16S rRNA Research Articles

Nano-Archives in Soils—What Microbial DNA Molecules Can Report About the History of Places

DNA encoding the 16S rRNA of bacteria is a type of nanometer-sized information storage that can be used to characterize bacterial communities in soils. Reading this molecular ’nano-archive’ is not only of interest for characterizing recent local ecological conditions but can also provide valuable information about human impacts on soils in the past. This is of great interest for archaeology and for understanding the ecological consequences of past human activities on recent ecological conditions. Powerful sequencing methods such as the Illumina process allow many different DNA sequences to be determined in parallel and provide very efficient data sets that reflect the composition of soil bacterial communities in topsoil layers as well as in translocated and covered soils of archaeological sites such as settlements, burials or workplaces. Here, a brief overview of recent developments in the use of these molecular nano-archives for the study of archaeological soil samples is given using typical examples.

Isolation and Identification of Hydrocarbon-Degrading Bacteria from Diesel-Contaminated Soils

Aim: To Isolate, screen and identify bacterial species with hydrocarbon biodegradative potentials from diesel-polluted soils using redox indicator (2% v/v of 2,6 – dichlorophenol indophenols- DCPIP) and Turbidity measurements. Place and Duration of Study: Microbiology laboratory in the Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, Effurun, between 2022 and 2024. Methodology: Soil samples from diesel-contaminated site were collected from diesel mechanic workshop, analysed using the spread plate isolation technique on Bushnell Haas mineral salt agar selective medium, were screened for Bacterial species with hydrocarbon degradative potential using the redox indicator (2% v/v of 2,6 – dichlorophenol indophenols- DCPIP) and Turbidity measurement. Selected Bacterial isolates were used for the hydrocarbon degradation studies, were characterized based on biochemical tests and identified with the aid of the Biolog database and 16S rRNA gene sequencing techniques. Results: Eight diesel degrading Bacteria species were identified, belonging to the following genera; Acinetobacter, Klebsiella, and Pseudomonas. Among these, the four most potent degraders were identified as Acinetobacter rudis (M2712942.1), Acinetobacter bereziniae (MT111619.1), Pseudomonas koreensis (MW794239.1), and Klebsiella aerogenes (CP070520.1) and the % diesel reduction achieved in 15 days were; 70%, 48%, 47% and 45%, while the % Turbidity increase were 84%, 79%, 78% and 76% respectively. Consequently, the partial 16S rRNA gene sequences revealed the two most potent diesel degrading bacterial strains were Acinetobacter rudis and Acinetobacter bereziniae with 70% and and 48% respectively. Conclusion: These findings demonstrate the potential of indigenous bacteria for effective bioremediation of petroleum-contaminated environments. The study provides critical insights into sustainable solutions for mitigating hydrocarbon pollution, contributing to advancements in environmental microbiology and ecosystem restoration.

Gut Microbiome as a Potential Marker of Hematologic Recovery Following Induction Therapy in Acute Myeloid Leukemia Patients.

The management of acute myeloid leukemia (AML) is hindered by treatment-related toxicities and complications, particularly cytopenia, which remains a leading cause of mortality. Given the pivotal role of the gut microbiota (GM) in hemopoiesis and immune regulation, we investigated its impact on hematologic recovery during AML induction therapy. We profiled the GM of 27 newly diagnosed adult AML patients using 16S rRNA amplicon sequencing and correlated it with key clinical parameters before and after induction therapy. Our investigation revealed intriguing associations between the GM composition and crucial recovery indicators, including platelet, lymphocyte, and neutrophil counts, and identified early GM signatures predictive of improved hematologic recovery. Remarkably, patients demonstrating superior recovery had higher alpha diversity and enrichment in health-associated taxa belonging to the genera Faecalibacterium, Ruminococcus, Blautia, and Butyricimonas at diagnosis. Despite certain study limitations, our findings suggest that evaluating GM features could serve as a potential marker for hematologic recovery. This preliminary work opens avenues for personalized risk assessment and interventions, possibly involving GM modulation tools, to optimize recovery in AML patients undergoing induction therapy and potentially enhancing overall outcomes in individuals with hematologic diseases.

Genome drafting of nosocomial infection CRE Klebsiella pneumoniae confirming resistance to colistin and eravacycline, carrying blaNDM-1, mcr-1, and blaKPC-2, in neonatology from November to December 2023

BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study was to characterize the phenotypic and genomic profiles of the CRKP isolates involved in the outbreak and to gain insights into their resistance mechanisms and transmission dynamics within the NICU.MethodsThe study was conducted between November and December 2023 in a 5-bed NICU. Monthly surveillance cultures were performed to monitor colonization and infection with multidrug-resistant organisms. CRKP isolates were obtained from blood and nasal swabs of affected neonates. Identification and antimicrobial susceptibility testing were initially conducted using the Vitek®2 system with an N-395 card and further confirmed by 16S rRNA sequencing. Whole-genome sequencing (WGS) and antimicrobial resistance (AMR) profiling were performed to identify resistance genes and virulence factors. For genetic analysis, both Illumina short-read and Nanopore long-read sequencing were used, followed by hybrid assembly for enhanced genome resolution. Plasmid and resistance gene profiles were determined using AMRFinder and PlasmidFinder databases.ResultsA total of three CRKP isolates (designated Kp1, Kp2, and Kp3) were identified. Kp1 and Kp2 belonged to sequence type (ST) ST23 and were genetically near-identical, differing by a single allele, while Kp3 was of a distinct sequence type, ST2096, with 245 allelic differences from Kp1 and Kp2. All isolates were resistant to colistin and carried resistance genes, including mcr-1 and blaNDM-1,blaKPC2 confirming carbapenem resistance. Efflux pump genes and aminoglycoside resistance genes were also detected, providing a multifaceted defence against antibiotics. Plasmid analysis identified several incompatibility groups (IncFI, IncHI, IncFIB, IncX), indicating the potential for horizontal gene transfer of resistance determinants.ConclusionThis study highlights the complexity of CRKP outbreaks in neonatal care, with isolates exhibiting resistance mechanisms that complicate treatment. The plasmid profiles suggest these strains are reservoirs for multidrug-resistant genes, emphasizing the need for strict infection control and ongoing genomic surveillance. For neonatal care, these resistance challenges increase the risk of treatment failures and mortality, underscoring the importance of enhanced infection prevention and novel therapeutic strategies.

Propidium Monoazide is Unreliable for Quantitative Live-Dead Molecular Assays.

Propidium monoazide (PMA) is a dye that distinguishes between live and dead cells in molecular assays like the Polymerase Chain Reaction (PCR). It works by cross-linking to the DNA of cells that have compromised membranes or extracellular DNA upon photoactivation, making the DNA inaccessible for amplification. Currently, PMA is used to detect viable pathogens and alleviate systemic bias in the microbiome analysis of samples using 16S rRNA gene sequencing. In these applications, treated samples consist of different amounts of dead bacteria and a range of bacterial strains, variables that can affect the performance of PMA and lead to inconsistent findings across various research studies. To evaluate the effectiveness of PMA, we used a sensitive qPCR assay and post-treatment sample concentration to determine PMA cross-linkage and activity accurately under varying sample conditions. We report that PMA is unreliable for viability assays when the concentration and composition of the bacterial mixtures are unknown. PMA is suitable only for qualitatively assessing viability in samples containing a known number of dead microbes or extracellular DNA.

Distinct Ocular Surface Microbiome in Keratoconus Patients Correlate With Local Immune Dysregulation.

Keratoconus (KC) is characterized by irregular astigmatism along with corneal stromal weakness and is associated with altered immune status. Tissue resident microbiomes are known to influence the immune status in other organs, but such a nexus has not been described in ocular conditions. Therefore, we examined the ocular surface microbiome of patients with KC and correlated it to the immune cell and tear molecular factor profiles. Sixty-two patients with KC and 21 healthy controls underwent corneal topography analysis and eye examination followed by a collection of Schirmer's strip, ocular surface wash, and ocular surface swabs. Microbiomes were analyzed by extracting DNA from the swabs followed by 16S rRNA gene V3-V4 amplicon sequencing and analyzed using QIIME. Fifty-two molecular factors from Schirmer's strip tear extracts and 11 immune cells from ocular wash were measured using multiplex ELISA and flow cytometry. Alpha diversity, linear discriminant analysis effect size (LEfSe), relative abundance and receiver operating characteristic - area under the curve (ROC-AUC) analysis were performed. Unsupervised clustering at the genus level with clinical parameters, soluble factors, and immune cells was performed. Fifty-two phyla/class, 132 order, 283 family, and 718 genera were identified in our cohort. Alpha diversity indices were comparable between patients with KC and the healthy controls. Dominant phyla across groups were Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Alphaproteobacteria increased in KC eyes whereas Actinobacteria, Firmicutes_Bacilli reduced compared with the healthy controls. We found a significant positive correlation of Microbacterium, Cutibacterium, and Brevundimonas genera abundance with keratometry and corneal thickness. Levels of IL-21, IL-9, Fractalkine, and VEGF positively correlated with Tetrasphaera (P < 0.05). β2-microglobulin and CD66bhigh cells correlated with Bacteroides (P < 0.05). CD45+ cells correlated with Escherichia_Shigella (P < 0.02). We discovered a unique microbiome signature of KC which correlated to disease grades and secreted molecular factors and immune cells. Therefore, the altered microbiome on the ocular surface may drive immune dysregulation in KC and provide scope for potential interventions in the future.

Genomic and phenotypic characterisation of Leeuwenhoekiella obamensis sp. nov., a novel marine bacterium isolated from the surface water of a Japanese fishing port.

A novel aerobic marine bacterium, FRT2T, isolated from surface water of a fishing port in Fukui, Japan, was characterised based on phylogenomic and phylogenetic analyses combined with classical phenotypic and chemotaxonomic characterisations. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FRT2T clustered with genus Leeuwenhoekiella. Closest relatives of FRT2T were Leeuwenhoekiella palythoae KMM 6264T and Leeuwenhoekiella nanhaiensis G18T with 16S rRNA gene sequence identities of 95.1% and 94.5%, respectively, suggesting that FRT2T is a novel species of genus Leeuwenhoekiella. Phylogenetic analysis of 81 bacterial core gene sequences also placed FRT2T in a highly supported lineage distinct from described Leeuwenhoekiella species. Values of digital DNA-DNA hybridisation and average nucleotide identity between FRT2T and type strains of species of genus Leeuwenhoekiella indicate that FRT2T is a novel species of the genus Leeuwenhoekiella. Cells were Gram-stain-negative rods with 0.3-0.8µm width and 1.6-4.1µm length. The bacterium was strictly aerobic, produced yellow-orange-pigments and showed gliding motility. Na+ was needed to grow FRT2T with optimal growth in the presence of 3.0-4.0% (w/v) NaCl. Growth pH and temperature ranges were 5.5-8.5 (optimum pH 6.5-7.5) and 10-39°C (optimum 25-35°C), respectively. Major cellular fatty acids were iso-C15:0, iso-C15:1, iso-C17:0 3-OH and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The only respiratory quinone was MK-6. Genomic G + C content of FRT2T was 38.9%. FRT2T represents a novel species, for which the name Leeuwenhoekiella obamensis sp. nov. is proposed, with type strain FRT2T (= BCRC 81451T = DSM 118489T = JCM 36940T).

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition

Background: In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing’s specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study. Methods: Fourteen participants followed one of three diets—exclusive juice, juice plus food, or plant-based food—for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition. Results: The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p &lt; 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance. Conclusions: These findings suggest that short-term juice consumption may negatively affect the microbiota.

Fecal microbiota is more stable during degradation and more diverse for ex situ cheetahs in Namibia compared to the USA

The relationships between gut microbiota and animal health are an important consideration increasingly influential in the management of wild and ex situ endangered species, such as the cheetah (Acinonyx jubatus). To better understand these relationships, fresh fecal samples are currently required as a non-invasive alternative for the gut microbiome. Unfortunately, fresh samples are challenging to collect in the wild. This study had two aims: 1) to determine the optimal collection time point for cheetah feces after deposit in their native environment of Namibia as a guide for wild cheetah fecal microbiome studies; and 2) to compare the fecal microbiota of two ex situ cheetah populations (Front Royal, VA, USA and Otjiwarongo, Namibia), which also consume different diets. We collected eight fresh fecal samples from cheetahs in Namibia and allowed them to decompose for four days, taking subsamples each day. The fresh Namibian samples (n = 8) were also used in objective two for comparison to fresh USA cheetah samples (n = 8). All samples were analyzed for bacterial community diversity and composition using 16S rRNA gene amplicon sequencing. First, over a five-day sampling period in Namibia, subsamples 1-3 days post-fresh showed no changes in bacterial diversity or composition compared to fresh subsamples. Second, fresh ex situ cheetah samples under Namibian conditions had increased bacterial taxa, more phylogenetically diverse bacterial communities, and compositionally distinct microbiomes from cheetahs managed in human care in the USA. However, when bacterial ASVs were weighted by relative abundance, both populations shared 69% of their total bacterial sequences indicating a conserved cheetah microbiota between the two populations. We also found few differences in predictive functions of the fecal microbiota between the populations, where only one disease-related pathway was higher in the USA samples. Overall, our findings suggest that in dry season conditions (no recorded rainfall) in Namibia, fecals may be usable for up to three days after defecation for microbial ecology studies. There are significant differences between ex situ Namibian and USA populations, and we suggest further investigation into the influence of diet, host demographics, and environment on the gut microbiota and health of cheetahs.

Effects of rumen fluid transplantation on the fecal flora of yaks

IntroductionThere are few studies on the effect of rumen fluid transplantation on the fecal flora of yaks. Yak fecal flora is closely related to their health. This study aimed to evaluate the effects of rumen fluid transplantation on growth performance and fecal flora indicators.MethodsTwenty 6-month healthy male yaks (weight: 57.20 ± 7.80 kg) were selected from grazing yaks in an alpine meadow pasture at an altitude of approximately 3,400 m. They were then transferred to a farm and randomly divided into a control group (CON; n = 10) and a rumen fluid transplantation group (RT; n = 10). Separate single-pen rearing was performed in two pens using the same rearing environment and feeding method, and all yaks were earmarked for identification. In addition, 10 yaks that had been adapted to stall fattening feed in 1 month were selected as the rumen fluid donor group to provide fresh rumen fluid. Ruminal fluid transplantation trials were conducted on the 1st, 3rd, and 5th weeks. Overall, 1 L of ruminal fluid was transplanted to each yak in the RT and CON groups. The formal trial then began with both groups fed the same diet. After this, yak feed intake was recorded daily; yaks were weighed on days 1, 30, and 60 of the formal trial; and yak feces were collected directly from the ground on days 1, 4, 7, 14, 30, and 60 to compare the microbial composition of the feces using 16S rRNA sequencing data.ResultsThe results showed that rumen fluid transplantation significantly increased the alpha diversity of fecal microflora (P &amp;lt; 0.05), and on day 30 of the experiment, both the operational taxonomic unit (OTU) and Shannon index were significantly higher in the RT group than the CON group (P &amp;lt; 0.05). In the principal coordinate analysis (PCoA) plot, the intestinal flora of the RT group was significantly different (P &amp;lt; 0.05) on days 1–7 but not significantly different after day 14. In contrast, the intestinal flora of the CON group was significantly different (P &amp;lt; 0.05) on days 1–14 but not significantly different after day 30. Compared with the CON group, the relative abundance of Firmicutes in the RT group was significantly lower on days 1, 4, 7, and 14 (P &amp;lt; 0.05); the relative abundance of Bacteroidetes in the RT group was significantly higher on days 1, 4, 14, and 30 and significantly lower on day 7 (P &amp;lt; 0.05); the relative abundance of Tenericutes in the RT group was significantly higher on day 30 (P &amp;lt; 0.05); the relative abundance of Actinobacteria in the RT group was significantly higher on day 60 (P &amp;lt; 0.05); the relative abundance of Ruminococcaceae_UCG-005 in the RT group was significantly lower on days 4, 7, 14, and 60 (P &amp;lt; 0.05); the relative abundance of Unidentified in the RT group was significantly higher on days 1, 4, and 7 days (P &amp;lt; 0.05); and the relative abundance of Rikenellaceae_RC9_gut_group, Bacteroides, and Christensenellaceae_R-7_group in the RT group was significantly higher on day 1 (P &amp;lt; 0.05). Moreover, Actinobacteria was positively correlated with ADG and negatively correlated with DMI; Tenericutes was positively correlated with weight and negatively correlated with F/G. Metabolism of terpenes and polyketones, metabolism of other amino acids, and energy metabolism were higher in the RT group than in the CON group. LEfSe analysis showed that 32 species were more abundant in the RT group and 11 in the CON group. In conclusion, our findings suggest that rumen fluid transplantation improved the stability of the intestinal tract of yaks, improved the immunity of yaks, and reduced the occurrence of intestinal diseases; rumen fluid transplantation remodeled the structure of the intestinal flora, shortened the time of remodeling the intestinal flora of yaks during the transition period, and accelerated yak adaptation to digest housed rations, reducing the DMI. The findings of this study provide new insights into yak microbial community transplantation and a reference for improving feed efficiency in the yak industry.

C-di-GMP inhibits rRNA methylation and impairs ribosome assembly in the presence of kanamycin.

Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous bacterial secondary messenger with diverse functions. A previous Escherichia coli proteome microarray identified that c-di-GMP binds to the 23S rRNA methyltransferases RlmI and RlmE. Here we show that c-di-GMP inhibits RlmI activity in rRNA methylation assays, and that it modulates ribosome assembly in the presence of kanamycin. Molecular dynamics simulation and mutagenesis studies reveal that c-di-GMP binds to RlmI at residues R64, R103, G114, and K201. Structural simulations indicate that c-di-GMP quenches RlmI activity by inducing the closure of the catalytic pocket. We also show that c-di-GMP promotes antibiotic tolerance through RlmI. Binding and methylation assays indicate that the inhibitory effect of c-di-GMP on RlmI is conserved across various pathogenic bacteria. Our data suggest an unexpected role for c-di-GMP in regulating ribosome assembly under stress through the inhibition of rRNA methyltransferases.

New insights in the systematics of the Hemiuroidea (Digenea: Hemiurata) based on the integrative taxonomy approach.

Opistholecithum sandugaense n. g. n. sp. was collected from the intestine of Oncorhynchus keta (Walbaum) in the Nezhinka (=Sanduga) River, Primorsky region, Russia. Based on the position of the vitellarium in hindbody and significant genetic differentiation, ten species from the genus Lecithaster Lühe, 1901 were transferred to the newly established Opistholecithum as follows: O. gibbosum (Rudolphi, 1802) n. comb., O. macrocotyle (Szidat & Graefe, 1967) n. comb., O. micropsi (Zdzitowiecki, 1992) n. comb., O. salmonis (Yamaguti, 1934) n. comb. According to the morphometrics and topology of the internal organs, O. sandugaense appears similar to O. salmonis. These species are distinct based on novel sequence data - 28S rRNA gene (p-distances 0.4%) and the cox1 mtDNA gene (p-distances 4.4-4.8%). Large-scale phylogeny reconstruction showed that the lecithasterid subfamily Lecithasterinae sensu stricto include two genera Lecithaster (type taxon) and Opistholecithum n. g.; other genera Lecithophyllum and Aponurus were transferred to the family Lecithophyllidae n. stat. Based on the morphological features, we consider four subfamilies Lecithasterinae, Trifoliovariinae, Prolecithinae and Macradenininae belonging to Lecithasteridae. Analysis of indels in the 28S divergent domains proved to be a robust technic for family delimitation within the superfamily Hemiuroidea. Especially it allows to reveal the molecular symplesiomorphies affecting phylogenetic reconstructions. Taxonomic rearrangements proposed in this study are supplemented by dichotomous keys: (1) for two genera of the subfamily Lecithasterinae; (2) for the genus Opistholecithum; (3) for the genus Lecithaster; (4) for six closely related hemiuroid families, with Lecithophyllidae n. stat. (genera Lecithophyllum, Aponurus, Monorchiaponurus, Weketrema) and Merlucciotrematidae n. fam. (Merlucciotrema).

Metabarcoding for the Monitoring of the Microbiome and Parasitome of Medically Important Mosquito Species in Two Urban and Semi-urban Areas of South Korea.

Interactions between microbial communities and the host can modulate mosquito biology, including vector competence. Therefore, future vector biocontrol measures will utilize these interactions and require extensive monitoring of the mosquito microbiome. Metabarcoding strategies will be useful for conducting vector monitoring on a large scale. We used 16S and 18S rRNA gene metabarcoding through iSeq100 sequencing to characterize the microbiome and eukaryome of Aedes albopictus (Skuse 1894) and Culex pipiens (Linnaeus 1758), two globally important vectors present in South Korea. Mosquitoes were collected from an urban and a semi-urban location in South Korea. Bacterial alpha and beta diversities varied by population. Pseudomonadota dominated the microbiomes of both species. The microbiome composition varied by population and was dominated by different taxa. At the genus level, Wolbachia sp. was the most enriched genus in Cx. pipiens, followed by Aeromonas sp. In Ae. Albopictus, the most abundant group was Enterococcus sp. The gregarine parasite Ascogregarina taiwanensis was highly prevalent in Ae. Albopictus and its absence was marked by the presence of seven bacterial taxa. To our knowledge, this is the first characterization of the microbiome of Ae. albopictus and Cx. pipiens in these regions of South Korea and contributes to the current information on the microbiome of mosquito species, which can be used in further studies to assess pathogen-microbiome and microbiome-microbiome interactions.

Lacticaseibacillus Casei JS-2 from ‘Jiangshui’ Reduces Uric Acid and Modulates Gut Microbiota in Hyperuricemia

Lacticaseibacillus casei (JS-2) is a novel probiotic isolated from “Jiangshui”, a kind of traditional folk fermented food, which has a significant effect on hyperuricemia (HUA). In vitro experimental results showed that JS-2 has a high degradation ability and selectivity for uric acid (UA). The animal test results indicated that after two weeks of treatment, JS-2 could significantly reduce the level of UA in the serum of HUA quails (p &lt; 0.01), and its effect is almost equivalent to that of the positive drug control group, benzbromarone. Further, after JS-2 treatment, the level of xanthine oxidase in quail serum decreased significantly. Analysis data of quail fecal metabolomics results showed that JS-2-altering metabolites were involved in amino acid, purine, and lipid metabolism. To investigate the mechanism underlying JS-2-mediated UA degradation in the quail model of HUA, 16S rRNA gene sequencing was conducted. It was found that the structure and function of the gut microbiota were restored after JS-2 intervention, and the abundance of short-chain fatty acid (SCFA)-producing bacteria (g__Ruminococcus_torques_group and g__Butyricicoccus) and bacteria with UA degradation capacity (g__unclassified_f__Lachnospiraceae and g__Negativibacillus) increased significantly; intestinal SCFAs, especially propionic acid, increased accordingly. These experimental data suggest that the beneficial effects of JS-2 may derive from changes in the gut microbiome, altering host–microbiota interactions, reducing UA levels by increasing UA excretion, and reducing absorption. These findings provided new evidence that JS-2 has the potential to be used as a naturally functional food for the prevention of HUA.

Carbon monoxide-oxidising Pseudomonadota on volcanic deposits

Carbon monoxide (CO) oxidising microorganisms are present in volcanic deposits throughout succession, with levels of vegetation and soil influencing the communities present. Carboxydovores are a subset of CO oxidisers that use CO as an energy source, which raises questions about the physiological and metabolic features that make them more competitive in harsh volcanic ecosystems. To address these questions, samples were taken from volcanic strata formed by eruptions from Calbuco Volcano (Chile) in 2015 (tephra) and 1917 (soil). Two carboxydovore members of the Burkholderiaceae family were isolated for further study to elucidate the benefits of carboxydovory for the survival of these strains in extreme volcanic ecosystems. The isolates were identified as Paraburkholderia terrae COX (isolated from the 2015 tephra) and Cupriavidus str. CV2 (isolated from the 1917 soil). 16S rRNA gene sequencing showed that within the family Burkholderiacea, the genus Paraburkholderia dominated the 2015 volcanic deposit with an average relative abundance of 73.81%, whereas in the 1917 volcanic deposit, Cupriavidus accounted for 33.64% (average relative abundance). Both strains oxidise CO across a broad range of concentrations (< 100 ppmv – 10,000 ppmv), and genome sequence analysis revealed a candidate form-I carbon monoxide dehydrogenase (CODH), which is likely to catalyse this process. Each strain oxidised CO specifically at stationary phase but the conditions for induction of CODH expression were distinct. Cupriavidus strain CV2 expressed CODH only when CO was added to cultures (100 ppm), while Pb. terrae COX expressed CODH regardless of supplementary CO addition. Based on comparative metabolic and phylogenetic analyses, Cupriavidus strain CV2 is proposed as a novel species within the genus Cupriavidus with the name Cupriavidus ulmosensis sp. nov. for the type strain CV2T (= NCIMB 15506 T, = CECT 30956 T). This study provides valuable insights into the physiology and metabolism of carboxydovores which colonise volcanic ecosystems.

The Occurrence of Borrelia burgdorferi sensu lato in Ixodes ricinus Ticks Collected from Nature-Educational and Tourist Trails in the Poprad Landscape Park

Throughout Europe, including Poland, Ixodes ricinus ticks are the main vector of numerous pathogenic agents that pose a serious threat to public health. Southern Poland attracts many tourists with its scenic landscapes and abundant recreational opportunities. These areas are ideal habitats for wild fauna, which serve as the main reservoirs and hosts for these pathogens and ticks. The large population and biodiversity of these hosts facilitate the proliferation of ticks. The aim of this study was to determine the potential exposure of humans to ticks and tick-borne pathogens such as Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, and Babesia spp., along the nature-educational and tourist trails of the Poprad Landscape Park. From 2020 to 2021, ticks were collected using the flagging method on three tourist trails and nature-educational paths within the Poprad Landscape Park. DNA was isolated from 213 I. ricinus ticks using the ammonia method. To detect pathogens in ticks, PCR and nested PCR methods were used. To detect B. burgdorferi s.l. and A. phagocytophilum, two pairs of primers specific to the flaB gene fragment and 16S rRNA gene fragment were used, respectively. For Babesia spp. detection, primers specific to the 18S rRNA gene were used. The amplification products were separated electrophoretically and visualized under ultraviolet light. In total, among the 213 examined ticks, B. burgdorferi s.l. was detected in 31% of the samples. Neither A. phagocytophilum nor Babesia spp. were detected in the studied material. These results indicate a potentially high risk of ticks and tick-borne B. burgdorferi s.l. infections for residents and tourists in the recreational areas of the Poprad Landscape Park.

A timescale for the evolutionary history of sea spiders (Arthropoda: Pycnogonida)

Abstract Sea spiders (Arthropoda: Pycnogonida) are an ancient lineage of chelicerates represented by a single living order, Pantopoda, and a patchy fossil record that provides limited information of their evolutionary timescale. The sudden appearance of Pantopoda in the Middle Jurassic has led several authors to propose a recent (Early Jurassic) origin and rapid diversification of modern pycnogonids. In contrast, a recent molecular clock study suggested Pantopoda originated before the Devonian, and diversified slowly, though the calibrations on which it was based have since been revised. Here, we conduct timetree inference analyses using a set of 13 mitochondrial protein-coding genes, 18S rRNA sequences and 98 Ultra Conserved Elements from 198 pycnogonid taxa, with calibrations reflecting the most recent interpretations of the sea spider fossil record. Our analyses estimate that pycnogonids diverged from other arthropods during the Cambrian (539-510 Ma), indicating about 100 Myr between Pycnogonida origin and pantopod diversification. The pycnogonid crown group (=Pantopoda) diversified during the Late Palaeozoic, in an interval spanning the Early Silurian and the Late Devonian (435-367 Ma), preceding the appearance of the first pantopod fossil by ~206.5 Myr. Our analysis also implies that pantopod families originated between the Late Devonian and the Late Jurassic (378-154 Ma). This leads to very different estimates to previous studies based on the fossil record. However, previous molecular divergence time analyses yielded a similar evolutionary timescale, despite a notably different set of calibrations. This effective corroboration of previous evidence indicates that the underpinning molecular evidence is informative and that the inferred long ghost lineages faithfully reflect the patchy nature of the pycnogonid fossil record which results from their low fossilisation potential. Regardless, our results predict further fossil discoveries from different environments and periods, which might at least partially rewrite pycnogonid history.

Exploring the Post Mortem Interval (PMI) Estimation Model by circRNA circRnf169 in Mouse Liver Tissue

Estimating the post mortem interval (PMI) is a crucial and contentious issue in forensic research, particularly in criminal cases. Traditional methods for PMI estimation are limited by constraints and inaccuracies. Circular RNA (circRNA), formed through exon or intron looping to create a complete circular structure without a 5′ end cap and a 3′ poly(A) tail, exhibits exceptional stability, abundance, and tissue-specific characteristics that make it potentially valuable for PMI estimation. However, research on the exploration or application of circRNA in PMI estimation has been limited. This study aims to investigate the correlation between circRNA and PMI. In this study, liver tissue samples were collected from mice at six different time points at 4 °C, 18 °C, 25 °C, and 35 °C, respectively. The reference gene 28S rRNA and the biomarker circRnf169 were successfully screened. Quantitative PCR was employed to examine the correlation between circRnf169 levels and PMI. At 4 °C, the level of circRnf169 decreased with prolonged PMI, whereas at 18 °C, 25 °C, and 35 °C, the circRnf169 RNA was degraded rapidly, indicating that circRnf169 is suitable for PMI estimation at low temperatures or early PMI. These findings suggest the establishment of mathematical model for early PMI based on circRnf169 using liver tissue, which may serve as a reliable marker. Further research is required in order to develop more markers in mice and/or to validate these mathematical models in human samples.

Prokaryotic and eukaryotic periphyton responses to warming, nutrient enrichment and small omnivorous fish: a shallow lake mesocosms experiment.

Global change stressors, including climate warming, eutrophication, and small-sized omnivorous fish, may exert interactive effects on the food webs and functioning of shallow lakes. Periphyton plays a central role in the primary production and nutrient cycling of shallow lakes but constitutes a complex community composed of eukaryotes and prokaryotes that may exhibit different responses to multiple environmental stressors with implications for the projections of the effects of global change on shallow lakes. We analyzed the effects of warming, nutrient enrichment, small omnivorous fish and their interactions on eukaryotic and prokaryotic periphyton structures in shallow lake mesocosms. We performed 16S and 18S rRNA high-throughput sequencing to elucidate the effect of the abovementioned stressors. We found that warming promoted periphytic alpha diversity and network complexity, with multi-tolerant genera becoming dominating (e.g. Spirosomaceae and Azospirillaceae). Contrastingly, nutrient enrichment led to reduced prokaryotic diversity and network complexity and stability, with weak disruption of the eukaryotic structure. Small omnivorous fish were major drivers of changes eukaryotic periphyton, facilitating diversity and network complexity, and increasing prokaryotic and eukaryotic biomarker diversity. Omnivorous fish reduced the grazing pressure on periphyton mainly through selective grazing on zooplankton, contributing to periphytic structural stability and functional diversity, especially the proliferation of prokaryotic biomarkers. Nutrient enrichment counteracted the positive effects of warming on periphyton, while concerted action with omnivorous fish led to high TN and TP concentrations and accelerated the negative development of periphytic alpha diversity and network structure. The co-occurrence of the three environmental pressures ultimately resulted in a disruption of periphytic biodiversity and community structure and weakened connectivity with the environment. Our study provided new insights into the understanding of the response of prokaryotic and eukaryotic community structure and ecological functions of freshwater periphyton to global environmental change.

Prospective analysis of biomarkers associated with successful faecal microbiota transplantation in recurrent Clostridioides difficile Infection.

Faecal microbiota transplantation (FMT) is an established treatment for recurrent Clostridioides difficile infection (R-CDI). This study aimed to identify calprotectin and microbiome characteristics as potential biomarkers of FMT success. We conducted a prospective study of patients who underwent oral FMT (single dose of 4-5 capsules) for R-CDI (January 2018 to December 2022). Samples were collected at three time points: at CDI diagnosis, within 24hours prior to FMT administration, and 30days post-FMT. Calprotectin levels were assessed and the V4 region of the 16S rRNA gene was sequenced to analyse the microbiota composition. Sequencing data analysis and statistical analysis were performed using MOTHUR and R. Ninety-seven patients underwent FMT (totalling 105 procedures). A total of 221 samples were processed, including 21 donor samples, 24 capsule contents, and 176 patient faecal samples (39 at diagnosis, 63 pre-FMT, and 74 post-FMT). FMT achieved an overall success rate of 85.1% (86/101 cases). The abundance of Bacteroides, Ruminococcus, Megamonas, and certain Prevotella operational taxonomic units (OTUs) was significantly higher in capsules associated with 100% success compared to less effective capsules. FMT engraftment was observed in 95% of patients with favourable outcomes versus 62% of those with recurrences (p = 0.006). Additionally, a negative correlation was found between calprotectin levels and specific microbial genera, suggesting an association with successful outcomes. This study highlights differences in the evolution of faecal microbiota, bacterial engraftment, and inflammation markers (e.g., calprotectin) between patients with varying FMT outcomes. Potential biomarkers for successful FMT were identified, providing valuable insights for optimizing FMT strategies.