16S rDNA Research Articles

Integrated gut microbiome and UHPLC-MS metabolomics to reveal the prevention mechanism of pidanjiangtang granules on IGT Rats

IntroductionPidanjiangtang (PDJT) is a traditional Chinese medicine formula empirically used to treat impaired glucose tolerance (IGT) based on the "Pidan" theory from the classic ancient book Nei Jing. However, the mechanism of PDJT intervention for IGT remains to be studied. ObjectiveThis study aims to explore the mechanism of PDJT granules intervention in IGT by integrating gut microbiome and UHPLC-MS untargeted metabolomics. Materials and methodsThe IGT model was established in 6-week-old male Sprague-Dawley (SD) rats by feeding them a high-fat diet and using an STZ injection. The low, medium, and high doses of PDJT were used for six weeks. metformin (Glucophage) was used as the positive control drug. The efficacy of PDJT was evaluated using fasting blood glucose (FBG), blood glucose maximum (BGmax), blood lipid, and inflammatory factor levels. Finally, 16S rDNA gut microbiome sequencing with metabolomics analysis was used to explore the pharmacological mechanism of PDJT intervention in IGT. ResultsPDJT could reverse the phenotype of IGT rats, reduce blood glucose levels, improve lipid metabolism disorder, and reduce inflammatory response. Gut microbiome analysis found that PDJT can improve gut microbiota composition and abundance of three phyla (Firmicutes, Bacteroidota, Desulfobacterota) and four genera (unclassified_f__Lachnospiraceae, Ruminococcus, Allobaculum, Desulfovibrio), which play an important role in the process of PDJT intervention on glucose metabolism and lipid metabolism in IGT rats. UHPLC-MS untargeted metabolomics showed that PDJT could regulate the levels of 258 metabolites in lipid metabolism pathways, inflammatory response pathways, fat and protein digestion, and absorption. The combined analysis of the two omics showed that improving the body's metabolism by gut microbes may be the possible mechanism of PDJT in treating IGT. Thus, this study provides a new method to integrate gut microbiome and UHPLC-MS untargeted metabolomics to evaluate the pharmacodynamics and mechanism of PDJT intervention in IGT, providing valuable ideas and insights for future research on the treatment of IGT with traditional Chinese medicine.

Temporal dynamic of soil microbial communities and antibiotic resistance markers exposed to increasing concentrations of sulfamethoxazole

The reuse of treated wastewater (TWW) for irrigation is widely applied to alleviate pressure on freshwater resources. However, TWW contains antibiotics that once in soils, can exert selective pressure, promoting the emergence and spread of antimicrobial resistance (AMR) in the environment. Current environmental risk assessments for antibiotic residues rely on indicators such as Predicted No Effect Concentrations (PNECs), usually determined in liquid media. These PNECs aim to predict antibiotic concentrations that may promote resistance in the environment. Given the complexity of soil matrices, few studies have established PNEC values for soil, which likely differ significantly from aquatic environments.To address this gap, we developed a simplified experimental model using soil microcosms irrigated with TWW and the antibiotic sulfamethoxazole (SMX) to estimate threshold concentrations favouring resistance transfer or/and emergence within the soil microbiome. We identified SMX concentrations between 0.01 and 0.1 mg/kgdry soil that likely increased the abundance of sulfonamide resistance genes in soil. A time window of 1 to 7 days post-exposure showed a temporary rise in sul1 and intl1 gene abundance (over 1 log/soil 16S rDNA), the appearance of SMX transformation products, and an increase in some Rhodocyclaceae. After 1.5 months of incubation and complete SMX transformation, the relative abundance of sul1 and intl1 remained about 0.5 log higher than in SMX-free controls and soils with SMX levels below 0.1 mg/kg dry soil. A persistent transformation product, 4-N-glucuronide-SMX, was also observed.Here, the estimated PNEC for SMX in soil, between 0.01 and 0.1 mg/kg, exceeds typical SMX concentrations found in soils exposed to TWW. This may suggest low impact on resistance selection for this compound in the context of TWW exposure. However further studies on other soils, water, and antibiotics need to be conducted to expand our knowledge on soil PNECs.

A new genus and a new species of microcotylids (Polyopisthocotyla, Platyhelminthes), gill parasite of the pink dentex Dentex gibbosus (Teleostei, Sparidae) off Tunisia and notes on Polyopisthocotyla and Monopisthocotyla from Dentex spp.

The study of the polyopisthocotylan parasites of marine fishes in the western Mediterranean is carried on using an integrative approach combining morphology and DNA barcodes. Ktarius patrickbrueli n. gen. n. sp (Polyopisthocotyla, Microcotylidae), from the gills of pink dentex Dentex gibbosus (Teleostei, Sparidae) from the western Mediterranean Sea off Tunisia, is described. Anatomical and morphological features of the new genus are described, and the molecular barcodes for nuclear and mitochondrial markers (28S rRNA and cox1) are generated. The new genus is closely related to Microcotyle by sharing a symmetrical haptor, inverted question mark-shaped ovary and unarmed vagina. However, Ktarius n. gen. can be distinguished from Microcotyle and other Microcotylinae taxa by an unarmed male copulatory organ, formed by a long muscular cirrus, a basal layer of concentric muscles, and an elongated thick-walled ejaculatory bulb. A partial 28S rDNA sequence of K. patrickbrueli n. gen. n. sp. was obtained and found to be distinct from all known microcotylid sequences, with a p-distance of 5–13%. A phylogenetic tree constructed from available microcotylid sequences revealed that K. patrickbrueli n. gen. n. sp. clustered in a strongly supported clade of Microcotylinae, containing species of Omanicotyle, Bivagina, and Microcotyle confirming its belonging to the Microcotylinae subfamily. The cox1 sequences of K. patrickbrueli n. gen. n. sp. were highly divergent from the closely related genus Pauciconfibula and confirmed its distinction. This new genus is the third polyopisthocotylan genus to be described from sparids of Dentex.

Description and phylogenetic position of an unusual genus and species of allocreadiid trematode from a characid freshwater fish in South America

The worldwide distributed family Allocreadiidae Looss, 1902 is predominantly parasitic in freshwater fish and occasionally in amphibians and reptiles. It contains 15 genera, of which only Allocreadium, Creptotrema, Wallinia and Creptotrematina have been reported in Argentina. The records of Allocreadium species still require further verification. The discovery of an allocreadiid digenean parasitizing Pseudocorynopoma doriae led us to erect a new genus for which the name Martorellia n. gen is proposed. It is characterized by poorly developed ventrolateral muscular lobes and a transversely elongated ovary, with the most characteristic feature being the presence of vitelline follicles in two fields (one anterior at level of ventral sucker and one posterior to the testis), which are not confluent in the middle. The phylogenetic tree reconstructed with 28S rDNA sequences placed the new genus as the sister taxa of Creptotrematina. Although both genera are separated by a small genetic distance, it is comparable with those separating other allocreadiid genera. The discovery of Martorellia liciae gen et sp. nov. provides further evidence of the great diversity of Allocreadiidae in South America. The analysis of new samples from different South American hosts with an integrative taxonomic approach as the one used here allows a better understanding of the evolutionary history and biogeography of allocreadiids in the Americas.

Taxonomic revision of the genus Sarcosphaera (Ascomycota: Pezizales) in Europe and North America revealed unexpected diversity

Sarcosphaera (Ascomycota: Pezizales) is a genus of rare spring fungi, currently encompassing a single species, S. coronaria, which is red-listed in many European countries. The genus is characterized by large bright-colored fruit-bodies and high arsenic content. This study investigates the genetic diversity across Europe and North America. Using integrated molecular techniques, including ITS and 28S rDNA sequencing, we aimed to resolve the taxonomic ambiguities and assess their arsenic hyperaccumulation capabilities, a rare trait among fungi. We identified the presence of two species in the Western Palearctic (S. coronaria, S. crassa) and at least 12 additional lineages in North America, indicating a more complex taxonomic structure than previously recognized. To consolidate the taxonomy and nomenclature of these fungi, we selected reference specimens for S. coronaria and S. crassa and discussed their morphological and ecological differences. Two genera, Caulocarpa (C. montana) and Hydnotryopsis (H. setchellii), a genus comprising hypogeous fungi, are newly placed in the genus Sarcosphaera. Sarcosphaera is thus another genus where the rapid evolution of hypogeous forms from their above-ground ancestors took place. Furthermore, two new Sarcosphaera species, S. columbiana and S. pacifica, are described from the Pacific Northwest. Investigation of arsenic content of Sarcosphaera species revealed that arsenic mass fractions in ascocarps vary significantly between species and even within species across different geographical locations. Our findings have important implications for the taxonomy and conservation of the S. coronaria species complex and also point to future directions for further research in the taxonomy, geomycology, and toxicology of this group of fungi.

Nuclear ribosomal transcription units in Asian Paragonimus species (Paragonimidae: Platyhelminthes): genetic characteristics, polymorphism, and implications for intersuperfamilial phylogeny.

The entire transcribed sequences (from the 5' terminus of 18S to the 3' terminus of 28S rRNA genes) of the ribosomal transcription units (rTU*) of five Asian Paragonimus species were obtained and characterized. The rTU* length was 7661bp for P. heterotremus (LC strain, Vietnam), 7422bp for P. iloktsuenensis (Amami strain, Japan), 6932bp for P. skrjabini miyazakii (OkuST1 strain, Japan), 7422bp for P. ohirai (Kino strain, Japan), and three strains of P. westermani: 8616bp (Megha strain, India), 7292bp (Bogil strain, South Korea), and 7052bp (QT2 strain, Vietnam) without intergenic spacer region (IGS). All seven Asian Paragonimus strains' genetic characteristics were described, including the length of individual genes/regions, repeat polymorphism, base composition, and skewness. To investigate the superfamilial relationships in the Xiphidiata, with a focus on the Troglotrematoidea and its associated superfamilies, we used the PhyML software package to create three comprehensive maximum-likelihood phylogenies. The datasets used were 83 concatenated 28S + 18S, 83 single complete 18S, and 157 single, partial 28S rDNA sequences, respectively, from entire rTUs and/or accessible ribosomal sequences of the same species from the suborders Xiphidiata, Echinostomata, and Haplosplanchnata, with a Schistosoma sequence as an outgroup. Three phylogenetic trees revealed that Echinostomata and Haplosplanchnata are monophyletic, while Xiphidiata is polyphyletic and contains the monophyletic Troglotrematoidea. The concatenated 18S + 28S and single 18S phylogenies revealed well-bootstrap supported seven superfamilies (Troglotrematoidea, Haploporoidea, Gorgoderoidea, Brachycladioidea, Microphalloidea, Plagiorchioidea, and Opecoeloidea) that are monophyletic in the Xiphidiata. The Haploporoidea was a basal superfamily nested close to the Gorgoderoidea and Troglotrematoidea and was not supported as a distinct suborder Haploporata. Six of seven xiphidiatan superfamilies were monophyletic in the partial 28S phylogeny, with the exception of Opecoeloidea, which was separated into two different subclades: Opecoelidae and Stenakridae/Zdzitowieckitrematidae. The monophyletic Haploporoidea/Haploporata was separated from the Gorgoderoidea associates and placed in a marginal group in Xiphidiata. There were two notable clusters in the Paragonimidae: mixed-Paragonimus, which included a fairly compact group of P. heterotremus strains, and P. westermani/siamensis, which was divided into geographical/country strain groups. In conclusion, combined ribosomal rDNA sequences were more effective than single rDNA markers in resolving interfamilial and familial relationships. The ribosomal datasets presented here will be useful for taxonomic reassessment, as well as evolutionary and population genetics research in the Troglotrematoidea and other superfamilies in the Xiphidiata and the class Trematoda.

Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage

This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4–5.8, 5.8–6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC–MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4–5.8 and 5.8–6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.

Dermacentor species (Acari: Ixodidae) in western Canada, with detection of Dermacentor similis.

Numerous tick species are undergoing significant range expansion in Canada, including several Dermacentor spp Koch (Acari: Ixodidae). With the recent description of Dermacentor similis Lado in the western United States, additional research is required to determine the current range of this species. Five hundred ninety-eight Dermacentor spp. were collected from companion animals in the western Canadian provinces of British Columbia, Alberta, and Saskatchewan. Ticks were morphologically identified to species, followed by PCR and gel electrophoresis of the ITS-2 partial gene target (n = 595). Ninety-seven percent (n = 579/595) generated valid banding patterns. The banding pattern for the majority (74%, n = 206/278) of Dermacentor spp. from southern British Columbia was consistent with D. variabilis (Say), while 26% (n = 72/278) was consistent with D. andersoni Stiles. For samples from Alberta, 38% (n = 3/8) had banding patterns consistent with D. variabilis and 63% (n = 5/8) with D. andersoni. All (n = 293) ticks from Saskatchewan had banding patterns consistent with D. variabilis. After the description of D. similis was published, DNA sequencing of mitochondrial (16S rDNA gene, COI gene) and nuclear (ITS-2) markers was used to confirm the identity of 40 samples. Twenty-seven samples that had banding patterns consistent with D. variabilis from British Columbia were confirmed to be D. similis. One sample from Alberta and five from Saskatchewan were confirmed to be D. variabilis and seven samples from British Columbia were D. andersoni. The ITS-2 amplicons were not useful for differentiating between D. variabilis and D. similis. These results provide evidence of D. similis in western Canada and highlight that sequences of the mitochondrial genes are effective for distinguishing D. andersoni, D. variabilis, and D. similis.

Effects of water-insoluble wheat bran-fraction powder on disease activity and caecal microbiota in dextran sodium sulphate-induced inflammatory bowel disease mouse model.

Water-soluble arabinoxylan exerts anti-colitic effect and exhibits ameliorative activity in an inflammatory bowel disease (IBD) mouse model. Water soluble fibre from wheat bran (WB) also exhibits anti-colitic effect. However, arabinoxylan is a primary compound of insoluble polysaccharide (hemicellulose) in WB. This study aimed to clarify the anti-IBD effects of the WB water-soluble (WBS) and water-insoluble (WBI) fractions. WB suspension was autoclaved and fractionated to WBS and WBI. C57BL/6 mice were divided into control (CT), dextran sodium sulphate (DSS), WBI, and WBS groups. They were fed as follows from day 1: CT, standard diet and distilled water; DSS and WBI, 3% (w/v) DSS in drinking water; WBI, 8% (w/w) WBI diet; and WBS, 50% (v/v) WBS and 3% (w/v) DSS in water. DSS group mice showed diarrhoea, body weight reduction, and blood in faeces by day 5 and colon tissue damage by day 6. These inflammatory indices were significantly inhibited by treatment with WBI. Amplicon sequencing of the 16S rDNA (V4) gene of the caecal contents of the CT, DSS, and WBI groups showed that the abundances of Escherichia, Allobaculum, and Bacteroidaceae increased and that of Faecalibaculum decreased in the DSS group. KEGG pathway prediction showed that amino acid metabolism and lipopolysaccharide biosynthesis decreased and increased, respectively, in the DSS group. However, WBI treatment tended to suppress these effects. WBI, rather than WBS, reduces inflammation and maintains the gut microbiota. However, further studies are warranted to elucidate the properties of the WBI active components and efficacy of WBI metabolites on gut microbiota, particularly on Faecalibaculum.

Super Astragalus polysaccharide in specific gut microbiota metabolism alleviates chronic unpredictable mild stress-induced cognitive deficits mice

Chronic stress affects intestinal microbiota. Astragaloside IV (AS), called super Astragalus polysaccharide, is a monomer component of traditional herbs Astragalus membranaceus which belongs to medicinal food homology (MFH), exerts a neuroprotection effect, but the underlying mechanism has not yet been elucidated. Intestinal flora is also involved in the biotransformation of the active ingredients of MFH species, thus affecting their physiological and pharmacological properties. In this study, we found that AS improved CUMS-induced cognitive impairment, inhibited neuroinflammation, and restored intestinal barrier damage, but the improvement was suppressed by the elimination of gut microbiota, suggesting a key regulatory role for the microbiota. The results of 16S rDNA sequencing showed that AS treatment significantly increased the relative abundance of Lactobacillus reuteri (L. reuteri) and Bacteroides acidifaciens. Furthermore, supplementation of L. reuteri rather than Lactobacillus plantarum restored the effect of AS-supplied dysbiosis mice via inhibition of inflammatory repose and the maintenance of the intestinal epithelial barrier, indicating that dietary AS requires L. reuteri to ameliorate cognitive injury. These findings provide evidence for new therapeutic strategies to treat chronic stress and support the role of specific bacteria in the intestinal environment that metabolizes the AS.

Identification and Characterization of a surfactin from Pseudomonas gessardii: A Symbiotic Bacterium with Potent Anticancer Activity

Prasiola japonica, traditionally used as food and folk medicine in South Korea, exerts pharmacological properties, including antioxidant, anti-inflammatory, antidiabetic, and anticancer effects. In this study, we explored symbiotic microbes associated with P. japonica and identified Pseudomonas gessardii as a nonpathogenic symbiotic bacterium through 16S rDNA sequencing. Bioactivity-guided fractionation of P. gessardii ethanol extracts, utilizing a series of non-polar to polar solvents, led to the isolation of a single bioactive compound (SF10) from the ethyl acetate fraction. Structural analysis using LC-MS and NMR spectroscopy identified SF10 as surfactin C15, a lipopeptide consisting of 7 amino acids and a β-hydroxy fatty acid chain containing 15 carbon atoms. This represents the first discovery of surfactin production in P. gessardii, expanding known surfactin-producing genera beyond Bacillus. In HT-29 colorectal cancer cells, surfactin C15 demonstrated significant anticancer activity through multiple mechanisms: inhibition of cancer stem cell marker CD133 expression, upregulation of pro-apoptotic factors (CHOP, PUMA, DR5), and modulation of cell cycle regulators (p21, cyclin E1, CDK5). Furthermore, surfactin C15 induced necrotic cell death, confirmed by increased lactate dehydrogenase release and flow cytometry analysis showing dose-dependent increases in necrotic cell populations. This study reveals a novel source of surfactin with unique cancer cell-targeting properties, particularly through its ability to induce necrosis in colorectal cancer cells, suggesting potential therapeutic applications in cancer treatment.

Bioaerosol emission and exposure risk from a wastewater treatment plant in winter and spring

The potential health risks posed by bioaerosols containing pathogens originating from wastewater treatment plants (WWTPs) have gaining intensive attention. This study designated sampling locations within a WWTP situated in Xi'an, a major city in northwest China. The airborne bacterial concentration, taxonomic composition, and the associated health risks were analyzed in the aeration tanks with bottom microporous aeration system. The Anaerobic-Anoxic-Oxic (AAO) tank emitted significantly higher culturable bacteria (1.58×104 CFU m−3 in spring, 6.69×103 CFU m−3 in winter) compared to Double-ditch (DE) oxidation ditch and aerated grit chamber (AGC) chamber, aligning with 16S rDNA quantification results. The bacterial concentrations are higher in spring than that in winter, with the AAO tank posing the highest exposure risk during the spring season. The dominant genera in the air samples include Cutibacterium, Lawsonella, Acinetobacter, Pseudomonas, and Aeromonas. Among the identified genus, 139 bacterial genera were identified as potential human pathogens like Neisseria, Moraxella, Haemophilus, Escherichia-Shigella and Streptococcus. These pathogens further elevate exposure risks from WWTP bioaerosols. This study provides relevant information on the seasonal health risk variations tied to bioaerosol emissions from diverse aeration tanks with bottom microporous aeration system in the mega city of northwest China, emphasizing the imperative to enhance the management and control measures for bioaerosols originating from the AAO tank.

Cloning, Expression, Purification and Enzymatic Characterization of Low-temperature Cholesterol Esterase from Marine Panthenia Agglutinosa

BACKGROUND: The low-temperature cholesterol esterase is primarily used in industries such as papermaking and healthcare. OBJECTIVE: To discover a microorganism with high cholesterol esterase activity and tolerance to low temperatures, leading to the promotion of the sustainable utilization of marine cold-adapted microbial resources and fostering industrial development. MATERIALS AND METHODS: This study isolated a strain producing low-temperature cholesterol esterase from marine samples in the China Bohai Sea. The strain was identified through 16S rDNA sequencing and named Panthenia agglutinosa Y03. The cholesterol esterase gene (PaChe) from P. agglutinosa Y03 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme PaChe was purified and characterized. The structure of PaChe was predicted using AlphaFold2, and molecular docking was performed with cholesterol linoleate as the ligand. RESULTS: The enzyme protein has a molecular weight of 56.35 KDa, a theoretical pI of 7.24, lacks a signal peptide, and exhibits structural features of the α/β hydrolase superfamily protein. The concentration of the purified PaChe is 0.5 mg/mL, with a specific activity of 42.7 U/mg. The optimal working temperature is 30 °C, and the enzyme retains activity at 4 °C , demonstrating weaker thermal stability. The optimal pH is 7, and the enzyme maintains over 70% activity at pH 9. Na +, Ca 2+ and Mg 2+ are the primary activators, while Ba 2+, Fe 2+, Mn 2+, Cu 2+ and chemical agents such as SDS as inhibitors, with Cu2+ exhibiting particularly significant inhibitory effects. CONCLUSION: This study establishes the theoretical groundwork for the development and utilization of a novel lowtemperature cholesterol esterase.

Lactobacillus plantarum LP104 improved intestinal and brain inflammation by modulating TLR4 pathway and gut flora in alcohol liver injury mice

In this study, Lactobacillus plantarum LP104 (LP104) originating from kimchi was treated to C57BL/6N mice fed a chronic-plus-single-binge ethanol diet for ten days, aiming to evaluate the effects of the probiotics on intestinal and brain inflammation in the alcohol-induced liver injury model. Dietary supplementation with LP104 significantly reduced the concentrations of alanine aminotransferase (ALT), aspartate aminotransferase (AST), total cholesterol (TC), triglycerides (TG) and low-density lipoprotein cholesterol (LDL-C) in alcoholic hepatic injury mice. The 16S rDNA sequencing results inferred that LP104 modulated the intestinal microbiota by depleting inflammation-related bacterial genera Proteobacteria and enriching Lactobacillus and Roseburia. Furthermore, LP104 intervention attenuated alcohol-induced gut inflammation by the TLR4 signaling pathway, which regulated the expressions of intestinal tight junction proteins such as ZO-1, Claudin-1 and Occludin. Subsequently, LP104 intake exerted neuroprotection by restoring neurotrophic factor levels and the blood-brain barrier (BBB) function to decrease lipopolysaccharide (LPS) levels in the serum. The western blotting results suggested LP104 ameliorated alcohol-induced brain inflammation by inhibiting the LPS/TLR4 signaling pathway in mice. Spearman's correlation analysis demonstrated that differential intestinal bacterial taxa were connected with the expressions of inflammation-related proteins in both gut and brain of alcohol liver injury mice.

The microbiota comparative analysis of the characteristics between colorectal adenomatous polyps and normal mucosal intestinal.

The aim of this study is to systematically examine and compare the characteristics distinguishing colorectal adenomatous polyps from normal mucosal intestinal microbiota. A total of 30 specimens were obtained from patients diagnosed with colorectal adenomatous polyps (adenoma group) who underwent endoscopic removal at Wenzhou People's Hospital between September 2021 and November 2021. Concurrently, 30 normal mucosal specimens were collected from patients without adenomatous polyps (control group). Subsequently, microbiome total DNA extraction was carried out, followed by PCR amplification targeting the V3-V4 region of the 16S rDNA. High-throughput sequencing was conducted using the Illumina MiSeq platform. Subsequent to sequencing, bioinformatics analysis was used to assess the diversity, composition, and functional aspects of the intestinal microbiota in both study groups. A notable dissimilarity in the microbiota structure was identified, specifically within the transverse colon, between these two groups ( P < 0.05). Species composition analysis revealed that Escherichia , Fusobacterium , and Bacteroides were predominant bacteria in both groups, with Escherichia and Enterobacter displaying significant differences at the genera level between the control group and the adenoma group ( P < 0.05). Correlation analysis and functional prediction demonstrated substantial disparities in interactions among dominant intestinal microbial genera within patients from both groups. Additionally, it was discovered that the intestinal microbiomes in patients in the adenoma group exhibited a significantly higher pathogenic potential. Upon conducting a comprehensive analysis, it was discerned that the microbiota present in the transverse colon of the control group exhibited distinctive characteristics that may contribute to the maintenance of intestinal health.

Lactiplantibacillus plantarum P101 Ameliorates TiO2 NP-Induced Bone Injury in Young Rats by Remodeling the Gut Microbiota and Inhibiting the Production of Pro-Inflammatory Cytokines.

To evaluate the therapeutic effect of oral administration of Lactiplantibacillus plantarum P101 (P101) on skeletal injury in young rats exposed to titanium dioxide nanoparticles (TiO2 NPs), and explore the potential mechanism. Four-week-old male rats were orally administration to TiO2 NPs and supplemented with P101 2hours later for 4weeks. The growth and development, food intake, bone metabolism and serum inflammatory markers of the rats were evaluated. Their tibias were observed and evaluated using microcomputed tomography (micro-CT), tartrate-resistant acid phosphatase (TRAP) staining, immunohistochemistry (IHC) and real-time quantitative PCR (RT-qPCR). We observed the tibia growth plate using safranin and fast green staining. 16S rDNA sequence analysis of fecal samples was performed to observe changes in the gut microbiota. Our results showed that TiO2 NPs can lead to bone growth inhibition and osteoporosis, induce intestinal flora imbalance, and induce inflammation in young rats. Further mechanistic studies suggested that TiO2 NPs disrupts intestinal flora and increases serum IL-1β levels, which increased the expression of RANKL in bone, thereby enhancing osteoclast differentiation and function, leading to bone loss. Through a P101 supplementation experiment, we found that P101 ameliorated the inflammation and osteoporosis on bone caused by TiO2 NPs. This study showed that the mechanism by which P101 alleviates bone damage caused by TiO2 NPs may be through restoring intestinal microbial homeostasis and inhibiting inflammatory response.

Short-chain fatty acids enhance muscle mass and function through the activation of mTOR signalling pathways in sarcopenic mice.

Sarcopenia is a prevalent muscle disorder in old people leading to higher fracture rate, mortality, and other adverse clinical outcomes. Evidence indicates that short-chain fatty acids (SCFAs), which are beneficial gut microbial metabolites, were reduced in old people with sarcopenia. This study aimed to determine whether the use of SCFAs as a supplement can be a therapeutic strategy of sarcopenia in a pre-clinical model. Seven-month-old pre-sarcopenic senescent accelerated mouse prone 8 (SAMP8) mice received daily SCFAs cocktail (acetate, butyrate, and propionate) for 3months. Age-matched senescence accelerated mouse resistant 1 (SAMR1) and SAMP8 mice receiving sodium-matched drinking water were control groups. The gut microbiota composition analysis of aged mice with or without sarcopenia was conducted by 16S rDNA sequencing. Gut barrier-related proteins and lipopolysaccharide (LPS) concentration were biomarkers of gut permeability. Colon inflammation levels, circulatory SCFAs concentration, muscle quality, function, and underlying pathways were detected by cell number counting, RT-qPCR, gas chromatography-mass spectrometry, measurements of muscle wet weight and grip strength, ex vivo functional test, treadmill endurance test, transcriptomic sequencing, morphological and immunofluorescent staining, as well as western blot. To investigate the role of mTOR signalling pathways in SCFAs treatment, C2C12 myotubes were treated with rapamycin. Aged SAMP8 mice had different microbiota composition, and lower serum butyric acid compared with SAMR1 mice (P<0.05). SCFAs treatment reversed the increment of colon inflammation (2.8-fold lower of il-1β) and gut barrier permeability (1.7-fold lower of LPS) in SAMP8 mice. Increased muscle mass, myofibre cross-sectional area, grip strength, twitch and tetanic force were found in SCFAs-treated mice compared with control SAMP8 mice (P<0.05). Anti-fatigue capacity (1.6-fold) and muscle glycogen (2-fold) also improved after SCFAs treatment (P<0.05). Transcriptomic analysis showed that AMPK, insulin, and mTOR pathways were involved in SCFAs treatment (P<0.05). Regulation of AKT/mTOR/S6K1 and AMPK/PGC1α pathways were found. SCFAs attenuated fat infiltration and improved mitochondria biogenesis of atrophic muscle. In vitro studies indicated that SCFAs inhibited FoxO3a/Atrogin1 and activated mTOR pathways to improve myotube growth (P<0.05), and rapamycin attenuated the effect of SCFAs through the inhibition of mTOR pathways. This study demonstrated that bacterial metabolites SCFAs could attenuate age-related muscle loss and dysfunction, and protein synthesis-related mTOR signalling pathways were involved both in vivo and in vitro.

Karyotype diversity of Polybia (gr. occidentalis) species complex (Hymenoptera: Vespidae): Taxonomic and evolutionary implications

AbstractPolybia is a common wasp genus found in most of South America. Polybia (gr. occidentalis) encompasses several species that are difficult to identify because of their similar morphologies. Our goal was to cytogenetically characterize three species belonging to Polybia (gr. occidentalis) and discuss the importance of cytogenetic data for integrative taxonomy. Polybia colonies were sampled from different regions of Brazil to perform classical and molecular cytogenetic analyses. Polybia paulista and Polybia sp. 1 showed 2n = 34 and 18S rDNA loci on two chromosomes, whereas Polybia sp. 2 showed 2n = 40 and 18S rDNA clusters on four chromosomes. The microsatellites GA(15), GAG(10), CAA(10), TTAGG(6), and TCAGG(6) showed similar distributions among the species, forming blocks in the euchromatic regions of the chromosomes, whereas CGG(10) did not yield any positive markings. In contrast, TAT(10) hybridized on the centromeric heterochromatin, showing differences in the number of marked chromosomes among the species. Therefore, it may potentially be a species‐specific cytotaxonomic marker in this group of wasps, but this feature needs further investigation. Fluorochromes evidenced that AT‐rich DAPI+ sequence distribution was coincident with heterochromatin, while the distribution of CG‐rich CMA3+ sequences was coincident with the 18S rDNA region. The present study revealed differences in diploid number, heterochromatin content, 18S rDNA sites, and microsatellite patterns between morphologically similar species, demonstrating the usefulness of cytotaxonomy in studying species complexes.

Molecular phylogeny of Boninia (Platyhelminthes: Polycladida), with description of a new species from the Pacific coasts of Panama.

Mesopsammic polyclad members in the family Boniniidae have attracted attention in terms of their evolutionary shifts of microhabitat and their unique morphology such as a pair of pointed tentacles extending from the anterolateral margins and prostatoid organs harbouring stylets. Here, we establish a new species of this family as Boninia panamensis sp. nov. from the Pacific coasts of Panama, based on its morphological characteristics of (i) four cerebral and 61-80 marginal eyespots, (ii) two prostatoid organs located anterior and posterior to the penis papilla, and (iii) two uterine canals departing from the anterior part of the Lang's vesicle. We also report Boninia cf. uru from Hawai'i, USA, based on its morphological identity with B. uru from Okinawa, Japan, along with their genetic distances for the partial cytochrome c oxidase subunit I (COI ) sequences, which were beyond the range of intraspecific differences observed in congeners in this study. Boninia oaxaquensis is also reported from Panama as a new locality for the species. Involving the above-mentioned three species sequenced herein, we reconstructed molecular phylogenetic trees of Boninia based on the four gene markers (18S rDNA, 28S rDNA, 16S rDNA and COI ). Our phylogenetic trees indicated the synapomorphy within the genus Boninia of the small numbers of stylets (2-4) and the connection route of the uterine canals to the Lang's vesicle. The results also showed a characteristic distribution pattern in which pairs of species in distinct lineages occurred sympatrically with different microhabitats, as observed in Boninia uru and Boninia yambarensis in Okinawa and B. panamensis sp. nov. and B. oaxaquensis in Panama. In addition, we discuss possible speciation pathways in this genus based on the tree topology. ZooBank: urn:lsid:zoobank.org:pub:D414BACD-C14A-4B34-8AF9-7ACBA28F46D0.

First Report of Leaf Spot on Lonicera japonica Caused by Aspergillus niger in China.

Honeysuckle (Lonicera japonica Thunb, LJ) is a common medicinal and edible plant (He et al. 2022). It has been utilized in various industries such as biomedicine, animal husbandry, and food production (Li et al. 2014; Su et al. 2020). In June 2023, a significant leaf lesion was observed on approximately 20% of honeysuckle "Juhua No.1" leaves in a 3.33-ha field at the base of Julu County, Hebei province, China. Almost all leaves were infected. Leaf spot disease occurred in the field honeysuckle throughout the flowering period, especially after picking. The disease mainly infected the leaves of honeysuckle, forming irregular spots on the edge of the leaf surface with black-brown edges, the midrib and lateral veins were affected (Figure S1A). In advanced stages, the entire leaf would become necrotic. For pathogen isolation, small pieces (4×4 mm) of the infected tissue from diseased leaves were surface sterilized with 75% ethanol and 5% sodium hypochlorite, rinsed with the sterile water, incubated on PDA. Finally, six isolated pathogens were obtained. Hyphae were white. The mycelium was multicellular, had diaphragm. Conidiophores protruded from the stroma, started as spherical structures and gradually developed into radial, black-brown formations. Spore acrosome was subglobose, bilayered pedicels covering acrosome, 40-60 µm in diameter, yellowish brown (Figures S1B, S1C). Based on morphological and cultural characteristics, the leaf spot disease fungus was tentatively identified as Aspergillus spp. (Wei 1979). To test the pathogenicity of pathogen, leaves of three healthy potted honeysuckle "Juhua No.1" plants were inoculated by sprayed with conidial suspensions (106 spores/ml) (Figure S1D). Negative controls were established by inoculating leaf with sterile distilled water. All plants were incubated in a greenhouse at 28 ± 2℃. The experiment was replicated three times. After 10 days, typical leaf spot symptoms were observed on inoculated leaves, whereas no symptoms were found on the control groups. The re-isolated fungus from the inoculated leaves displayed the same morphological traits (Figures S1E-S1H), again identified as Aspergillus spp., confirming Koch's postulates, designated as H2. To confirm the pathogen's identity, genomic DNA was extracted from the pathogenicity isolate H2. The 18S rDNA and the ITS genes were amplified and sequenced using primer pairs S1/S2 (Zhang et al. 2018) and ITS1/ITS4 (Zhang et al. 2023), respectively. Results of BLAST searches showed that the 18s rDNA and ITS sequences of H2 were highly homologous (>99%) with Aspergillus niger. The close genetic relationship indicated that H2 belonged to the genus Aspergillus (Figure S2a). We further sequenced the whole genome of H2. The sequence data were available in the NCBI GenBank (Accession number: PRJNA1117256). We also analyzed the ANI (Yoon et al. 2017) and digital DNA-DNA blotting (dDDH) (Figures S2b, S2c). The ANI values of H2 compared to Aspergillus niger CBS 554.65 and Aspergillus niger KJC3 were higher than 95%. The dDDH values of H2 compared to Aspergillus niger CBS 554.65 and Aspergillus niger KJC3 were higher than 70%. Above all results, honeysuckle leaf spot disease was identified as Aspergillus niger. This is the first report of leaf spot on Lonicera japonica caused by Aspergillus niger in China. Our findings expand the geographical range of A.niger-infected plants, also provide reference for scientific prevention and control of honeysuckle leaf spot disease.