potential impact for our understanding of the colonization process and as therapeutic modalities. Here, we present an in-depth characterization-including the complete genome sequence-of the non-toxigenic C. difficile strain L-NTCD03. This strain belongs to PCR ribotype 416, clade 4 and multilocus sequence type 39. It is resistant to multiple antimicrobials, but not those used for treatment of CDI. We validated the relevance of the cfr(B) gene from this strain in antimicrobial resistance to clindamycin, linezolid, retapamulin, and streptogramin A. We found the L-NTCD03 strain to be non-toxic in various assays. Altogether, L-NTCD03 is a promising candidate for developing into a live biotherapeutic product.

Radiation resistance in Deinococcus requires an SOS-independent response mechanism, controlled by M78 family (COG2856) metallopeptidase IrrE and XRE family transcriptional repressor DdrO, to induce expression of DNA repair genes after exposure to radiation. DdrO must form dimers to bind target DNA sites. IrrE inactivates DdrO by cleaving the C-terminal dimerization domain of DdrO. However, the molecular basis of the interaction between IrrE and DdrO is still unknown. Here, we showed that IrrE is monomeric in solution and forms heterodimers with DdrO, with the N-terminal DNA-binding domain of DdrO contributing to the interaction. We further revealed that the initially isolated radiation-sensitive irrE mutant strain encodes an oxidation-sensitive IrrE protein affected in DdrO cleavage. Predicted COG2856/XRE regulatory protein pairs are present in many environmental, pathogenic, and industrial bacteria. Single-stranded DNA enhanced the cleavage activity of IrrE from Deinococcus as well as from closely related Marinithermus and Oceanithermus species, but not of the distant homologs ImmA from Bacillus subtilis and Rir from Streptococcus thermophilus. The formation of a heterotrimer containing IrrE, DdrO, and single-stranded DNA was also demonstrated. Together, these findings provide new insights into the molecular interplay between the key regulators IrrE and DdrO.

Escherichia coli TisB/IstR1 is a type I toxin-antitoxin system. The TisB toxin targets the inner membrane and disrupts the proton motive force (PMF). Under normal growth conditions, tisB transcription is repressed by the LexA SOS repressor, and IstR1 blocks its translation. DNA damage lifts LexA repression, allowing tisB mRNA to overcome IstR1 inhibition and produce TisB. Although spontaneous tisB expression has been reported, its physiological significance remains unclear. We show that tisB is spontaneously induced and TisB is synthesized during the transition to stationary phase, coinciding with decreased LexA repression and a transient decline in istR1 promoter activity. Deletion of tisB does not affect exponential growth but delays entry into and exit from stationary phase, reduces fitness under nutrient limitation and alkaline pH, and impairs stringent response induction, intracellular pH homeostasis, and glycogen accumulation-phenotypes consistent with metabolic dysregulation. These findings indicate that low-level spontaneous TisB production modulates metabolism during the transition to stationary phase. By collapsing the PMF, TisB attenuates nutrient uptake and promotes early stringent-response-driven dormancy before nutrient exhaustion. Our results reveal a physiological role for TisB, positioning it as a metabolic rheostat that fine-tunes adaptation to environmental fluctuations.

Candida glabrata is a clinically significant cause of candidemia, yet how it supplies uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) for cell-wall chitin synthesis remains unclear. Here, we identify an N-acetylglucosamine (GlcNAc) kinase encoded by CAGL0M00682g and designated CgNgk1. In vitro, purified CgNgk1 preferentially phosphorylated GlcNAc with markedly higher catalytic efficiency than other sugars and accepted multiple nucleoside triphosphates, including ATP, as phosphoryl donors. Site-directed mutagenesis indicated that Asp197 and Lys155 are required for catalysis and ATP binding, respectively. In vivo, CgNgk1 overexpression in C. glabrata increased intracellular UDP-GlcNAc in a GlcNAc dose-dependent manner, whereas the kinase-dead D197N variant had no effect. CgNgk1-mediated GlcNAc phosphorylation elevated cell-wall chitin and heightened sensitivity to sodium dodecyl sulfate, heat, and low pH, but did not affect β-1,3-glucan-related phenotypes such as zymolyase or caspofungin sensitivity. Under GlcNAc supplementation, CgNgk1-overexpression specifically decreased cellular susceptibility to flucytosine, while responses to voriconazole and amphotericin B were unchanged. Overexpression of the putative hexosamine-pathway regulator CgIsr1 lowered intracellular UDP-GlcNAc, consistent with an intact endogenous pathway. These findings demonstrate that imported GlcNAc is routed via CgNgk1 to UDP-GlcNAc to promote chitin biosynthesis, and that quantitative control of this route shapes cell-wall integrity and modulates responses to host-relevant stresses and antifungal agents.

In recent years, concerns over declining biodiversity in urban spaces have increased. Urban Bokashi composting (i.e. microaerobic or anaerobic fermentation of food waste indoors) has been suggested as a possibility to promote microbial diversity in the domestic environment. However, studies on microbial communities in household-scale Bokashi and their potential impacts on health and environment are lacking. Thus, the present pilot study investigated microbial communities in different stages of the Bokashi composting process in collaboration with six Bokashi practitioners by looking into physicochemical characteristics as well as microbial community composition (16S amplicon sequencing, 34 samples) and functional potential (shotgun metagenome sequencing, 11 samples). The collective results indicate that i) microbial communities in Bokashi compost differed between stages, but also between households, ii) microbial communities were dominated by lactic acid bacteria like Lentilactobacillus or Lacticaseibacillus, iii) metabolic pathways for the production of diverse organic acids were detected, iv) application of Bokashi ferment or leachate to soil can supply nutrients and organic acids to promote plant growth but does not substantially affect soil microbial community composition, and v) potentially pathogenic organisms were detected in extremely low abundances. Thus, urban Bokashi is likely not associated with increased health risks and positive impacts are feasible.

Toxoplasmosis is a parasitic infection with significant implications for human health, particularly in its ocular form, which can lead to severe visual impairment. While both basic and clinical research have made considerable strides in understanding the biology and treatment of this parasite, challenges remain. Recent advancements in diagnostics, mainly through multimodal imaging, have improved the identification of active disease and predicting outcomes. Experimental therapies are also emerging, offering new hope for more effective treatments. However, the most critical insight from recent research, particularly emphasized at the 17th International Congress on Toxoplasmosis, is the necessity of a collaborative approach. Integrating basic and clinical research is essential for translating molecular and pathophysiological findings into effective clinical practices. This synergy is crucial for advancing treatment strategies and improving patient outcomes in ocular toxoplasmosis.

The deep sea is a largely unexplored extreme environment supporting a diverse biological community adapted to low temperatures and high pressures. Such environments support microbial life that may be a source of novel antibiotics and other drugs. Whilst this is often the case, many species with bioactive capabilities may be missed with traditional culturing methods. In this study, a total of 16 different concentrations and types of media were employed, to culture 389 bacterial isolates using Dilution to Extinction methods and Actinobacteria Directed Cultivation techniques. This generated 72 (18.6%) isolates with narrow and broad-spectrum activity against ESKAPE pathogens including Escherichia coli (E. coli), methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococci. We also report that an early-stage ‘One Strain Many Compounds’ approach can reveal a greater number of bioactive isolates that otherwise would have been missed; 12 isolates initially deemed ‘inactive’ were seen to exhibit activity towards S. aureus and/or E. coli. We emphasize the importance of a thorough initial screening method to capture bioactive isolates and show how selecting only morphologically distinct isolates for screening may result in species with promising bioactivity being overlooked. Our findings justify on-going investigation of Pheronema sponges for bioactive microbiota.

Microorganisms released into the atmosphere by various disturbances can travel significant distances before depositing, yet their impact on community assembly remains unclear. To address this, we examined atmospheric and lithospheric bacterial communities in 179 samples collected at two distinct Icelandic volcanic sites: a small volcanic island Surtsey, and a volcanic highland Fimmvörðuháls using 16S rRNA amplicon sequencing. Airborne microbial communities were similar between sites while significant differences emerged in the communities on lava rocks after 1-year exposure. SourceTracker analysis revealed distinct bacterial populations in the atmosphere and the lava rocks with surrounding soil contributed more significantly to lava rock microbial composition. Nevertheless, shared genera among air, rocks, and local sources, suggested potential exchange between these environments. The prevalent genera shared between rocks and potential sources exhibited stress-resistant properties, likely helping their survival during air transportation and facilitating their colonization of the rocks. We hypothesize that the atmosphere serves as a conduit for locally sourced microbes and stress-resistant distant-sourced microbes. Additionally, bacterial communities on the lava rocks of Fimmvörðuháls showed remarkable similarity after 1 and 9 years of exposure, suggesting rapid establishment. Our study reveals that atmospheric deposition significantly influences bacterial community formation, potentially influencing ecosystem dynamics and microbial communities' resilience.

Enterococcus faecium is an opportunistic pathogen able to colonize the intestines of hospitalized patients. This initial colonization is an important step in the downstream pathogenesis, which includes outgrowth of the intestinal microbiota and potential infection of the host. The impact of intestinal overgrowth on host-enterococcal interactions is not well understood. We therefore applied a RNAseq approach in order to unravel the transcriptional dynamics of E. faecium upon co-culturing with human derived colonic epithelium. Co-cultures of colonic epithelium with a hospital-associated vancomycin resistant (vanA-type) E. faecium (VRE) showed that VRE resided on top of the colonic epithelium when analyzed by microscopy. RNAseq revealed that exposure to the colonic epithelium resulted in upregulation of 238 VRE genes compared to the control condition, including genes implicated in pili expression, conjugation (plasmid_2), genes related to sugar uptake, and biofilm formation (chromosome). In total, 260 were downregulated, including the vanA operon located on plasmid_3. Pathway analysis revealed an overall switch in metabolism to amino acid scavenging and reduction. In summary, our study demonstrates that co-culturing of VRE with human colonic epithelium promotes an elaborate gene response in VRE, enhancing our insight in host-E. faecium interactions, which might facilitate the design of novel anti-infectivity strategies.