It has been proposed by Ettema and colleagues, in the two-domain framework for the tree of life, that Eukarya emerged from Heimdallarchaeia, as sister group to Hodarchaeales. Looking at the individual trees of the protein markers used by these authors, I notice that Eukarya are only sister to Hodarchaeales or other Heimdallarchaeia in a minority of trees, whereas they are located far apart from these Asgard archaea in most other trees. Examination of single trees also reveals massive gene transfers from Crenarchaeota and/or Korachaeota to hyperthermophilic Njordarchaeales, explaining why their belonging to Asgard archaea is sometimes difficult to recover. Finally, I discuss several points raised by Ettema and colleagues, such as the phylogeny of Asgard archaea and the hyperthermophilic nature of their last common ancestor. The patchy localization of Eukarya in individual trees relative to Hodarchaeales and other Heimdallarchaeia, as well as the patchy distribution of eukaryotic signature proteins among Asgard archaea, is best explained by suggesting that multiple gene transfers take place between proto-eukaryotes and Asgard archaea in both directions. This suggests that the co-evolution of proto-eukaryotes and Asgard archaea has played a major role in eukaryogenesis but also in shaping the physiology and diversification of Asgard archaea.

Aeromonas hydrophila, an opportunistic pathogen, often encodes Type VI Secretion System (T6SS) genes. However, the specific functions of T6SS, particularly in the context of clinical strains, remain poorly understood. In this study, we characterize a multi-drug-resistant strain, AH54, which possesses a complete and functional T6SS, composed of a structural cluster and two homologous auxiliary clusters (Aux1 and Aux2). Each auxiliary cluster encodes two distinct effector proteins: a rearrangement hotspot (Rhs) protein and a proline–alanine–arginine repeat (PAAR) protein—Rhs1/PAAR1 in Aux1 and Rhs2/PAAR2 in Aux2. Our findings reveal that AH54 assembles a fully operational T6SS capable of delivering these effectors, driving inter-bacterial antagonism. Interestingly, the T6SS activity in AH54 is temperature-regulated, with enhanced secretion and antibacterial activity at lower temperatures. To protect itself from self-intoxication, AH54 produces immunity proteins (Tsi1–Tsi4) that neutralize the toxic effectors. While PAAR1 and PAAR2 are critical for Hcp secretion, immunity proteins Tsi3 and Tsi4 do not cross-protect against PAAR effectors, suggesting distinct roles for each PAAR protein in optimizing AH54's competitive fitness. In addition, using a Dictyostelium discoideum phagocytosis model, we demonstrate that Rhs2, a metal ion-dependent DNase effector, plays a crucial role in protecting AH54 from eukaryotic predation via T6SS. These findings highlight the pivotal role of T6SS in bacterial competition and pathogenesis, offering new insights into the virulence mechanisms of A. hydrophila.

The global spread of hypervirulent Klebsiella pneumoniae (hvKp) poses a serious public health threat. In this study, we conducted genomic epidemiology analysis on 2097 global hvKp isolates, including our 900 isolates sequenced through the Illumina platform (177 of them fully sequenced through PacBio platform), representing the most comprehensive genomic analysis of hvKp to date. Our results identified six dominant clonal groups (CGs), particularly including CG23 and CG258, and 17 major virulence determinant combinations (VDCs) comprising 10 virulence gene profiles (VGPs), four types of virulence plasmids, four ICEKp variants, Tn7399, and all_island. Each CG harbored distinct advantageous VDCs, indicating strong genomic correlation and co-evolution. Additionally, the phylogeny and evolutionary history of CG23 and CG258 were characterized in depth. Notably, 41.58% of the 2097 isolates were multidrug-resistant and 33.29% were carbapenem-resistant, indicating serious antimicrobial resistance. Overall, our study provides a global genomic landscape of hvKp, emphasizing the genetic basis for their global dissemination and the need for precise prevention and control.

Inflammatory bowel disease (IBD) is a chronic condition characterized by intestinal inflammation and gut dysbiosis, with limited treatment options primarily focused on immune-modulating therapies. Among potential therapeutic agents, butyrate has emerged as a promising candidate due to its anti-inflammatory and gut-restorative properties. However, direct administration of butyrate poses significant challenges, including its rapid absorption, uneven distribution within the intestinal tract, and an unpleasant odor that reduces patient compliance. To address these issues, we evaluated the therapeutic potential of Bacillus subtilis BM107, a strain selected for its superior butyrate-producing capabilities and established bacterial safety. BM107 efficiently hydrolyzed tributyrin (TB), a butyrate prodrug, producing substantial butyrate levels in TB-supplemented media. In a dextran sodium sulfate-induced colitis mouse model, co-administration of BM107 and the TB diet significantly improved inflammatory indices, such as reduced disease activity index scores, increased colon length, and restored body weight. Additionally, this combination treatment markedly improved gut microbiome composition, restoring microbial diversity and balance. Furthermore, butyrate levels in the cecum contents of the TB + BM107 group were restored to levels comparable to those in healthy controls, demonstrating the ability of this approach to promote gut homeostasis and intestinal recovery. These findings highlight the therapeutic potential of BM107 combined with a TB diet as a safe, effective, and innovative strategy for addressing gut dysbiosis and inflammation in IBD, paving the way for the development of microbiome-based bacterial therapeutics to improve patient outcomes.

Infections with Shiga toxin (Stx)-producing Escherichia coli (STEC) strains can result in a wide range of clinical presentations. Despite STEC O157:H7 being the serotype most frequently associated with hemolytic uremic syndrome (HUS), in some patients, a self-limited gastrointestinal infection is observed. We have previously demonstrated that genetic differences between BALB/c and C57BL/6 mice account for a different outcome after an experimental gastrointestinal STEC O157:H7 infection, in which the better outcome observed in BALB/c mice was associated with a Th-2 biased immune response. The objective of this study was to determine the role of anti-STEC antibodies during STEC O157:H7 infections. We first demonstrated that the B-cell-dependent response triggered upon STEC O157:H7 infection is necessary to keep BALB/c mice healthy and reciprocally C57BL/6 mice pre-challenged with an Stx2-deficient STEC O157:H7 strain were able to survive, remaining healthy after a subsequent STEC O157:H7 infection. We further proved that anti-STEC O157:H7 antibodies raised after infection have binding specificity against STEC O157:H7 bacteria, recognize H7, and have neutralizing capacitiy, by interfering with important pathogenic mechanisms such as motility and adhesion to intestinal epithelial cells. We conclude that local and/or systemic specific antibodies against STEC mediate prevention of lethal complications during STEC O157:H7 infections.

Antibiotic resistance has caused a severe reduction in bacteriostatic action and clinical therapy, demanding effective agents or strategies. Tellurite is an ancient yet powerful antimicrobial agent with an ambiguous mechanism. In this study, we uncovered the underlying action mechanism of tellurite by disturbing the cellular homeostasis of proton and metal ions. Tellurite, entering into Escherichia coli MG1655 cells, synchronously imported excess protons and induced intracellular acidification. The intracellular pH declined upon exposure to 0.5 μg/ml of tellurite (the minimal inhibitory concentration, MIC) for 15 min, decreasing from 7.5 to 6.3 in 3 h. A dramatic decrease (31%–73%) in cellular magnesium contents and cytoplastic Mg²⁺ levels occured early after a 5-min treatment with tellurite, primarily via the enhanced efflux by FocB/MdtL/MdtG and the reduced influx by MgtA/CorA. Disruption of cellular Mg²⁺ homeostasis by tellurite severely hindered ribosome assembly, retarded protein synthesis, and disturbed cellular metabolism. This action logic was applicable to various pathogens. Furthermore, a combination of trace tellurite (0.01/0.1× MIC) synergistically augmented the efficacy of antibiotics at sublethal doses (0.5× MIC) against hypervirulent and drug-resistant bacterial strains in vitro and in vivo, significantly enhancing the survival rate and the wound-healing rate of infected animals. These discoveries regarding this metalloid present a promising perspective for combating stubborn and drug-resistant pathogens.

The filamentous prophage Pf4 is activated to produce phage virions during Pseudomonas aeruginosa biofilm formation, a process crucial for maintaining biofilm architecture and enhancing pathogenicity. However, the environmental cues triggering Pf4 activation have been inadequately explored. In this study, we discovered that oxidative stress, a significant stressor encountered by pathogens in biofilms or within eukaryotic hosts, triggers the production of the filamentous phage Pf4 in P. aeruginosa MPAO1 through OxyR. Under oxidative stress, the expression of oxyR is induced, leading to increased OxyR binding to the promoter region of the Pf4 excisionase gene xisF4, thereby facilitating Pf4 prophage excision and virion production. Thus, our study elucidates a mechanism by which bacteria exploit cytotoxic oxidative stress as a potent stimulant to activate the filamentous phage Pf4 within biofilms.

Extractable glycolipids of mycobacteria, such as lipooligosaccharides (LOSs), play crucial roles in responding to environmental stress and modulating the host immune response. Although the biosynthesis of LOS is likely regulated at multiple levels to ensure proper composition of the cell wall, the key regulators remain unknown. In this study, we investigated B11, a conserved mycobacterial small RNA (sRNA), and found that it post-transcriptionally regulates LOS synthesis in Mycobacterium marinum. Through a combination of RNA-seq and mass spectrometry screening, we identified specific genes within the LOS synthesis locus that are directly regulated by B11. We confirmed in vivo sRNA-mRNA interactions using MS2-tagged RNA affinity purification, and found that B11 utilizes the cytosine-rich loop of its Rho-independent transcriptional terminator to interact with guanine tracks adjacent to the ribosome binding sites of its target genes, thereby impeding translation and promoting mRNA degradation. Moreover, deletion of B11 altered the colony morphology associated with LOS composition. These comprehensive functional studies of the mycobacterial sRNA B11 reveal sRNA-based regulation of LOS synthesis, providing new insights into the regulatory mechanisms controlling the biosynthesis of the complex mycobacterial cell wall.