16S Ribosomal DNA Research Articles

Heat exposure promotes sarcopenia via gut microbiota-derived metabolites.

The unprecedented rise in global ambient temperatures in the last decade has significantly impacted human health, yet how heat exposure affects the development of sarcopenia remains enigmatic. Here, we demonstrate that chronic heat exposure induces skeletal muscle volume loss, leading to muscle strength and functional decline in mice. The microbiota composition of heat-exposed mice was analyzed using 16S ribosomal DNA analysis. Liquid chromatography-mass spectrometry (LC-MS) was used to explore the effects of heat exposure on the blood metabolome and to further analyze the correlation between blood metabolism and gut microbiota. Transplantation of microbiota from heat-exposed mice to germ-free mice was sufficient to increase adverse effects on skeletal muscle function in the host. Mechanistically, using an untargeted metabolomics strategy, we reveal that altered gut microbiota due to high temperatures is associated with elevated serum levels of homocitrulline. Homocitrulline causes mitochondrial dysfunction in myocytes by exacerbating ferroptosis levels. And Nrf2 activator (Oltipraz) supplementation alleviates muscle atrophy and dysfunction induced by heat exposure. Our findings reveal the detrimental effects of heat exposure on muscle function and provide new strategies for treating sarcopenia.

New Occurrence of Nigrospora oryzae Causing Leaf Blight in Ginkgo biloba in China and Biocontrol Screening of Endophytic Bacteria

Ginkgo biloba is a multifunctional composite tree species that has important ornamental, economic, medicinal, and scientific research value. In October 2023, the foliage of G. biloba on the campus of Nanjing Forestry University exhibited leaf blight. Black-brown necrotic spots were observed on a large number of leaves, with a disease incidence of 86%. After isolating a fungus from symptomatic leaves, pathogenicity was tested to satisfy Koch’s postulates. Using morphological features and multi-gene phylogenetic analyses of an internal transcribed spacer (ITS), elongation factor 1-alpha (EF1-α), and beta-tubulin (β-tub), the isolates YKB1-1 and YKB1-2 were identified as Nigrospora oryzae. N. oryzae was previously reported as an endophyte of G. biloba. However, this study shows it to be pathogenic to G. biloba, causing leaf spots. Two endophytic bacteria were isolated from asymptomatic leaves of diseased G. biloba trees, and their molecular identification was performed using 16S ribosomal DNA (16S rDNA). GBB1-2 was identified as Bacillus altitudinis, while GBB1-5 was identified as Bacillus amyloliquefaciens. The screening and verification of endophytic bacteria provide a new strategy for the control of N. oryzae.

Impact of periodontal therapy on oral bacterial composition in individuals diagnosed with advanced periodontal disease.

Introduction. Negative changes in the microbial composition have been extensively studied in individuals with periodontal disease.Gap Statement. The changes in the oral microbiota after treating this disease are still unknown.Aim. We sought to elucidate the distinctive traits of salivary microbiota in individuals displaying healthy gums and those with severe periodontitis (SP) and examine the influence of periodontal therapy.Methodology. Periodontal pocket depths were examined to determine disease severity. The presence and quantity of oral Helicobacter pylori (associated with periodontal disease) were determined. Sequencing of 16S ribosomal DNA and bioinformatic analyses were performed to assess oral bacterial compositions in patients.Results. Sequencing analysis of 16S ribosomal DNA revealed a significant reduction in the abundance of operational taxonomic units (OTUs) and Chao1 and Abundance coverage-based estimator(ACE) indices in the oral cavities of individuals with SP compared to those of the healthy controls. However, these parameters showed significant recovery after appropriate treatment severe periodontitis after treatment (TSP). Additionally, the levels of harmful Bacillales and Spirochetes significantly increased, whereas the presence of beneficial Euryarchaeota significantly decreased in the SP group. The TSP group exhibited considerably augmented abundances of Burkholderiaceae and Veillonella, while noteworthy reductions in the pathogenic microbiota (Clostridia, Fusobacteria and Spirochaetes) were noticed compared to those of the SP group. Functionally, these modified OTUs were extensively implicated in 41 metabolic pathways.Conclusion. Our study demonstrates that nonsurgical periodontal therapy can effectively reduce the diversity of the oral microbiota, thereby potentially enhancing the treatment efficacy in patients with periodontal disease.

Chromosomal Localization and Diversity Analysis of 5S and 18S Ribosomal DNA in 13 Species from the Genus Ipomoea

Background: Sweet potato (Ipomoea batatas (L.) Lam.), a key global root crop, faces challenges due to its narrow genetic background. This issue can be addressed by utilizing the diverse genetic resources of sweet potato’s wild relatives, which are invaluable for its genetic improvement. Methods: The morphological differences in leaves, stems, and roots among 13 Ipomoea species were observed and compared. Chromosome numbers were determined by examining metaphase cells from root tips. Fluorescence in situ hybridization (FISH) was used to identify the number of 5S and 18S rDNA sites in these species. PCR amplification was performed for both 5S and 18S rDNA, and phylogenetic relationships among the species were analyzed based on the sequences of 18S rDNA. Results: Three species were found to have enlarged roots among the 13 Ipomoea species. Chromosome analysis revealed that I. batatas had 90 chromosomes, Ipomoea pes-tigridis had 28 chromosomes, while the remaining species possessed 30 chromosomes. Detection of rDNA sites in the 13 species showed two distinct 5S rDNA site patterns and six 18S rDNA site patterns in the 12 diploid species. These rDNA sites occurred in pairs, except for the seven 18S rDNA sites observed in Ipomoea digitata. PCR amplification of 5S rDNA identified four distinct patterns, while 18S rDNA showed only a single pattern across the species. Phylogenetic analysis divided the 13 species into two primary clades, with the closest relationships found between I. batatas and Ipomoea trifida, as well as between Ipomoea platensis and I. digitata. Conclusions: These results enhance our understanding of the diversity among Ipomoea species and provide valuable insights for breeders using these species to generate improved varieties.

A new species of Thoracophelia (Annelida, Opheliidae) from the Yellow Sea of South Korea.

Thoracophelia Ehlers, 1897 is a genus of Opheliidae characterised by the body divided into three distinct regions, modified parapodia in chaetiger 10 and a ventral groove restricted to the posterior half of the body. To date, 18 species have been described in the genus. Amongst them, six species have been recorded in northeast Asia. A new species, Thoracopheliafoliformis sp. nov., was discovered in the intertidal zone of the Yellow Sea, South Korea. This is the first Thoracophelia species report from the Yellow Sea. This new species is closely related to T.dillonensis (Hartman, 1938) from California and T.ezoensis Okuda, 1936 from Japan in having pectinate branchiae. However, the new species can be distinguished from the two species by the unique combination of the following characteristics: 15 pairs of wrinkled pectinate branchiae with 12-15 filaments at best development and a foliaceous mid-ventral plate in the pygidium instead of one or two thick ventral cirri. Detailed descriptions and illustrations of T.foliformis sp. nov. are provided. Sequences of the mitochondrial cytochrome c oxidase subunit I (COI), nuclear 18S ribosomal DNA (rDNA) and 28S rDNA of the new species were determined and analysed.

Stability of Gastric Fluid and Fecal Microbial Populations in Healthy Horses under Pasture and Stable Conditions.

Equine gastrointestinal microbial communities vary across the gastrointestinal tract and in response to diet or disease. Understanding the composition and stability of gastric fluid microbiota in healthy horses is a prerequisite to understanding changes associated with the development of disease. The objective of this study was to describe microbial communities in the gastric fluid and feces of healthy horses longitudinally. Horses were maintained on pasture (6 weeks), stabled (5 weeks), then returned to pasture. A consistent forage diet was provided throughout. Native gastric fluid and feces were collected weekly for full-length 16S ribosomal DNA sequencing and microbial profiling analysis. Fewer taxa were identified in the gastric fluid (770) than in the feces (5284). Species richness and diversity were significantly different between sample types (p < 0.001), but not between housing locations (p = 0.3). There was a significant effect of housing and horse on the Bray-Curtis compositional diversity of gastric (p = 0.005; p = 0.009) and fecal (p = 0.001; p = 0.001) microbiota. When horses moved from pasture to stable, the relative proportions of gastric fluid Lactobacillaceae increased and Streptococcaceae decreased, while fecal Firmicutes increased and Bacteriodota decreased. Within each housing condition, there was no significant week-to-week variation in gastric (p = 0.9) or fecal (p = 0.09) microbiota. Overall, these findings support the maintenance of stable gastric and fecal microbial populations under each management condition, providing a basis for further investigation of gastric fluid microbiota in diseases of the foregut.

Auricularia auricula polysaccharide alleviates cyclophosphamide-induced liver injury in mice involving remodeling of the gut bacteriome, mycobiome, and metabolome

In this study, a novel polysaccharide (AHP) from Auricularia auricula was isolated and purified, showing protective effects against CTX-induced liver injury in mice. To study the action mechanism of AHP, a liver injury model was established by intraperitoneally injection 80 mg/kg of CTX for 3 consecutive days. The focus was on how AHP regulated the gut bacteriome and mycobiome to help alleviate metabolic disorders associated with liver injury. Results showed that AHP amended liver injury by improving liver function, stabilizing oxidative stress homeostasis, reducing inflammatory invasion and activating Akt/GSK3β/Nrf-2/HO-1 signaling pathway. The 16S ribosomal DNA (16S rDNA) and Internal Transcribed Spacer-1 (ITS1) sequencing results demonstrated that AHP supplementation significantly restored the gut bacteriome and mycobiome composition in CTX-induced liver injury mice, by enriching the abundance of beneficial bacteriome (unclassified_Muribaculaceae, Faecalibaculum and Alloprevotella) and mycobiome (Fusarium), reducing the abundance of harmful bacteriome (Akkermanisa) and mycobiome (Fusicolla and Cladosporium). Analysis of untargeted metabolomics indicated that AHP altered the levels of metabolites associated with both bile acid and arachidonic acid metabolism, showing a significant connection to the AHP-regulated bacteriome and mycobiome. To conclude, the findings suggested that AHP was a viable and secure candidate for use as a hepatoprotective medication.

Quantification of the thermal history of insects in foods using real-time PCR-based DNA fragmentation analysis

A major challenge faced by the food industry is the contamination of food by insects. Once an insect is found in a food product, it is important to determine how it entered the food. Given that the thermal history of insects provides a clue to unraveling this mystery, in this study, we have developed a novel real-time PCR-based DNA fragmentation analysis method to quantify the thermal history of insects found in foods.We selected two species of cockroaches (Periplaneta fuliginosa and Blattela germanica) as investigative targets because cockroach contamination often causes significant economic losses in the food industry. A set of real-time PCRs was designed for each species to amplify the species-specific regions of 18S ribosomal DNA at approximate 100 and 300 bp. The degree of DNA fragmentation was evaluated using the differences between the amplification curves for the 100- and 300-bp sequences. We observed that the degree of DNA fragmentation was quantifiable when the insect was heated to >100 °C. Therefore, we determined whether cockroaches contaminate retort foods during the manufacturing or household consumption stages. This novel analytical method is expected to improve food safety and product reliability by identifying the cause of insect contamination.

Characterization of four novel actinospore types of fish parasitic myxozoans and the occurrence of Branchiodrilus hortensis and Ophidonais serpentina from fish farms of Hungary

Six distinct actinospore types were identified in the intestinal epithelium of oligochaetes collected from the Szigetbecse and Makád fish farms of Ráckeve Danube Arm Fishing Association, in Hungary. Four new types: triactinomyxon type, raabeia type, aurantiactinomyxon type 1, and aurantiactinomyxon type 2, were described morphologically and molecularly from three invertebrate host species: Limnodrilus hoffmeisteri, Ophidonais serpentina, and Tubifex tubifex. The 18S ribosomal DNA (rDNA) analysis revealed that these new types of actinospores did not match any myxospore sequences available in GenBank. Phylogenetic analysis placed the triactinomyxon type within the Myxobolus clade that parasitizes cyprinid fish, while the raabeia type and aurantiactinomyxon type 2 were both placed within the Myxobolus clade associated with Perciformes fish. Aurantiactinomyxon type 1 was clustered in a clade containing gill-infecting Henneguya spp. from Esociformes fish. However, no myxospores have been found yet to link to the newly sequenced actinospores reported in this survey. This study also reports the first occurrence of two oligochaetes species, Branchiodrilus hortensis and Ophidonais serpentina in Hungary, specifically in fish farms of Ráckeve Danube Arm Fishing Association. Moreover, this is the first report on the involvement of Ophidonais serpentina in the life cycle of myxozoans.

Antibacterial and Anticancer Properties of Endophenazines from Streptomyces prasinus ZO16, an Endophyte in Zingiber officinale Rosc.

&lt;b&gt;Background and Objective:&lt;/b&gt; This study investigated a bacterial strain, ZO16, isolated from ginger (&lt;i&gt;Zingiber officinale&lt;/i&gt;) roots. Analysis of its 16S ribosomal DNA (rDNA), along with chemical and physical properties, revealed it to be &lt;i&gt;Streptomyces prasinus&lt;/i&gt;. This study aimed to isolate and characterize the main bioactive compounds from ZO16, evaluating their antibacterial and anticancer properties. &lt;b&gt;Materials and Methods:&lt;/b&gt; Techniques like column chromatography and thin-layer chromatography (TLC) were used to purify the key compounds from ZO16's culture extract. Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry were utilized to confirm the identities of the purified compounds as endophenazine A (compound 1) and endophenazine B (compound 2). The antibacterial and anticancer properties of these compounds were then evaluated. &lt;b&gt;Results:&lt;/b&gt; The isolated compounds displayed antibacterial activity against &lt;i&gt;Staphylococcus aureus&lt;/i&gt; ATCC 25923 and Methicillin-Resistant &lt;i&gt;Staphylococcus aureus&lt;/i&gt; (MRSA). The minimum inhibitory concentration (MIC) of the isolated compounds against bacteria ranged from 8 to 32 μg/mL, while the minimum bactericidal concentration (MBC) was between 32 and 128 μg/mL. These compounds exhibited effectiveness against tested cancer cells with IC&lt;sub&gt;50&lt;/sub&gt; values ranging from 30.40 to 32.51 μg/mL for cervical cancer (HeLa), 78.32 to 86.45 μg/mL for liver cancer (HepG2) and 23.41 to 28.26 μg/mL for breast cancer (MDA-MB-231) cells. However, these compounds also showed moderate toxicity towards non-cancerous Vero cells (IC&lt;sub&gt;50&lt;/sub&gt; = 317.44-328.63 μg/mL). &lt;b&gt;Conclusion:&lt;/b&gt; The findings of this study suggest that &lt;i&gt;Streptomyces prasinus&lt;/i&gt; strain ZO16 produces compounds with antibacterial and anticancer properties. Further investigation of these compounds has the potential to contribute to the development of improved methods for controlling and treating bacterial infections and some cancers.

Bifidobacterium longum subsp. infantis NKU FB3-14 attenuates loperamide-induced constipation through regulation of gut microbiota

Abstract Objectives Constipation is a prevalent gastrointestinal issue, and the efficacy of probiotics in alleviating constipation has been well proved. This study aimed to investigate the impact of Bifidobacterium longum subsp. infantis NKU FB3-14 on loperamide- induced constipation by focusing on improving intestinal barrier function and modulating gut microbiota composition Materials and Methods The constipated model mice induced by loperamide were treated with NKU FB3-14, and the laxative effect was assessed based on the fecal water content, first black stool time and gastrointestinal transit rate. Gastrointestinal regulatory peptides in serum, intestinal neurotransmitter and inflammatory cytokines in colon tissues were measured using ELISA kits. Changes of gut microbiota composition were analyzed through 16S ribosomal DNA sequencing identification. Additionally, HPLC detection was performed to quantify short chain fatty acids levels in feces Results Treatment with NKU FB3-14 led to increase the fecal water content, shorten the first black stool time and improve small intestine transit rate. Motilin and substance-P significantly decreased in the model group, and only motilin increased in FB3-14 group; somatostatin and vasoactive intestinal peptide were decreased in model mice and both increased in FB3-14 group; 5-HT levels in the colon tissue were upregulated following NKU FB3-14 treatment. Histological examination revealed thinner colonic mucosa in the model group along with significant in TNF-α, IL-1β and IL-17 levels form the colon tissues which were all relieved by NKU FB 3-14 treatment. Furthermore, NKU FB3-14 intervention resulted in reduced abundance of Desulfobacterota and Desulfovibrio while increasing the abundance of Ruminococcaceae and Eubacterium; higher level of butyric acid was observed in feces Conclusions In summary, our findings demonstrated that NKU FB3-14 treatment significantly enhanced the intestinal motility, regulated the expression levels of gastrointestinal regulatory peptides, prevented damage to colonic barriers as well as ameliorated gut microbiota imbalance associated with loperamide-induced constipation.

The rhizobacterial Priestia megaterium strain SH-19 mitigates the hazardous effects of heat stress via an endogenous secondary metabolite elucidation network and molecular regulation signalling

Global warming is a leading environmental stress that reduces plant productivity worldwide. Several beneficial microorganisms reduce stress; however, the mechanism by which plant–microbe interactions occur and reduce stress remains to be fully elucidated. The aim of the present study was to elucidate the mutualistic interaction between the plant growth-promoting rhizobacterial strain SH-19 and soybeans of the Pungsannamul variety. The results showed that SH-19 possessed several plant growth-promoting traits, such as the production of indole-3-acetic acid, siderophore, and exopolysaccharide, and had the capacity for phosphate solubilisation. The heat tolerance assay showed that SH-19 could withstand temperatures up to 45 °C. The strain SH-19 was identified as P. megaterium using the 16S ribosomal DNA gene sequence technique. Inoculation of soybeans with SH-19 improved seedling characteristics under high-temperature stress. This may be due to an increase in the endogenous salicylic acid level and a decrease in the abscisic acid level compared with the negative control group. The strain of SH-19 increased the activity of the endogenous antioxidant defense system, resulting in the upregulation of GSH (44.8%), SOD (23.1%), APX (11%), and CAT (52.6%). Furthermore, this study involved the transcription factors GmHSP, GmbZIP1, and GmNCED3. The findings showed upregulation of the two transcription factors GmbZIP1 (17%), GmNCED3 (15%) involved in ABA biosynthesis and induced stomatal regulation, similarly, a downregulation of the expression pattern of GmHSP by 25% was observed. Overall, the results of this study indicate that the strain SH-19 promotes plant growth, reduces high-temperature stress, and improves physiological parameters by regulating endogenous phytohormones, the antioxidant defense system, and genetic expression. The isolated strain (SH-19) could be commercialized as a biofertilizer.

Faecal source apportionment using molecular methods: A proof of concept using the FEAST algorithm

Faecal contamination of freshwater and marine environments represents a significant risk for public health, recreational activity and food safety, and tools for evaluating complex multi-source contamination remain largely in the development phase. We evaluated the efficacy of the Fast Expectation Maximization (FEAST) microbial source tracking (MST) algorithm to apportion sources of faecal contamination among four mammalian species of interest in coastal waters in New Zealand. Using 16S ribosomal DNA metabarcoding of faecal samples from cows, fur seals, and sheep, as well as human wastewater, we aimed to differentiate and quantify the contribution of these sources in mixed faecal samples. Multivariate analysis confirmed significant differences in the microbial communities associated with each mammalian source, with specific bacterial classes indicative of different sources. The FEAST algorithm was tested using mixed DNA and mixed faecal samples, and we found that the algorithm correctly assigned the dominant source from all samples, but underestimated the dominant source's proportional contribution. This underestimation suggests the need for further refinement and validation to ensure accurate source apportionment in environmental samples where the faecal signal is likely to be a minor component. Despite these limitations, the findings of our study, in combination with the evidence from others who have tested the FEAST algorithm in environmental settings, indicates that it represents an advance on existing tools for microbial source tracking and may become a useful addition to the toolbox for environmental management.

Combined Application Strategy of Biochar/Phosphate Fertilizer Affects the rice Production by Regulating Soil Bacteria Taxa Composition

Phosphate fertilizer affects the rice yield and has a critical role in arable land management. Biochar regulates soil nutrient and soil microbe taxa composition. Our study aimed to elucidate the effects of co-application for biochar-phosphate on soil nutrient indicators, soil microorganisms, and crop production. Our experiment was set up as follows: 0 t/hm2, 28 t/hm2, and 55 t/hm2 biochar application rates with 20 kg/hm2, 40 kg/hm2, and 60 kg/hm2 phosphate fertilizer. The rice yield and soil nutrient indexes were observed and the differences between groups were analyzed based on multiple comparisons. 16S ribosomal DNA sequencing was used to analyze the soil bacteria structure. Redundancy analysis was performed to obtain the correlation relationships between microbial community marker species, soil nutrient indexes, and rice yield. The results showed that a higher application rate of biochar led to a significant alteration in the soil water content, bulk density, alkali-hydrolyzed nitrogen, and available phosphate content. In addition, high concentrations of biochar-phosphate fertilizer application elevated the soil bacterial diversity. Biochar had various effects on the relative abundance of soil bacteria taxa. Our study provided a theoretical basis for exploring efficient fertilization strategies in the rice cultivation industry and shed light on the extensive biochar application in agriculture production.

Copula lucentia sp. nov., a new box jellyfish (Cnidaria: Cubozoa: Carybdeida) from Western Mediterranean Sea

A new species of box jellyfish, Copula lucentia sp. nov., is described from El Campello, Spain, and compared to the holotype of Copula sivickisi that was successfully recovered after being lost for almost 60 years. So far, the only cubozoan species recorded in the Western Mediterranean was Carybdea marsupialis. The genus Copula just included the type species (Copula sivickisi) reported from different localities in the Pacific, Atlantic, and Indian Oceans. Morphologically, this new species possesses the typical characteristics of the genus Copula (four adhesive pads on the apex and a vertical keyhole-shaped rhopalial niche ostium) but it can be differentiated from the C. sivickisi holotype by the velarial canal pattern. In C. lucentia sp. nov., the velarial canal roots taper towards the velarial rim and each root bears one to two narrow triangular canals with sharp tips, resembling a bird beak. In contrast, the velarial canal roots of C. sivickisi bear two short, broad canals that increase breadth towards the velarial rim and split up into three- to six-lobed, finger-like canals with rounded tips, giving the canal pattern a paw-like appearance. Molecular analyses of mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 16S ribosomal DNA genes confirm the distinction of the new species and show that there are even more Copula species than expected, but which will not be focused on here. This study highlights not only that there are species yet to be discovered in the Mediterranean Sea but that a revision of the genus Copula is necessary.

Exploring the Microbial Diversity of Botswana’s Traditional Sourdoughs

Sourdough is one of the oldest technologies employed by humans to leaven bread because of its ability to enhance the flavour and structure of bread using micro-organisms. However, there is a lack of comprehensive information in Botswana regarding the diversity of sourdough starters and the fermentative micro-organisms responsible for spontaneous fermentation. The present study aimed to explore the microbial species diversity of sourdoughs in Botswana and gain insight into the unique microbial communities involved in sourdough production. A total of nine samples were collected from different areas in Botswana. The microbial diversity in sourdoughs was characterized through the sequencing of amplicons of the 16S ribosomal DNA and internal transcribed spacer regions. In silico polymerase chain reaction–restriction fragment length polymorphism and phylogenetics were utilized to determine the genetic diversity among the isolates. The dominant yeast species identified were Saccharomyces cerevisiae, Wickerhamomyces anomamlus, Pichia kudriazverii and kazachstania humilis. Additionally, the presence of Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, Liquorilactobacillus nageli and Bacillus cereus was also detected. It is worth noting that two species of acetic acid bacteria (AAB), namely Acetobacter pasteurianus and A. indonesiensis, were isolated, though in low levels, but the finding is significant in sourdough fermentation. The low occurrence of AAB (acetic acid bacteria) species observed in this study could be an important finding, as these bacteria are considered understudied, yet they are known to contribute significantly to the final product.

Structure and Evolution of Ribosomal Genes of Insect Chromosomes.

Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them.

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients.

Carbapenem-resistant Acinetobacter baumannii (CRAB) pneumonia has been a serious problem in the intensive care unit (ICU). However, defined characteristics of respiratory microbiome in CRAB pneumonia are lacking nowadays. This study aimed to analyze respiratory microbiome of CRAB pneumonia compared to non-CRAB pneumonia and reveal the clinical significance of respiratory microbiome data in these patients. Patients diagnosed with severe pneumonia with mechanical ventilation were enrolled in the ICU of a tertiary care hospital. Respiratory specimens were collected on days 1, 4, 7, and 14 in each participant via tracheal aspiration. Clinical data and outcomes of each enrolled patient were collected via electronic medical records. Microbiome analysis was conducted with collected respiratory specimens undergone by next-generation sequencing of microbial 16S ribosomal DNA. Six CRAB pneumonia, 4 non-CRAB pneumonia and 5 healthy controls were enrolled. In CRAB pneumonia, CRAB was detected in 3 patients by sputum culture at day 1, while it was negative at day 1 and detected later in the others by follow-up sputum culture. Beta diversity plot analysis showed differences between each group. Shannon index was decreased markedly at day 4 in CRAB pneumonia compared to the others. Among CRAB pneumonia cases, 3 respiratory specimens were culture-negative, but positive by microbiome analysis. Lower respiratory microbiome in CRAB pneumonia had distinct characteristics and early loss of diversity compared to non-CRAB pneumonia, which might be related to poor clinical course. Moreover, CRAB acquisition and colonization would be predicted by preemptive microbiome analysis, which will contribute to effective infection control in the ICU.

Combining Gram stain and 16S qPCR improved diagnostic accuracy for suspected pneumonia and could become a new metric in the rapid diagnosis of lower respiratory tract infections.

Introduction. The frequency of multidrug-resistant organisms (MDROs) in hospitals and the risk of delaying effective treatment result in the culture of respiratory secretions for nearly all patients with suspected pneumonia. Culture delays contribute to over prescribing and use of broader spectrum antibiotics.Gap statement. The need for improved rapid diagnostics for early assessment of suspected hospital pneumonia.Aim. To validate a new metric, enhanced Gram stain (EGS), to provide a rapid diagnostic test of high diagnostic accuracy that could be assessed in clinical trials of the use of antibiotics in suspected pneumonia.Methodology. Ninety-two residual lower respiratory samples previously tested by culture and Gram stain were re-tested by 16S ribosomal DNA real-time polymerase chain reaction (16S qPCR) and reported as a combined metric with Gram stain termed EGS. The EGS was assessed for diagnostic accuracy, standard performance measurements and correlation against culture. For samples with discordance between culture and EGS, 16S ribosomal DNA whole operon sequencing (16S rDNA WOS) was used for test resolution. An amended EGS (A-EGS was reassessed against culture.Results. Gram stain, 16S qPCR, EGS and A-EGS had respective diagnostic accuracies of 77.01 %, 82.76 %, 84.04 % and 94.19 %. The same platforms had respective correlation with culture of r = 0.67, r = 0.71, r = 0.81 and r = 0.89. EGS had the highest negative predictive value (NPV) of 93.18 % (81.99 %-97.62 %). Adding an 16S qPCR result is achievable in most routine laboratories and, combined with Gram stain, could improve early decision-making in patients with suspected hospital pneumonia.Conclusion. EGS could improve early decision-making in patients with suspected hospital pneumonia and could be assessed in clinical trials. The 16S rDNA WOS results in the A-EGS also supported the use of pathogen genomic sequencing in early decision making of suspected pneumonia.

Chromosome Mapping of Ribosomal DNA Clusters in Four Leaf-cutting Ant Species of the Genus Acromyrmex, with Description of a Triploid Individual in A. laticeps

The increase of cytogenetic data in the leaf-cutting genus Acromyrmex has shown interesting contributions to the evolutionary and taxonomic approaches, including the creation of a new genus and the description of chromosomal patterns allowing comparative studies within Acromyrmex as well as between this genus and other similar taxa. The conserved chromosome number in Acromyrmex is a notable feature, with some distinguishable chromosomes among the species. In this study, we describe the diploid karyotype of Acromyrmex laticeps in addition to an individual with all the metaphases triploids, suggesting a triploid individual. To the best of our knowledge, this is the first report of polyploidy in a fungus-growing ant. Furthermore, we mapped 18S ribosomal DNA on the chromosomes of A. laticeps and three other Acromyrmex species. Among them, three species showed the ribosomal DNA cluster pattern observed in other previously studied members of this genus, with a terminal location in the largest subtelocentric pair. Meanwhile, Acromyrmex balzani had these ribosomal DNA clusters in its entire short arm. The role of triploidy in ant evolution has also been discussed. The increase in chromosomal data of leaf-cutting ants may provide significant insights into the evolution of this peculiar ant group.