The publication and scientific implementation of scholarly articles is a collaborative effort that unites readers, authors, editors, and referees. A scientific journal thereby serves as a vital platform, enabling these interactions and fostering a shared commitment to advancing the quality and impact of scientific communication. In this short editorial, we celebrate the milestone of publishing the 500th article in Microbial Cell by highlighting these collective efforts. Importantly, from the outset of the journal more than ten years ago, we have cultivated a handcrafted organ that is produced by scientists for scientists. In that frame, we have followed and advocated a radical open access approach that fuels interaction and visibility of such cooperative endeavors for the public good.

Molecular de-extinction has emerged as a novel strategy for studying biological molecules throughout evolutionary history. Among the myriad possibilities offered by ancient genomes and proteomes, antimicrobial peptides (AMPs) stand out as particularly promising alternatives to traditional antibiotics. Various strategies, including software tools and advanced deep learning models, have been used to mine these host defense peptides. For example, computational analysis of disulfide bond patterns has led to the identification of six previously uncharacterized β-defensins in extinct and critically endangered species. Additionally, artificial intelligence and machine learning have been utilized to uncover ancient antibiotics, revealing numerous candidates, including mammuthusin, and elephasin, which display inhibitory effects toward pathogens in vitro and in vivo. These innovations promise to discover novel antibiotics and deepen our insight into evolutionary processes.

Cholelithiasis is one of the most common diseases of the biliary system. Neutrophil extracellular traps (NETs) in the liver play an important role in accelerating the formation of gallstones. The upstream mechanism of NETs formation remains unclear. In this study, 16S rRNA sequencing was used to screen the differential gut microbiota in mice with gallstones. Transcriptome sequencing was used to screen the differentially expressed core genes and signalling pathways of Clostridium scindens that acted on human colonic epithelial cells. Western blotting was used to verify the protein expression of TLR2 and the NF-κB pathway. RT-PCR was used to verify the mRNA expression of TLR2, CXCL1 and the NF-κB pathway. ELISA was used to verify CXCL1 expression in the supernatant or portal vein blood of mice. Immunofluorescence was used to detect NETs formation in cocultured neutrophils in vitro or in mouse livers. Clostridium scindens was the key differential strain in the formation of gallstones in mice. After treatment with Clostridium scindens, both in vitro and in vivo, the expression of TLR2 was upregulated, the secretion of CXCL1 was increased by regulating the NF-κB pathway. Finally, the formation of NETs and stones was significantly increased. This study reveals a new mechanism of the gut-liver immune axis in the formation of gallstones. Clostridium scindens acts on colonic epithelial cells through TLR2 to regulate the NF-κB pathway and increase the secretion of CXCL1. CXCL1 enters the liver via the portal vein and increases the formation of NETs in the liver, thereby accelerating gallstone formation.

Persister cells are a clinically relevant sub-population of an isogenic bacterial culture that is tolerant to bactericidal antibiotics. With the aim to investigate the ribosomal protein content of persister cells, we employed the bacteriolytic properties of ampicillin to separate persister from sensitive cells. Thereby, we observed processing of several ribosomal proteins. Promisingly, we detected a variant of the large subunit protein uL2 that lacks the last 59 amino acids from its C-terminus (tL2) and which previously has been described as an inhibitor of DNA replication in vitro. Considering the increasing number of moonlighting functions described for ribosomal proteins, we investigated a potential regulatory role of tL2 in persister cells after ampicillin treatment. In contrast to our assumption, our findings show that the generation of tL2 after ampicillin treatment must be attributed to proteolysis upon cell lysis. Ultimately, no tL2 was detected intracellularly of purified persister cells isolated by an improved protocol employing proteinase K treatment. We therefore exclude the possibility of tL2 regulating DNA replication in ampicillin tolerant E. coli cells. Nevertheless, this study clearly highlights the necessity of further purification steps in addition to ampicillin treatment for the study of persister cells and invites for the careful re-examination of previously published results.

Peroxisomes are organelles that are crucial for cellular metabolism, but they also play important roles in non-metabolic processes such as signalling, stress response or antiviral defense. To uncover the consequences of peroxisome deficiency, we compared Saccharomyces cerevisiae wild-type with pex3 cells, which lack peroxisomes, employing quantitative proteomics and transcriptomics technologies. Cells were grown on acetate, a carbon source that requires peroxisomal enzymes of the glyoxylate cycle to generate energy and essential carbohydrates, and that does not repress the expression of peroxisomal genes. Our integrative omics analysis reveals that the absence of peroxisomes induces distinct responses at the level of the transcriptome and proteome. Transcripts of genes and corresponding proteins that are associated with peroxisomal β-oxidation were mostly increased in pex3 cells. In contrast, levels of peroxins were regulated at protein but not at transcript level. Membrane-bound peroxins were reduced, whereas the soluble receptors Pex5 and Pex7 were increased in abundance in pex3 cells. Interestingly, we found several non-peroxisomal transcript and proteins regulated in pex3 cells including mitochondrial proteins involved in respiration or import processes, which led to the identification of the mitochondrial pyruvate carrier Mpc1/3 as so far unnoticed transporter present in the peroxisomal membrane. Our results reveal the impact of the absence of peroxisomes in pex3 yeast cells and represent a rich resource of genes/proteins for follow-up studies to obtain a deeper understanding of peroxisome biology in a cellular context.