The composition of the gut microbiota changes throughout life and is shaped by various external influences, particularly major physiological stressors such as surgery. The extent of these changes and their impact remain poorly understood. This prospective cohort study aimed to investigate changes in the gut microbiota following colorectal surgery and to identify factors that modify these alterations. Paired pre- and postoperative stool samples from 59 patients at the University Medical Centre Freiburg were analyzed using 16S rRNA and ITS2 gene sequencing. Analyses included alpha and beta diversity, LEfSe differential feature analysis, network analysis with Louvain clustering, KEGG pathway annotation, and correlation with clinical parameters. Bacterial diversity significantly decreased postoperatively (Shannon index: p < 0.001), while fungal diversity remained largely unchanged (p > 0.05). Beta diversity revealed increased inter-patient variability in bacterial communities after surgery (PERMANOVA p = 0.001). Preoperative network analyses identified 18 microbial network clusters and interkingdom associations between bacteria and fungi. KEGG pathway mapping showed cluster-specific metabolic profiles, including enrichment in degradation pathways, antimicrobial resistance mechanisms, and bacterial secretion systems. The contrasting responses of bacterial and fungal communities highlight the importance of considering the entire gut microbiome in perioperative care and suggest a central role for interkingdom interactions in maintaining gut homeostasis during surgical recovery.

Moraxella species are fastidious Gram-negative bacteria capable of causing opportunistic infections, including bloodstream infections, especially in immunocompromised patients. Data on their epidemiology, antimicrobial susceptibility, and phylogenomics in Europe remains limited. We conducted a multicentre, retrospective, observational study across 56 European hospital centres between January 1st 2020 and December 31st 2024. All Moraxella species isolated from blood cultures (BCs) were included. Species distribution and antimicrobial susceptibility profiles were analysed. We also performed a phylogenomic analysis of Moraxella genomes deposited in GenBank. A total of 709 Moraxella isolates were included. Moraxella osloensis (61.1

Background: The human microbiome is a complex ecosystem that has a significant impact on health. Dysbiosis, an imbalance in microbial communities, is often associated with various diseases and could therefore be a target for therapeutic interventions and preventive measures. Objectives: The aim of this article is to critically examine the concept of dysbiosis and to present concepts and supportive measures for promoting a healthy intestinal microbiome. Materials and methods: This is a narrative review that summarizes and critically evaluates current scientific literature on the microbiome, dysbiosis, nutrition, lifestyle, and probiotic interventions. Results: The term "dysbiosis" is not clearly defined scientifically and therefore does not always imply functional and health-relevant changes in the microbiome. The composition of the microbiome is significantly influenced by diet, physical activity, and environmental factors. Plant-based foods, polyphenols, and fermented products promote microbial diversity and in addition the production of short-chain fatty acids, which modulate inflammatory and metabolic processes. Regular physical activity also increases diversity and supports metabolic resilience. Conclusion: Promoting a health-associated microbiome requires an integrative approach combining diet, exercise, and, if necessary, targeted microbial modulation.

Introduction Aeromonas species are Gram-negative bacilli capable of causing bloodstream infections in both immunocompromised and otherwise healthy individuals. However, data on their epidemiology and antimicrobial resistance remain limited in Europe. Methods We conducted a multicentre, retrospective, observational study that included all Aeromonas species isolates recovered from blood cultures in 56 European hospitals between January 1st 2020 and December 31st 2024. Epidemiological features and antimicrobial susceptibility profiles were analyzed. Results A total of 590 Aeromonas isolates were included. Most were recovered from polymicrobial blood cultures (73.1%), and catheter-related bloodstream infections were frequent (21.7%). The most commonly reported species were A. caviae (30.1%), isolates without conclusive species identification (Aeromonas spp., 24.8%), A. hydrophila (20.7%), and A. veronii (19.1%). At the genus level, susceptibility to aztreonam, ceftazidime, and cefepime exceeded 90%. Resistance to fluoroquinolones (∼10%) and sulfamethoxazole/trimethoprim (up to 11%) was observed. Species-level analyses showed higher resistance rates to fluoroquinolones and sulfamethoxazole/trimethoprim among A. caviae and A. hydrophila, and increased resistance to ceftazidime among Aeromonas spp. Conclusions Aeromonas species in Europe showed high susceptibility to ceftazidime and cefepime, alongside with emerging resistance to fluoroquinolones and sulfamethoxazole/trimethoprim. Species-specific findings should be interpreted cautiously due to limitations in routine identification methods, underscoring the need for sustained surveillance and harmonised diagnostic standards across Europe.

Das menschliche Mikrobiom ist ein komplexes Ökosystem, das maßgeblich die Gesundheit beeinflusst. Die Dysbiose, ein Ungleichgewicht der mikrobiellen Gemeinschaften, wird häufig mit verschiedenen Erkrankungen assoziiert und könnte so eine Möglichkeit für therapeutische Interventionen und präventive Maßnahmen sein. Ziel dieses Artikels ist es, den Begriff der Dysbiose kritisch zu beleuchten und Konzepte sowie supportive Maßnahmen zur Förderung eines gesunden intestinalen Mikrobioms darzustellen. Es handelt sich um eine narrative Übersichtsarbeit, die aktuelle wissenschaftliche Literatur zu Mikrobiom, Dysbiose, Ernährung, Lebensstil und probiotischen Interventionen zusammenfasst und kritisch bewertet. Der Begriff „Dysbiose“ ist wissenschaftlich nicht eindeutig definiert und impliziert daher nicht immer funktionelle und gesundheitlich relevante Veränderungen des Mikrobioms. Die Zusammensetzung des Mikrobioms wird wesentlich durch Ernährung, körperliche Aktivität und Umweltfaktoren geprägt. Pflanzliche Lebensmittel, Polyphenole sowie fermentierte Produkte fördern die mikrobielle Diversität sowie die Produktion kurzkettiger Fettsäuren, die entzündliche und stoffwechselrelevante Prozesse modulieren. Regelmäßige körperliche Aktivität steigert ebenfalls die Diversität und unterstützt die metabolische Resilienz. Die Förderung eines gesundheitsassoziierten Mikrobioms erfordert einen integrativen Ansatz aus Ernährung, Bewegung und bei Bedarf gezielter mikrobieller Modulation.

SMAC is a mitochondrial intermembrane space protein, which is released during apoptosis and whose known function is antagonism of inhibitor of apoptosis proteins in the cytosol, to facilitate caspase activation. Recent data suggest that SMAC can also be released by sub-lethal signals in the apoptosis pathway, in the absence of cell death. We here explored potential functions of SMAC in non-apoptotic cells. We found that a portion of SMAC is spontaneously released into the cytosol in the absence of apoptosis, regulated by the BCL-2-family proteins BAX and BAK and the fission GTPase DRP1. In cancer cell lines, SMAC was required for the activation of caspases in lethal and non-lethal conditions, while this contribution to caspase-activation was much smaller in non-malignant fibroblast lines. In cells with high levels of cytosolic SMAC, SMAC deficiency reduced in vitro migration, invasion and anchorage-independent growth as well as metastasis in a xenograft model in zebrafish. SMAC-deficient cells further showed a reduced activity in interferon signaling, associated with reduced cytosolic presence of mitochondrial DNA and activation of the stimulator of interferon genes (STING), and SMAC expression levels correlated with interferon-induced genes in cancer data sets. We further found that SMAC can regulate mitochondrial morphology and integrity. Finally, high gene-expression of SMAC was associated with poor prognosis in patients of several cancer types. These results identify SMAC as a regulator of inflammation and growth behavior of cancer cells. They further report a mitochondrial function of SMAC and demonstrate a role of SMAC in human cancer biology across several cancer entities.

INTRODUCTION:Non-fermenting Gram-negative bacilli (NFGNB) other than Pseudomonas and Acinetobacter species remain largely underrepresented in systematic surveillance programs across Europe. METHODS:We conducted a multicentre retrospective observational study analysing all minor NFGNB isolates recovered from blood cultures in 56 European Hospital Centres over a 5-year period (2020-2024). Diagnostic approach, epidemiology and antimicrobial susceptibility according to European Committee on Antimicrobial Susceptibility Testing v. 15.0 were investigated. RESULTS:A total of 4420 minor NFGNB isolates were included. In 43.6% of cases, the isolates were recovered from polymicrobial blood cultures, and 40.6% were detected during microbiologically defined catheter-related bloodstream infections. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-ToF) mass spectrometry was the most widely used tool for species identification (98%). Antimicrobial susceptibility testing was conducted in all centres, using mostly broth microdilution commercial systems (57%), disk diffusion (57%) and gradient diffusion MIC strip (54%) methods, mainly according to European Committee on Antimicrobial Susceptibility Testing guidelines (67.9%). The most prevalent species were Stenotrophomonas maltophilia (52.4%), Achromobacter xylosoxidans (7.8%), Sphingomonas paucimobilis (5.3%) and the Burkholderia cepacia complex (4.8%). S. maltophilia displayed a high rate of resistance to sulfamethoxazole/trimethoprim (11%), and 2% of the isolates were found to be likely resistant to cefiderocol. A. xylosoxidans showed high resistance to meropenem (10%), piperacillin/tazobactam (24%) and sulfamethoxazole/trimethoprim (53%) when tested by MIC methods, while showing over 90% susceptibility to meropenem when tested by disk diffusion. S. paucimobilis displayed over 90% susceptibility to amoxicillin/clavulanate, ampicillin/sulbactam, imipenem, meropenem and tetracycline. CONCLUSIONS:This study provides an updated overview of the diagnostic approaches and epidemiology of minor NFGNB across Europe, supporting future comparative analyses and improved diagnostic and antimicrobial strategies.

Background:The patient´s microbiome has become a focal point in cancer research. Even for pancreatic cancer, alterations in the microbiome appear to influence cancer formation and progression. The aim of our single-center analysis was the examination of microbiological colonization of pancreas tissue at the time of surgery and its potential influence on complications and outcome. Methods:We prospectively evaluated patients undergoing pancreatic surgery over a three-year period from June 2018 to June 2021. We focused on the microbiological colonization of pancreatic tissue which was acquired during pancreatic surgery. Tissue samples were cultivated at our institute of microbiology. Patients´ characteristics, complications and postoperative outcome were analyzed using a prospectively maintained SPSS database. Results:Between June 2018 and June 2021, we collected pancreatic tissue samples of a total of 178 patients undergoing pancreas resections, mostly due to ductal adenocarcinoma (PDAC; 50.6%). We could cultivate bacterial or fungal species in pancreatic tissue samples of 50 of our patients (28.1%). The majority of cases were characterized by the presence of a single microbial species, but 20 patients (11.2%) showed colonization with up to four different species. Among the bacterial species detected were Enterococcus faecium, Enterococcus faecalis, Escherichia coli, Staphylococcus aureus, Enterobacter cloacae and Klebsiella pneumonia. We found significantly more microbiological culture growth in patients with a preoperative biliary stent (74.0% vs. 15.6%, p < 0.001). Concerning postoperative complications, we found no difference concerning pancreatic fistula, but colonization with E. coli was associated with a significantly higher rate of postpancreatectomy hemorrhage (30.0% vs. 8.9%, p = 0.032). Interestingly, survival of PDAC patients seems to be negatively affected by positive microbiological findings at the time of surgery, but without reaching statistical significance (p = 0.770). Conclusion:In this first analysis of our patient cohort, we could show a microbiological colonization of pancreatic tumor tissue in almost a third of our patients. There seems to be only a minor impact on postoperative complications, but long-term outcome seems to be worse in patients with a positive pancreas microbiome. Further observation is needed to evaluate the influence of the tumor microbiome on the long-term oncological outcome in PDAC patients.

Introduction: Despite being implicated in a wide spectrum of community-and healthcare-acquired infections, anaerobes have not yet been incorporated into systematic surveillance programs in Europe. Methods: We conducted a multicentre retrospective observational study analysing all anaerobic strains isolated from blood cultures in 44 European Hospital Centres over a 4-y period (2020-2023). Diagnostic approach, epidemiology, and antimicrobial susceptibility according to EUCAST v. 15.0 were investigated. Results: Our study included 14,527 anaerobes, most of which were Gram-positive (45%) or Gram-negative (40%) bacilli. MALDI-TOF coupled to mass spectrometry was the most widely used tool for species identification (98%). Antimicrobial susceptibility testing was performed in the vast majority of centres, using mostly gradient diffusion strip (77%) and disk diffusion (45%) methods according to EUCAST guidelines. The most prevalent species were Cutibacterium acnes (18.7%), Bacteroides fragilis (16.3%), Clostridium perfringens (5.3%), Bacteroides thetaiotaomicron (4.2%), Fusobacterium nucleatum (3.5%), and Parvimonas micra (3.4%). C. acnes showed high resistance to benzylpenicillin (18%), clindamycin (39%), and imipenem (19% and 13% by MIC methods and disk diffusion, respectively). B. fragilis showed high resistance to amoxicillin/clavulanate (24%), piperacillin/tazobactam (22% and 14% by MIC methods and disk diffusion, respectively), clindamycin (22% by both MIC methods and disk diffusion), meropenem (13%), and metronidazole (10%, only by disk diffusion). A similar resistance pattern was observed in B. thetaiotaomicron, Bacteroides ovatus, and Parabacteroides distasonis. C. perfringens showed high resistance to clindamycin (69% and 45% by MIC methods and disk diffusion, respectively), while benzylpenicillin and metronidazole maintained over 90% activity. F. nucleatum showed high resistance to benzylpenicillin (11%), while Fusobacterium necrophorum showed alarming rates of resistance to clindamycin (12%), meropenem (16%) and metronidazole (11%). Conclusions: This study presented an up-to-date analysis of the diagnostics and epidemiology of anaerobic bacteria in Europe, providing insights for future comparative analyses and the development of antimicrobial diagnostic and management strategies, as well as the optimization of current antibiotic treatments. (c) 2025 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

SMAC is a mitochondrial intermembrane space protein, which is released during apoptosis and whose known function is antagonism of inhibitor of apoptosis proteins in the cytosol, to facilitate caspase activation. Recent data suggest that SMAC can also be released by sub-lethal signals in the apoptosis pathway, in the absence of cell death. We here explored potential functions of SMAC in non-apoptotic cells. We found that a portion of SMAC is spontaneously released into the cytosol in the absence of apoptosis, regulated by the BCL-2-family proteins BAX and BAK and the fission GTPase DRP1. In cancer cell lines, SMAC was required for the activation of caspases in lethal and non-lethal conditions, while this contribution to caspase-activation was much smaller in non-malignant fibroblast lines. In cells with high levels of cytosolic SMAC, SMAC deficiency reduced in vitro migration, invasion and anchorage-independent growth. SMAC-deficient cells further showed a reduced activity in interferon signalling, associated with reduced cytosolic presence of mitochondrial DNA and activation of the stimulator of interferon genes (STING), and SMAC expression levels correlated with interferon-induced genes in cancer data sets. We further found that SMAC can regulate mitochondrial morphology and integrity. Finally, high gene-expression of SMAC was associated with poor prognosis in patients of several cancer types. These results identify SMAC as a regulator of inflammation and growth behaviour of cancer cells. They further report a mitochondrial function of SMAC and demonstrate a role of SMAC in human cancer biology across several cancer entities. ### Competing Interest Statement The authors have declared no competing interest.

The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.

ObjectivesAscites, often associated with critical pathologies such as liver cirrhosis or bowel perforation, can be complicated by fungal infection, increasing mortality especially in intensive care settings and demanding rapid diagnosis and adequate treatment. Traditional microbiological diagnostic methods have limited sensitivity in accurately identifying fungal pathogens in ascitic fluid. Alternative diagnostic methods may offer important insights to enable guiding of antifungal therapy and refining empirical treatment strategies. The objective of this study was to evaluate the potential of next-generation sequencing methods to identify specific fungal pathogens responsible for ascitic fluid infections.MethodsWe prospectively collected 50 ascitic fluid samples from ICU patients with suspected ascites infection. In addition to standard culture-based microbiological testing, an ascitic fluid aliquot underwent fungal DNA isolation and was analyzed by next-generation sequencing (NGS) methods for identification of fungal species.ResultsOf 50 ascitic samples collected, five samples showed growth of Candida spp. in culture. After DNA isolation and ITS2 PCR, detectable amplification was achieved in 10 samples. Sequencing of the 50 patients’ samples identified facultative pathogenic fungi in 19 patients. In 15 cases, culture alone would not have permitted the identification of all facultative pathogenic fungi. The identification of fungal DNA by sequencing was significantly associated with poor patient outcome and a number of clinical parameters.ConclusionsOur results show a higher sensitivity for NGS-based diagnostic methods in the identification of ascitic fluid fungal infections compared to culture-based diagnostics. This may be beneficial especially for patients in a critical care setting, who have an increased prevalence of comorbidities and high mortality. The implementation of such methods in standard diagnosis will require increased standardization of the workflows and interpretation of the sequencing results with respect to patients’ clinical picture.

IntroductionAlterations of the gut microbiome are involved in the pathogenesis of Crohn’s disease (CD). The role of fungi in this context is unclear. This study aimed to determine postoperative changes in the bacterial and fungal gut communities of CD patients undergoing intestinal resection, and to evaluate interactions between the bacteriome and mycobiome and their impact on the patients’ outcome.MethodsWe report a subgroup analysis of a prospective cohort study, focusing on 10 CD patients whose fecal samples were collected for bacterial 16S rRNA and fungal ITS2 genes next-generation sequencing the day before surgery and on the 5th or 6th postoperative day.ResultsNo significant differences in bacterial and fungal diversity were observed between preoperative and postoperative stool samples. By in-depth analysis, significant postoperative abundance changes of bacteria and fungi and 17 interkingdom correlations were detected. Network analysis identified 13 microbial clusters in the perioperative gut communities, revealing symbiotic and competitive interactions. Relevant factors were gender, age, BMI, lifestyle habits (smoking, alcohol consumption) and surgical technique. Postoperative abundance changes and identified clusters were associated with clinical outcomes (length of hospital stay, complications) and levels of inflammatory markers.ConclusionsOur findings highlight the importance of dissecting the interactions of gut bacterial and fungal communities in CD patients and their potential influence on postoperative and disease outcomes.

Cancers of the biliary tract are more common in Asia than in Europe, but are highly lethal due to delayed diagnosis and aggressive tumor biology. Since the biliary tract is in direct contact with the gut via the enterohepatic circulation, this suggests a potential role of gut microbiota, but to date, the role of gut microbiota in biliary tract cancers has not been elucidated. This scoping review compiles recent data on the associations between the gut microbiota and diagnosis, progression and prognosis of biliary tract cancer patients. Systematic review of the literature yielded 154 results, of which 12 studies and one systematic review were eligible for evaluation. The analyses of microbiota diversity indices were inconsistent across the included studies. In-depth analyses revealed differences between gut microbiota of biliary tract cancer patients and healthy controls, but without a clear tendency towards particular species in the studies. Additionally, most of the studies showed methodological flaws, for example non-controlling of factors that affect gut microbiota. At the current stage, there is a lack of evidence to support a general utility of gut microbiota diagnostics in biliary tract cancers. Therefore, no recommendation can be made at this time to include gut microbiota analyses in the management of biliary tract cancer patients.

Micronuclei are DNA-containing structures separate from the nucleus found in cancer cells. Micronuclei are recognized by the immune sensor axis cGAS/STING, driving cancer metastasis. The mitochondrial apoptosis apparatus can be experimentally triggered to a non-apoptotic level, and this can drive the appearance of micronuclei through the Caspase-activated DNAse (CAD). We tested whether spontaneously appearing micronuclei in cancer cells are linked to sub-lethal apoptotic signals. Inhibition of mitochondrial apoptosis or of CAD reduced the number of micronuclei in tumor cell lines as well as the number of chromosomal misalignments in tumor cells and intestinal organoids. Blockade of mitochondrial apoptosis or deletion of CAD reduced, while experimental activation CAD, STING-dependently, enhanced aggressive growth of tumor cells in vitro. Deletion of CAD from human cancer cells reduced metastasis in xenograft models. CAD-deficient cells displayed a substantially altered gene-expression profile, and a CAD-associated gene expression 'signature' strongly predicted survival in cancer patients. Thus, low-level activity in the mitochondrial apoptosis apparatus operates through CAD-dependent gene-induction and STING-activation and has substantial impact on metastasis in cancer.

The bacterium Helicobacter pylori induces gastric inflammation and predisposes to cancer. H. pylori -infected epithelial cells secrete cytokines and chemokines and undergo DNA-damage. We show that the host cell’s mitochondrial apoptosis system contributes to cytokine secretion and DNA-damage in the absence of cell death. H. pylori induced secretion of cytokines/chemokines from epithelial cells, dependent on the mitochondrial apoptosis machinery. A signalling step was identified in the release of mitochondrial Smac/DIABLO, which was required for alternative NF-κB-activation and contributed to chemokine secretion. The bacterial cag -pathogenicity island and bacterial muropeptide triggered mitochondrial host cell signals through the pattern recognition receptor NOD1. H. pylori -induced DNA-damage depended on mitochondrial apoptosis signals and the caspase-activated DNAse. In biopsies from H. pylori -positive patients, we observed a correlation of Smac-levels and inflammation. Non-apoptotic cells in these samples showed evidence of caspase-3-activation, correlating with phosphorylation of the DNA-damage response kinase ATM. Thus, H. pylori activates the mitochondrial apoptosis pathway to a sub-lethal level. During infection, Smac has a cytosolic, pro-inflammatory role in the absence of apoptosis. Further, DNA-damage through sub-lethal mitochondrial signals is likely to contribute to mutagenesis and cancer development.

Data on molecular characterization of coagulase-negative staphylococci causing neonatal sepsis in low-income countries are highly limited. This report highlights the isolation of three Staphylococcus epidermidis strains, NGASs, from blood samples from neonates, with unknown transmission sources. Pathogenic factors and sources of transmission of these strains warrant further investigation.