Czech Academy of Sciences, Institute of Animal Physiology and Genetics

Background Diabetic foot infections (DFIs) contribute to the global disability burden. Beta-lactams are the most commonly used antibiotics for treating DFIs. However, the use of antibiotics may lead to disruption of the healthy balance of the gut microbiota, causing dysbiosis. Methods Patients with infected diabetic foot ulcers (iDFUs) were treated with two kinds of beta-lactams (amoxicillin/clavulanic acid or ceftazidime) according to microbial sensitivity of causative agents via bolus or continuous administration modes. Changes in the gut microbiome of patients were analyzed. Diabetic patients without iDFUs were used as a control group. 16 S ribosomal RNA gene amplicon sequencing was performed on stool samples collected from participants. Results Alpha diversity and beta diversity of gut microbiota of treated patients did not show significant differences between bolus and continuous modes. However, significant differences were observed between gut microbiota diversity of treated patients and control group. PCoA plots showed individualized responses of the patient’s gut microbiota to antibiotics at different times using both administration forms associated with the pre-treatment state of microbiota composition. Enterococcus, Sellimonas, and Lachnoclostridium were the common bacterial markers differentially abundant in the gut microbiota of antibiotic-treated patients with iDFUs while Roseburia, Dorea, and Monoglobus were mainly abundant in the gut microbiota of patients without iDFUs. Predicted pathways like “Transporters”, “ABC transporters” and “Phosphotranspherase system (PTS)” were upregulated in the gut microbiome of patients treated with bolus regime which may lead to increased intestinal barrier permeability. Conclusion The present study reported alterations in gut microbiota composition and functionality and provided the bacterial markers as well as potential metabolic signatures associated with each administration mode in patients with iDFUs, which may be used as a reference set for future studies of the effect of antibiotics administration on the gut microbiome of patients with iDFUs. This study shed light on the importance of understanding the effect of antibiotic administration form on gut microbiome in patients with iDFUs. Trial registration The DFIATIM Clinical Trial (Full title: “Rationalisation of ATB therapy in diabetic foot infection and its impact on the intestinal microbiota”) is submitted to the European Union Clinical Trials Database under the EudraCT Number: 2019-001997-27. The date of registration is July 17th, 2020.

Host-specific Lactobacillus and Bifidobacterium species constitute the core microbiota of the honey bee digestive tract and are recognized for their probiotic properties. One of the properties of these bacteria is the inhibition of bacterial pathogens such as Paenibacillus larvae and Melissococcus plutonius, the causative agents of American and European foulbrood, respectively. Additionally, Serratia marcescens has emerged as a relevant opportunistic pathogen. Although several previously published studies have examined the inhibition of selected bacterial pathogens of bees by members of the bee physiological microbiota, none have simultaneously investigated the inhibition of multiple clinical isolates of P. larvae, M. plutonius, and S. marcescens using a wide range of bifidobacterial and lactobacilli strains isolated from various locations within a single country. Thus, this study evaluated the antimicrobial potential of Lactobacillus and Bifidobacterium strains against these pathogens, with a focus on strain-dependent inhibition. A total of 111 bacterial strains (62 Lactobacillus and 49 Bifidobacterium) were isolated from the digestive tracts of honey bees collected from eight sites across the Czech Republic. Using 16S rRNA gene sequencing, the isolates were classified and tested in vitro against four P. larvae isolates, one M. plutonius isolate, and the S. marcescens strain sicaria in modified BHI medium. Twenty-eight strains (~26%) exhibited strong inhibition (≥21 mm) against at least two P. larvae isolates, while 12 strains showed moderate inhibition (16–20 mm) against all four isolates. Inhibition of M. plutonius and S. marcescens was observed in three and twenty strains, respectively. The most effective strains belonged to Bifidobacterium asteroides, B. choladohabitans, B. polysaccharolyticum, Lactobacillus apis, L. helsingborgensis, L. kullabergensis, and L. melliventris. These results underscore the strain-dependent nature of antimicrobial activity and highlight the importance of selecting probiotic strains with broad-spectrum pathogen inhibition to support honey bee health.

1. The poultry sector is possibly the fastest growing and most flexible of all livestock sectors. At present, the main changes to the table egg production system include the gradual abandonment and closure of all cage-housing systems for laying hens, driven by animal welfare concerns and stricter legislation in many countries. In the future, keeping hens in enriched cage systems may be restricted or phased out in response to evolving animal welfare guidelines and public demand. To meet the welfare and behavioural requirements of the hens, it is desirable to choose housing on litter or housing in aviaries as a substitute for housing in enriched cages. 2. The objective of this systematic review was to examine non-cage housing systems and hemp-based dietary interventions in relation to skeletal health in laying hens. This review focussed on the risks associated with alternative housing systems, particularly the increased incidence of bone fractures and the potential of nutritional strategies to mitigate skeletal disorders, including osteoporosis. 3. The proportion of hens housed in non-cage alternative housing systems is currently increasing sharply but carries certain risks. One of the most significant concerns is skeletal integrity, as hens in aviaries experience a higher rate of keel bone fractures due to collisions, falls and deviations thought to be related to internal pressure. Numerous studies have shown that the incidence of keel bone damage (i.e. fractures and deviations) was greater in aviaries compared to enriched cage systems. 4. Optimal skeletal health can be supported through proper nutrition, which plays a crucial role in bone metabolism. Key nutritional elements, including calcium, vitamins D, E and K, polyunsaturated fatty acids and hemp-based products, have been shown to be beneficial in preventing skeletal disorders and associated fractures due to their specific roles in maintaining bone structure and strength.

Cell communication systems based on polypeptide ligands use transmembrane receptors to transmit signals across the plasma membrane. In their biogenesis, receptors depend on the endoplasmic reticulum (ER)-Golgi system for folding, maturation, transport and localization to the cell surface. ER stress, caused by protein overproduction and misfolding, is a well-known pathology in neurodegeneration, cancer and numerous other diseases. How ER stress affects cell communication via transmembrane receptors is largely unknown. In disease models of multiple myeloma, chronic lymphocytic leukemia and osteogenesis imperfecta, we show that ER stress leads to loss of the mature transmembrane receptors FGFR3, ROR1, FGFR1, LRP6, FZD5 and PTH1R at the cell surface, resulting in impaired downstream signaling. This is caused by downregulation of receptor production and increased intracellular retention of immature receptor forms. Reduction of ER stress by treatment of cells with the chemical chaperone tauroursodeoxycholic acid or by expression of the chaperone protein BiP resulted in restoration of receptor maturation and signaling. We show a previously unappreciated pathological effect of ER stress; impaired cellular communication due to altered receptor processing. Our findings have implications for disease mechanisms related to ER stress and are particularly important when receptor-based pharmacological approaches are used for treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12964-025-02208-w.

Background/Aim This study investigated the therapeutic potential of lipophosphonoxin (LPPO), an antibacterial agent, loaded into polycaprolactone nanofiber dressings (NANO-LPPO) for full-thickness wound healing. Using a porcine model, we aimed to assess the impact of areal weight of the dressing (10, 20 and 30 g/m²) on wound-healing outcomes and validate findings from previous murine studies. Materials and Methods Full-thickness wounds were created on porcine skin and treated with the NANO-LPPO dressings of differing thickness. Positive control (Aquacel Ag+) and standard control (Jelonet) groups were included for comparison. Wound-healing progression was evaluated macroscopically and on the histological level. Results Macroscopic observations indicated no signs of infection in any group, with wounds covered by scabs by day 14. Thicker dressings (areal weights of 30 and 20 g/m²) demonstrated superior performance in promoting the formation of granulation tissue and healing compared to the thinner version (areal weight of 10 g/m²). LPPO-loading enhanced scaffold wettability and biodegradability without impairing healing outcomes. Both control groups exhibited similar healing characteristics. Conclusion The findings underscore the importance of optimizing dressing thickness for effective wound healing. NANO-LPPO dressings exhibit translational potential as a therapeutic option for full-thickness wounds, warranting further preclinical and regulatory evaluation to support clinical application.

Incidence rates of colorectal cancer vary geographically and have changed over time¹. Notably, in the past two decades, the incidence of early-onset colorectal cancer, which affects individuals below 50 years of age, has doubled in many countries2, 3, 4–5. The reasons for this increase are unknown. Here we investigate whether mutational processes contribute to geographic and age-related differences by examining 981 colorectal cancer genomes from 11 countries. No major differences were found in microsatellite-unstable cancers, but variations in mutation burden and signatures were observed in the 802 microsatellite-stable cases. Multiple signatures, most with unknown aetiologies, exhibited varying prevalence in Argentina, Brazil, Colombia, Russia and Thailand, indicating geographically diverse levels of mutagenic exposure. Signatures SBS88 and ID18, caused by the bacteria-produced mutagen colibactin6,7, had higher mutation loads in countries with higher colorectal cancer incidence rates. SBS88 and ID18 were also enriched in early-onset colorectal cancers, being 3.3 times more common in individuals who were diagnosed before 40 years of age than in those over 70 years of age, and were imprinted early during colorectal cancer development. Colibactin exposure was further linked to APC driver mutations, with ID18 being responsible for about 25% of APC driver indels in colibactin-positive cases. This study reveals geographic and age-related variations in colorectal cancer mutational processes, and suggests that mutagenic exposure to colibactin-producing bacteria in early life may contribute to the increasing incidence of early-onset colorectal cancer.

Primary cilium projects from cells to provide a communication platform with neighboring cells and the surrounding environment. This is ensured by the selective entry of membrane receptors and signaling molecules, producing fine-tuned and effective responses to the extracellular cues. In this study, we focused on one family of signaling molecules, the fibroblast growth factor receptors (FGFRs), their residence within cilia, and its role in FGFR signaling. We show that FGFR1 and FGFR2, but not FGFR3 and FGFR4, localize to primary cilia of the developing mouse tissues and in vitro cells. For FGFR2, we demonstrate that the ciliary residence is necessary for its signaling and expression of target morphogenic genes. We also show that the pathogenic FGFR2 variants have minimal cilium presence, which can be rescued for the p.P253R variant associated with the Apert syndrome by using the RLY-4008 kinase inhibitor. Finally, we determine the molecular regulators of FGFR2 trafficking to cilia, including IFT144, BBS1, and the conserved T⁴²⁹V⁴³⁰ motif within FGFR2.

Fibroblast growth factors (FGFs) control organ morphogenesis during development as well as tissue homeostasis and repair in the adult organism. Despite their importance, many mechanisms that regulate FGF function are still poorly understood. Interestingly, the thermodynamic stability of 22 mammalian FGFs varies widely, with some FGFs remaining stable at body temperature for more than 24 h, while others lose their activity within minutes. How thermodynamic stability contributes to the function of FGFs during development remains unknown. Here we show that FGF10, an important limb and lung morphogen, exists as an intrinsically unstable protein that is prone to unfolding and is rapidly inactivated at 37 °C. Using rationally driven directed mutagenesis, we have developed several highly stable (STAB) FGF10 variants with a melting temperature of over 19 °C more than that of wildtype FGF10. In cellular assays in vitro, the FGF10-STABs did not differ from wildtype FGF10 in terms of binding to FGF receptors, activation of downstream FGF receptor signaling in cells, and induction of gene expression. In mouse embryonal lung explants, FGF10-STABs, but not wildtype FGF10, suppressed branching, resulting in increased alveolarization and expansion of epithelial tissue. Similarly, FGF10-STAB1, but not FGF10 wildtype, inhibited the growth of mouse embryonic tibias and markedly altered limb morphogenesis when implanted into chicken limb buds, collectively demonstrating that thermal instability should be considered an important regulator of FGF function that prevents ectopic signaling. Furthermore, we show enhanced differentiation of human iPSC-derived lung organoids and improved regeneration in ex vivo lung injury models mediated by FGF10-STABs, suggesting an application in cell therapy.

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, the Prdm9 gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have two Prdm9 alleles, WDS harbour 46 different alleles. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 10 and 14 out of 16 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary and biomedical studies with great potential for medical applications. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-025-86505-x.

In late stages of inherited and acquired retinal diseases such as Stargardt disease (STGD) or dry age‐related macular degeneration (AMD), loss of retinal pigment epithelia (RPE) cells and subsequently photoreceptors in the macular area result in a dramatic decline of central visual function. Repopulating this area with functional RPE cells may prevent or decline the progression of photoreceptor loss. In the present study, the viability, survival, and integration of human induced pluripotent stem cell (hiPSC)‐derived RPE cells (hiPSC‐RPE) is assessed generated using clinical‐grade protocol and cultured on a clinically relevant scaffold (poly‐L‐lactide‐co‐D, L‐lactide, PDLLA) after subretinal implantation in immunosuppressed minipigs for up to 6 weeks. It is shown that transplanted hiPSC‐RPE cells maintain the RPE cell features such as cell polarity, hexagonal shape, and cell–cell contacts, and interact closely with photoreceptor outer segments without signs of gliosis or neuroinflammation throughout the entire period of examination. In addition, an efficient immunosuppressing strategy with a continuous supply of tacrolimus is applied. Continuous verification and improvement of existing protocols are crucial for its translation to the clinic. The results support the use of hiPSC‐RPE on PDLLA scaffold as a cell replacement therapeutic approach for RPE degenerative diseases.

The ABCB1 gene, encoding the ATP-dependent translocase ABCB1, plays a crucial role in the clearance of amyloid-beta (Aβ) peptides and the transport of cholesterol, implicating it in the pathogenesis of Alzheimer's disease. The study aims to investigate the association between polymorphisms in the ABCB1 gene and cognitive decline in individuals with MCI, particularly focusing on language function. A longitudinal cohort study involving 1005 participants from the Czech Brain Aging Study was conducted. Participants included individuals with Alzheimer's disease, amnestic mild cognitive impairment (MCI), non-amnestic MCI, subjective cognitive decline, and healthy controls. Next-generation sequencing was utilized to analyze the entire ABCB1 gene. Cognitive performance was assessed using a comprehensive battery of neuropsychological tests, including the Boston Naming Test and the semantic verbal fluency test. Ten ABCB1 polymorphisms (rs55912869, rs56243536, rs10225473, rs10274587, rs2235040, rs12720067, rs12334183, rs10260862, rs201620488, rs28718458) were significantly associated with cognitive performance, particularly in language decline among amnestic MCI patients. In silico analyses revealed that some of these polymorphisms may affect the binding sites for transcription factors (HNF-3alpha, C/EBPβ, GR-alpha) and the generation of novel exonic splicing enhancers. Additionally, polymorphism rs55912869 was identified as a potential binding site for the microRNA hsa-mir-3163. Our findings highlight the significant role of ABCB1 polymorphisms in cognitive decline, particularly in language function, among individuals with amnestic MCI. These polymorphisms may influence gene expression and function through interactions with miRNAs, transcription factors, and alternative splicing mechanisms.

Porcupine (PORCN) is a membrane-bound protein of the endoplasmic reticulum, which modifies Wnt proteins by adding palmitoleic acid. This modification is essential for Wnt ligand secretion. Patients with mutated PORCN display various skeletal abnormalities likely stemming from disrupted Wnt signaling pathways during the chondrocyte differentiation. To uncover the mechanism of PORCN action during chondrogenesis, we used two different PORCN inhibitors, C59 and LGK974, in several model systems, including micromasses, 3D cell cultures, long bone tissue cultures and zebrafish animal model. PORCN inhibitors enhanced cartilaginous extracellular matrix (ECM) production and accelerated chondrocyte differentiation, which resulted in the earlier induction of cellular hypertrophy as well as cartilaginous mass expansion in micromass cultures and cartilaginous organoids. In addition, both PORCN inhibitors expanded the hypertrophic zone and reduced the proliferative zone in the growth plate. This led to a significant increase in cartilaginous tissue and ultimately resulted in the elongation of tibias in the mouse organ cultures. Also, LGK974 treatment of Danio rerio embryos induced expansion of craniofacial cartilage width together with the shortening of the body axis, which was consistent with a phenomenon occurring upon inhibition of non-canonical Wnt signaling. By combining PORCN inhibition with exogenous Wnt proteins activating either canonical/β-catenin (WNT3a) or non-canonical (WNT5a) signaling, we propose that the key mechanism mediating pro-chondrogenic effects of PORCN inhibition is the removal of canonical ligands that prevent chondrocyte differentiation. In summary, our results provide evidence of the distinct role of PORCN in both the early and late stages of cartilage development. Further, our data demonstrate that PORCN inhibitors can be used in the experimental and clinical strategies that need to trigger chondrocyte differentiation and/or cartilage outgrowth.

Oral squamous cell carcinoma (OSCC), a subset of head and neck cancers, primarily originates in the epithelial tissues of the oral cavity. Despite advancements in treatment, the mortality rate for OSCC remains around 50%, underscoring the urgent need for improved prognostic markers. This review explores the role of the BRCA1 and BRCA2 genes—traditionally associated with breast and ovarian cancers—in the context of OSCC. We discuss the molecular pathways involving BRCA genes, their potential as diagnostics and prognostic biomarkers, and their implications for personalized treatment strategies, including addressing chemotherapy resistance. Furthermore, this review emphasizes the significance of genome stability in cancer progression and examines both current and emerging methodologies for detecting BRCA mutations in OSCC patients. Despite limited prevalence of BRCA mutations in OSCC compared to other cancers, their role in DNA repair and therapeutic response underscores their potential as clinical biomarkers. However, standardized, multicenter studies are still needed to validate their utility in OSCC management. A better understanding of the role of BRCA genes in OSCC could pave the way for more effective therapeutic approaches and improved patient outcomes.

Regrettably, in November 2024 we received the sad news of the sudden passing of Prof. Petr Rab, a pioneering researcher in the field of fish cytogenetics. His contributions to the field of cytogenetics, particularly on freshwater fish cytogenetics, are unparalleled. This obituary was written with heartbreaking sadness and immense admiration for his kindness, distinctive humor, and wisdom that inspired and united those around him.

The food supplements gain an attractivity among consumers due to their pronounced health benefits. There is no legal frame for probiotic food supplements and the only controllable aspect is the agreement of the declaration with the real composition. The culture methods and subsequent identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) suffer from many inconsistencies like a different growing rate of each microorganism to their close DNA relatedness and similar profile undistinguishable by MALDI-TOF MS. Despite their inability to assess viability, qPCR methods have become more popular due to their sensitivity, specificity and speed. This paper reports about 29 originally designed qPCR assays for the detection of the probiotic species present in food supplements. Moreover, an innovative procedure for the quantification of components in supplements without necessity to run calibration curve was introduced and validated. The whole process was tested on 35 commercially available food supplements. More than half of them did not meet the declaration of the manufacturer. It was also found out that the qPCR was too sensitive as it detected low numbers of non-declared species in all analyzed samples. Therefore, a cut-off value of Cq > 30 had to be applied. The quantification of the individual probiotic species by qPCR showed a good agreement with the declaration of the manufacturers. The same was true for the total number of microorganisms with two exceptions. The developed qPCR assays provide a very simple and inexpensive tool for the detection and quantification of probiotic species in food supplements.

Background Java combtail fish Belontia hasselti (Cuvier, 1831), a member of the Osphronemidae family, inhabits lakes and rivers throughout Southeast Asia and Sri Lanka. Previous cytogenetic research revealed it possesses a diploid chromosome number of 48 chromosomes with a female-heterogametic ZZ/ZW sex chromosome system, where the W chromosome is distinguishable as the only metacentric element in the complement. Female-heterogametic sex chromosome systems seem to be otherwise surprisingly rare in the highly diverse order Perciformes and, therefore, B. hasselti provides an important comparative model to evolutionary studies in this teleost lineage. To examine the level of sex chromosome differentiation in B. hasselti and the contribution of repetitive DNAs to this process we combined bioinformatic analyses with chromosomal mapping of selected repetitive DNA classes, and comparative genomic hybridization. Results By providing the first satellitome study in Perciformes, we herein identified 13 satellite DNA monomers in B. hasselti , suggesting a very low diversity of satDNA in this fish species. Using fluorescence in situ hybridization, we revealed detectable clusters on chromosomes only for four satellite DNA monomers. Together with the two mapped microsatellite motifs, the repeats primarily accumulated on autosomes, with no distinct clusters located on the sex chromosomes. Comparative genomic hybridization showed no region with accumulated female-specific or enriched repeats on the W chromosome. Telomeric repeats terminated all chromosomes, and no additional interstitial sites were detected. Conclusion These data collectively indicate a low degree of sex chromosome differentiation in B. hasselti despite their considerable heteromorphy. Possible mechanisms that may underlie this pattern are discussed.

The effect of the dietary inclusion of Hermetia illucens larvae meal on the diversity of the methanogenic archaea in the caecum of laying hens (Hy-line Brown) was investigated using molecular methods. A total of 27 hens, selected equally for slaughter from 162 birds which were divided equally into 3 treatment groups including control group C with a diet containing corn-soybean meal and 2 experimental groups, HI25 and HI50, in which 25% and 50% of the soybean meal protein was replaced by the protein from a Hermetia illucens larvae meal, respectively. At 40 weeks of age, the methanogenic community of caecal content of 9 hens per group was analyzed using a 16S rRNA gene clone library. A total of 108 positive clones, 35 from the control group, 44 from the HI25 group and 29 from the HI50 group, were analyzed by Sanger sequencing. Methanomicrobiales, Methanobacteriales and Methanomassiliicoccales were the main orders found in groups C and HI25. Methanomassiliicoccales was absent in the HI50 group, which was dominated by the order Methanobacteriales. At the species level, Methanobrevibacter woesei was the most prevalent species in all three groups regardless of diet. Some species were found exclusively either in the control group (Methanogenic archaeon CH1270) or in the HI25 group (Methanorbis furvi strain Ag1). Methanogenic diversity was significantly lower in the HI50 group compared to the control and HI25 groups and Methanomassiliicoccaceae archaeon DOK was completely suppressed in HI50 group. Our preliminary results indicate that ingestion of Hermetia illucens larvae meal has considerable effect on the methanogenic community, promoting the abundance of Methanobrevibacter woesei and suppressing Methanomassiliicoccaceae archaeon DOK in the caeca of laying hens.