In the present study, we examined the influence of the dietary inclusion of black soldier fly (BSF) larvae meal on the diversity and composition of the bacterial community in the caecum of Barbary partridges (Alectoris barbara). A total of 54 partridges were divided equally into three treatment groups. The control group (C) received a diet containing corn-soybean meals and the two experimental groups received diets in which soybean meal protein was partially substituted with BSF larvae meal at proportions of 25% (H25) and 50% (H50). The bacterial community of the caecal samples was analysed in 30 slaughtered animals (10 per group) at 64 days of age. High-throughput sequencing targeting the V4-V5 region of the 16 S rRNA gene was used. Firmicutes were the most abundant phylum in all studied categories. This phylum was dominated by the families Ruminococcaceae and Lachnospiraceae. The caecal microbiota was significantly altered at the genus level. The linear discriminant analysis effect size (LefSe) analysis for the differential taxa abundance revealed several significant dissimilarities between the control group (C) and the groups with 25% and 50% insect meal replacement, with 13 and 20 taxa with significantly different abundances, respectively. Several of these taxa are associated with gut health, fiber fermentation, and metabolic functions, indicating a biological importance of the observed microbial shifts. Compared with the control group, the partridges fed 25% BSF larvae meal had a significantly higher bacterial phylogenetic abundance and richness, which may contribute to improved gut health and a more stable microbial environment. The beta diversity measures revealed that all three groups of animals were significantly spatially separated. The results demonstrated the significant impact of black soldier fly larvae meal on the caecal microbiota of Barbary partridges. The positive influence of the insect meal used was indicated by increased bacterial diversity in the H25 group and increased relative abundance of several potentially beneficial genera in both experimental groups.

• Klíčová slova
• Barbary partridges, Black soldier fly, Gut microbiota, Insect,
• MeSH
• Bacteria genetika   klasifikace   MeSH
• biodiverzita MeSH
• cékum * mikrobiologie   MeSH
• dieta * MeSH
• Diptera * MeSH
• Galliformes * mikrobiologie   MeSH
• krmivo pro zvířata * MeSH
• larva MeSH
• RNA ribozomální 16S genetika   MeSH
• střevní mikroflóra * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

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.

• Klíčová slova
• Antibiotics, Beta-lactam, Bolus, Continuous, Diabetes, Diabetic foot infection, Diabetic foot ulcers, Gut microbiota,
• MeSH
• antibakteriální látky * aplikace a dávkování   terapeutické užití   MeSH
• Bacteria klasifikace   genetika   účinky léků   izolace a purifikace   MeSH
• ceftazidim aplikace a dávkování   terapeutické užití   MeSH
• diabetická noha * farmakoterapie   mikrobiologie   MeSH
• dysbióza mikrobiologie   MeSH
• feces mikrobiologie   MeSH
• kombinace amoxicilinu a kyseliny klavulanové aplikace a dávkování   MeSH
• lidé středního věku MeSH
• lidé MeSH
• RNA ribozomální 16S genetika   MeSH
• senioři MeSH
• střevní mikroflóra * účinky léků   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antibakteriální látky * MeSH
• ceftazidim MeSH
• kombinace amoxicilinu a kyseliny klavulanové MeSH
• RNA ribozomální 16S MeSH

DNA metabarcoding provides a scalable alternative to traditional botanical surveys, which are often time-consuming and reliant on taxonomic expertise. Here, we compare DNA metabarcoding with quadrat-based botanical surveys to assess plant species composition in experimental grassland plots under four defoliation regimes (continuous grazing, rotational grazing, frequent cutting and conservation cutting). Botanical surveys identified 16 taxa, while metabarcoding detected 25 taxa, including the dominant species Holcus lanatus and Lolium perenne. Despite detecting more taxa, there were some discrepancies in identification, with the sequence data only able to resolve some taxa at the genus level (e.g., Agrostis spp. instead of Agrostis capillaris) and potential species misidentifications (e.g., Cardaminopsis helleri vs. Cardamine flexuosa). However, both methods provided comparable results and revealed statistically significant differences in species composition between treatments, with higher diversity in cut versus grazed plots. The semi-quantitative nature of metabarcoding limits its capacity to accurately reflect species abundance, posing challenges for ecological interpretations where precise quantification is required. However, it provides a broader view of biodiversity and can complement traditional methods, offering new opportunities for efficient biodiversity monitoring. The findings support the integration of DNA metabarcoding into biodiversity assessments, particularly when used alongside traditional techniques. Further refinement of bioinformatics tools and reference databases will enhance their accuracy and reliability, enabling more effective monitoring of grassland biodiversity and sustainable management practices. This study highlights DNA metabarcoding as a valuable tool for understanding plant community responses to management interventions.

• Klíčová slova
• DNA metabarcoding, botanical survey, ecological monitoring, grassland biodiversity, species composition,
• Publikační typ
• časopisecké články MeSH

Developing microbiome-based markers for pediatric inflammatory bowel disease (PIBD) is challenging. Here, we evaluated the diagnostic and prognostic potential of the gut microbiome in PIBD through a case-control study and cross-cohort analyses. In a Korean PIBD cohort (24 patients with PIBD, 43 controls), we observed that microbial diversity and composition shifted in patients with active PIBD versus controls and recovered at remission. We employed a differential abundance meta-analysis approach to identify microbial markers consistently associated with active inflammation and remission across seven PIBD cohorts from six countries (n = 1,670) including our dataset. Finally, we trained and tested various machine learning models for their ability to predict a patient's future remission based on baseline bacterial composition. An ensemble model trained with the amplicon sequence variants effectively predicted future remission of PIBD. This research highlights the gut microbiome's potential to guide precision therapy for PIBD.

• Klíčová slova
• Gastroenterology, Microbiome,
• Publikační typ
• časopisecké články MeSH

RATIONALE: Severe alcohol-associated hepatitis (SAH) is the most critical, acute, inflammatory phenotype within the alcohol-associated liver disease (ALD) spectrum, characterized by high 30- and 90-day mortality. Since several decades, corticosteroids (CS) are the only approved pharmacotherapy offering highly limited survival benefits. Contextually, there is an evident demand for 3PM innovation in the area meeting patients' needs and improving individual outcomes. Fecal microbiota transplantation (FMT) has emerged as one of the new potential therapeutic options. In this study, we aimed to address the crucial 3PM domains in order to assess (i) the impact of FMT on mortality in SAH patients beyond CS, (ii) to identify factors associated with the outcome to be improved (iii) the prediction of futility, (iv) prevention of suboptimal individual outcomes linked to increased mortality, and (v) personalized allocation of therapy. METHODS: We conducted a prospective study (NCT04758806) in adult patients with SAH who were non-responders (NR) to or non-eligible (NE) for CS between January 2018 and August 2022. The intervention consisted of five 100 ml of FMT, prepared from 30 g stool from an unrelated healthy donor and frozen at - 80 °C, administered daily to the upper gastrointestinal (GI) tract. We evaluated the impact of FMT on 30- and 90-day mortality which we compared to the control group selected by the propensity score matching and treated by the standard of care; the control group was derived from the RH7 registry of patients hospitalized at the liver unit (NCT04767945). We have also scrutinized the FMT outcome against established and potential prognostic factors for SAH - such as the model for end-stage liver disease (MELD), Maddrey Discriminant Function (MDF), acute-on-chronic liver failure (ACLF), Liver Frailty Index (LFI), hepatic venous-portal pressure gradient (HVPG) and Alcoholic Hepatitis Histologic Score (AHHS) - to see if the 3PM method assigns them a new dimension in predicting response to therapy, prevention of suboptimal individual outcomes, and personalized patient management. RESULTS: We enrolled 44 patients with SAH (NR or NE) on an intention-to-treat basis; we analyzed 33 patients per protocol for associated factors (after an additional 11 being excluded for receiving less than 5 doses of FMT), and 31 patients by propensity score matching for corresponding individual outcomes, respectively. The mean age was 49.6 years, 11 patients (33.3%) were females. The median MELD score was 29, and ACLF of any degree had 27 patients (81.8%). FMT improved 30-day mortality (p = 0.0204) and non-significantly improved 90-day mortality (p = 0.4386). Univariate analysis identified MELD ≥ 30, MDF ≥ 90, and ACLF grade > 1 as significant predictors of 30-day mortality, (p = 0.031; p = 0.014; p = 0.034). Survival was not associated with baseline LFI, HVPG, or AHHS. CONCLUSIONS AND RECOMMENDATIONS IN THE FRAMEWORK OF 3PM: In the most difficult-to-treat sub-cohort of patients with SAH (i.e., NR/NE), FMT improved 30-day mortality. Factors associated with benefit included MELD ≤ 30, MDF ≤ 90, and ACLF < 2. These results support the potential of gut microbiome as a therapeutic target in the context of 3PM research and vice versa - to use 3PM methodology as the expedient unifying template for microbiome research. The results allow for immediate impact on the innovative concepts of (i) personalized phenotyping and stratification of the disease for the clinical research and practice, (ii) multilevel predictive diagnosis related to personalized/precise treatment allocation including evidence-based (ii) prevention of futile and sub-optimally effective therapy, as well as (iii) targeted prevention of poor individual outcomes in patients with SAH. Moreover, our results add to the existing evidence with the potential to generate new research along the SAH's pathogenetic pathways such as diverse individual susceptibility to alcohol toxicity, host-specific mitochondrial function and systemic inflammation, and the role of gut dysbiosis thereof. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-024-00381-5.

• Klíčová slova
• Alcohol toxicity, Cost-efficacy, Dysbiosis, Fecal microbiota transplantation, Gut microbiota, Health policy, Individualized patient profile, Mitochondrial health, Multi-level diagnostics, Patient stratification, Phenotyping, Predictive preventive personalized medicine (PPPM / 3PM), Severe alcohol-associated hepatitis, Survival, Systemic inflammation, Tailored therapy,
• Publikační typ
• časopisecké články MeSH

In this study, we investigated the influence of the inclusion of Tenebrio molitor (TM) larvae meal in the diet on the diversity and structure of the bacterial community in the caecal content of Barbary partridges. A total of 36 partridges, selected randomly for slaughter from 54 animals, were divided equally into three treatment groups, including the control group (C) with a diet containing corn-soybean meal and two experimental groups, in which 25% (TM25) and 50% (TM50) of the soybean meal protein was replaced by the meal from TM larvae. After slaughtering, the bacterial community of the 30 caecal samples (10 samples per each experimental group) was analysed by high-throughput sequencing using the V4-V5 region of the 16 S rRNA gene. Alpha diversity showed a higher diversity richness in the TM50 group. Beta diversity showed statistical dissimilarities among the three groups. Firmicutes was the dominant phylum regardless of the diet, with the predominant families Ruminococcaceae and Lachnospiraceae. Clostridia and Faecalibacterium were decreased in both TM groups, Lachnospiraceae was suppressed in the TM50 group, but still this class, genus and family were abundantly present in all samples. Several potentially beneficial genera, such as Bacillus, Ruminococcaceae UCG-009, Oscillibacter and UC1-2E3 (Lachnospiraceae) were increased in the TM50 group. The results showed a beneficial effect of the T. molitor larvae meal on the caecal microbiota of Barbary partridges, particularly in the TM50 group, which showed an increase in bacterial diversity.

• Klíčová slova
• Tenebrio molitor larvae meal, Caecal microbiota, Partridges,
• MeSH
• Bacteria klasifikace   genetika   izolace a purifikace   MeSH
• biodiverzita MeSH
• cékum * mikrobiologie   MeSH
• dieta MeSH
• Galliformes mikrobiologie   MeSH
• krmivo pro zvířata * MeSH
• larva * mikrobiologie   MeSH
• RNA ribozomální 16S genetika   MeSH
• střevní mikroflóra * MeSH
• Tenebrio * mikrobiologie   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

BACKGROUND: Climate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players," enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment. RESULTS: Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR. CONCLUSION: Our study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.

• Klíčová slova
• Ips acuminatus, Ips sexdentatus, amplicon sequence variances (ASVs), core bacteriome, holobiont, microhabitat,
• Publikační typ
• časopisecké články MeSH

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations.

• Klíčová slova
• FUNGuild, Norway spruce, PICRUSt2, amplicon sequencing, microbial communities, network analysis, precipitation, rhizosphere, seed orchards, soil metabolites,
• MeSH
• Bacteria genetika   klasifikace   metabolismus   MeSH
• déšť MeSH
• klimatické změny MeSH
• mikrobiota * genetika   MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• rhizosféra * MeSH
• semena rostlinná růst a vývoj   mikrobiologie   MeSH
• smrk * mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• půda MeSH

Assessments of biodiversity and ecosystem status can benefit from DNA metabarcoding as a means to streamline sample processing and specimen identification. Moreover, processing the fixation medium instead of the precious material introduces straightforward protocols that allow subsequent focus on certain organisms detected among the preserved specimens. In this study, we present a proof of concept via the analysis of freshwater invertebrate samples from the Tatra Mountain lakes (Slovakia). Besides highlighting a match between the lake-specific environmental conditions and the results of our fixative DNA metabarcoding, we observed an option to fine-tune the fixation time: to prefer two weeks over a day or a month. This effect emerged from the presence/absence of individual taxa rather than from coarse per-sample records of taxonomic richness, demonstrating that metabarcoding studies-and efforts to optimize their protocols-can use the robust metrics to explore even subtle trends. We also provide evidence that fixative DNA might better capture large freshwater species than terrestrial or meiofauna.

• MeSH
• bezobratlí genetika   klasifikace   MeSH
• biodiverzita * MeSH
• DNA genetika   izolace a purifikace   analýza   MeSH
• ekosystém MeSH
• jezera * MeSH
• taxonomické DNA čárové kódování * metody   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA MeSH

Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.

• Klíčová slova
• abiotic factors, freshwater environments, prokaryotes, protists, stratification, temporal dynamics,
• MeSH
• Bacteria * genetika   klasifikace   MeSH
• biodiverzita MeSH
• časoprostorová analýza MeSH
• ekosystém MeSH
• Eukaryota * genetika   klasifikace   MeSH
• jezera * mikrobiologie   MeSH
• mikrobiota * MeSH
• roční období MeSH
• strojové učení * MeSH
• taxonomické DNA čárové kódování * MeSH
• teplota MeSH
• Publikační typ
• časopisecké články MeSH