rDNA Sequences Research Articles

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study.

The oral microenvironment contributes to microbial composition and immune equilibrium. It is considered to be influenced by dietary habits. Phenylketonuria (PKU) patients, who follow a lifelong low-protein diet, exhibit higher prevalence of oral diseases such as periodontitis, offering a suitable model to explore the interplay between diet, oral microbiota and oral health. We conducted 16S rDNA sequencing on saliva and subgingival plaque from 109 PKU patients (ages 6-68 years) and 114 age-matched controls and correlated oral microbial composition and dental health. PKU patients exhibited worse dental health, reduced oral microbial diversity and a difference in the abundance of specific taxa, especially Actinobacteriota species, compared to controls. PKU patients with poor periodontal health exhibited higher alpha diversity than the orally healthy ones, marked by high abundance of the genus Tannerella. Notably, the observed taxonomic differences in PKU patients with normal indices of decayed/missing/filled teeth, plaque control record, gingival bleeding index and periodontal screening and recording index generally differed from microbial signatures of periodontitis. PKU patients' reduced microbial diversity may be due to their diet's metabolic challenges disrupting microbial and immune balance, thus increasing oral inflammation. Higher alpha diversity in PKU patients with oral inflammation is likely related to expanded microbial niches.

Comparative characterization of supragingival plaque microbiomes in malocclusion adult female patients undergoing orthodontic treatment with removable aligners or fixed appliances: a descriptive cross-sectional study

ObjectivesThis study aimed to explore the effects of removable aligners and fixed appliances on the supragingival bacterial communities in adult female patients undergoing orthodontic treatment.MethodsSupragingival plaque samples from 48 female individuals underwent microbiome analysis (16S rRNA gene sequencing) using PacBio Sequel sequencing. The study included 13 adults without orthodontic treatment needs as the control group (Group C), and 35 patients with comparable initial orthodontic conditions who received treatment at a university clinic in Beijing, China. The treatment involved either traditional fixed brackets (Group B, n = 17) or Invisalign® aligners (Group AT, n = 18). Bioinformatics methods were used for data analysis.ResultsFrom the 48 plaque samples, a total of 334,961 valid reads were obtained, averaging 6,978 sequences per sample. The 16S rDNA sequences were classified into 25,727 amplicon sequence variants (ASVs). Significant variances in alpha and beta diversity among the groups were noted. Group B microbiome exhibited an increased presence of Gram-negative bacteria. At the phylum level, Actinobacteriota was significantly more prevalent in Group C samples, while Bacteroidota was enriched in Group B samples. Family-level relative abundance analysis showed a notable increase in Saccharibacteria (formerly TM7) and Prevotellaceae in Group B. Genus-level analysis revealed a significant rise in Lautropia in Group AT. Fixed orthodontic appliances were linked to oral microbiome changes, notably an enhanced relative abundance of anaerobes, including periodontal pathogens.ConclusionThe observation points to the impact of orthodontic appliance on the oral microbial community, highlighting the difference between traditional braces (Group B) and clear aligners (Group AT)in terms of the predominance of anaerobic and gram negative bacteria. This emphasizes the importance of considering the microbiological effects when choosing orthodontic appliance and underscores the need for tailored oral hygiene practices for individuals undergoing these treatments. This research might provide insights that could assist in the development of innovative cleaning techniques and antibacterial materials.

Molecular identification and characterizations of rhizobacterial isolates collected from lentil rhizosphere of Indo-gangetic plains.

Plant growth promoting rhizobacteria (PGPR) are also known to colonize in the soil rhizosphere and prevent the development of other soil borne pathogens residing in the root surface. These microorganisms play a vital role in growth and development of the plant and also enhances the soil fertility by enriching the soil with different beneficial nutrients. This study was aimed at isolation of different rhizobacteria and their molecular characterization in search of efficient bacterial strains with multiple growth regulating activities. A total 36 bacteria were isolated from lentil root nodule as well as soil from different lentil growing fields with a view to screen/evaluate their plant growth promoting potential. Morphological characterization of isolated rhizobacterial candidates were done by observing the colonies on YEMA and nutrient agar media. Determination of CFU, Congo red test and gram staining tests were done to further screen them according to their morphology. All the isolates were then undergone molecular phylogenetic analysis using the partial sequences of the 16S rDNA. Based upon the Gram staining test, all the isolates were negative in gram reaction except six Bacillus isolates, PSB2 and AB3. Results of Ribosomal Database Project (RDP) and Basic Local Alignment Search Tool for Nucleotide Sequences (BLASTn) from 16S rDNA gene sequences showed that these isolates are genetically diverse. A total of 15 isolates of Rhizobium, 6 isolates of Bacillus, 3 isolates of Pseudomonas, 2 isolates of Phosphate Solubilizing Bacteria, 4 isolates of actinomycetes were identified by molecular sequencing of their 16S rDNA region and comparing them with the other isolates enlisted in the database of NCBI for the similarity percentage, query coverage. The purpose of the present study was to select native rhizosphere bacteria from the lentil nodule and soil of Lentil field and to evaluate their plant growth promoting potential as an alternative of chemical fertilizer for sustainable, environment friendly agriculture and assessment of their phylogenetic characterization.

Effects of microbes and metabolites on tobacco quality in “Humi” characteristic fermentation of cigar tobacco leaf

Fermentation is an important link in the process of cigar production, which directly determines the quality of tobacco leaves. “Humi” fermentation is a traditional method of manually adding materials, which can highlight the aroma characteristics and improve industrial availability of tobacco leaves. However, the mechanism of “Humi” fermentation is still unclear. This study was aimed to explore the effect of the “Humi” characteristic fermentation on the quality of cigar leaves, and the potential mechanisms. Cigar variety Dexue 1 was used. Three degrees of “Humi” water were prepared and water was used as control. 16 S rDNA sequencing and metabolomics analyses were carried out to determine the changes in microbes and metabolites during fermentation. “Humi” fermentation significantly improved the evaluation quality of cigar tobacco. The microbial richness and community diversity in “Humi” fermentation group were higher than that in natural fermentation group. Total 214 genera were detected, with Staphylococcus, Corynebacterium_1, and Oceanobacillus as the dominant genera in the “Humi” fermentation group. With the extension of fermentation time, the relative abundance of Corynebacterium_1 increased, and of Oceanobacillus and Staphylococcus first increased and then decreased. Moreover, Corynebacterium_1 were significantly negatively correlated with total nitrogen, protein and alkaloid content, and significantly positively correlated with amino acids, starch, reducing sugars and total sugars. Metabolome analysis revealed 2759 known metabolites in 36 samples and “Humi” fermentation increased the nitrogenous heterocyclic compounds, sugars, alkaloids and organic acids in tobacco leaves. These metabolites were closely related to the bacterial community. Our study provides a theoretical basis for inheriting and optimizing the “Humi” characteristic fermentation technology.

Unveiling the microbiota-metabolite-myocardium axis: a novel perspective on cardiovascular health

IntroductionCardiovascular diseases, including myocardial infarction, remain a leading cause of death globally. Emerging evidence suggests the gut microbiota plays a crucial role in cardiovascular health. This study aims to explore the impact of gut microbiota on myocardial infarction using a mouse model.MethodsThe research utilizes a multi-omics approach, including 16S rDNA sequencing and LC-MS-based metabolomics to analyze fecal and serum samples from mice modeled to mimic myocardial infarction. This methodology allows for a comprehensive analysis of microbial populations and their metabolic output.ResultsThe findings reveal a significant reduction in gut microbiota α-diversity in mice with induced myocardial infarction compared to healthy controls. Notably, there is an increase in populations of Fusobacteria and Clostridia. Metabolomic analysis indicates disruptions in amino acid and energy metabolism, suggesting a metabolic dysregulation linked to myocardial health.DiscussionThe study proposes a novel microbiota-metabolite-myocardium axis, where specific microbial metabolites may directly affect heart health. This connection points to the gut microbiota as a potential player in the pathogenesis of myocardial infarction and may open new therapeutic avenues targeting the gut microbiome to combat cardiovascular diseases.

A fungi hotspot deep in the ocean: explaining the presence of Gjaerumia minor in equatorial Pacific bathypelagic waters

A plant parasite associated with the white haze disease in apples, the Basidiomycota Gjaerumia minor, has been found in most samples of the global bathypelagic ocean. An analysis of environmental 18S rDNA sequences on 12 vertical profiles of the Malaspina 2010 expedition shows that the relative abundance of this cultured species increases with depth while its distribution is remarkably different between the deep waters of the Pacific and Atlantic oceans, being present in higher concentrations in the former. This is evident from sequence analysis and a microscopic survey with a species-specific newly designed TSA-FISH probe. Several hints point to the hypothesis that G. minor is transported to the deep ocean attached to particles, and the absence of G. minor in bathypelagic Atlantic waters could then be explained by the absence of this organism in surface waters of the equatorial Atlantic. The good correlation of G. minor biomass with Apparent Oxygen Utilization, recalcitrant carbon and free-living prokaryotic biomass in South Pacific waters, together with the identification of the observed cells as yeasts and not as resting spores (teliospores), point to the possibility that once arrived at deep layers this species keeps on growing and thriving.

Non-TGFβ profibrotic signaling in ulcerative colitis after in vivo experimental intestinal injury in humans.

Although impaired regeneration is important in many gastrointestinal diseases including ulcerative colitis (UC), the dynamics of mucosal regeneration in humans are poorly investigated. We have developed a model to study these processes in vivo in humans. Epithelial restitution (ER) and extracellular matrix (ECM) regulation after an experimental injury of the sigmoid colonic mucosa was assessed by repeated high resolution endoscopic imaging, histologic assessment, RNA sequencing, deconvolution analysis, and 16S rDNA sequencing of the injury niche microbiome of 19 UC patients in remission and 20 control subjects. Human ER had a 48-hour lag before induction of regenerative epithelial cells (WAE and TA cells) along with increase of fibroblast derived stem cell growth factor Gremlin 1 mRNA (GREM1). However, in UC deconvolution data showed aby rapid induction of inflammatory fibroblasts, and upregulation of major structural ECM collagen mRNAs and along with tissue inhibitor of metalloproteinase 1 (TIMP1) suggesting increased profibrotic ECM deposition. No change was seen in transforming growth factor β (TGFβ) mRNA whereas and the profibrotic cytokines interleukin 13 (IL13) and IL11 were upregulated in UC suggesting that human post injury responses could be TGFβ-independent. In conclusion, we found distinct regulatory layers of regeneration in the normal human colon and a potential targetable profibrotic dysregulation in UC that could lead to long-term end organ failure - i.e., intestinal damage.

Effects of Mactra chinenesis Peptides on Alcohol-Induced Acute Liver Injury and Intestinal Flora in Mice

Food-borne bioactive peptides have shown promise in preventing and mitigating alcohol-induced liver injury. This study was the first to assess the novel properties of Mactra chinenesis peptides (MCPs) in mitigating acute alcoholic liver injury in mice, and further elucidated the underlying mechanisms associated with this effect. The results showed that MCPs can improve lipid metabolism by modulating the AMPK signaling pathway, decreasing fatty acid synthase activity, and increasing carnitine palmitoyltransferase 1a activity. Meanwhile, MCPs ameliorate inflammation by inhibiting the NF-κB activation, leading to reduced levels of pro-inflammatory cytokines (tumor necrosis factor-α and interleukin-1β). Additionally, a 16S rDNA sequencing analysis revealed that MCPs can restore the balance of gut microbiota and increase the relative abundance of beneficial bacteria. These findings suggest that supplementation of MCPs could attenuate alcohol intake-induced acute liver injury, and, thus, may be utilized as a functional dietary supplement for the successful treatment and prevention of acute liver injury.

Revisiting the phylogeny and taxonomy of the genus Sidera (Hymenochaetales, Basidiomycota) with particular emphasis on S. vulgaris

The genus Sidera (Hymenochaetales, Basidiomycota) comprises white-rot, mono- or dimitic fungi with poroid or hydnoid hymenophore. It has a worldwide distribution albeit with fewer species present in the Southern Hemisphere. Although recent studies revealed the existence of several new Sidera species, there are still taxonomic inconsistencies and obscure phylogenetic relationships amongst certain taxa of the genus. In this work, a large number of Sidera collections were used to obtain an updated phylogeny, based on ITS and 28S rDNA sequences by including new material from Mediterranean Europe. The monophyly of the genus was strongly supported and all species with poroid hymenophore formed a highly-supported lineage with two major subclades. In total, 23 putative species were recognised. Amongst those, five are considered to possibly represent entities new to science, but further work is required since they are represented by single specimens or environmental sequences. Examined collections originally named S. lenis from southern Europe were grouped within S. vulgaris. Similarly, several collections under various names were hereby identified as S. vulgaris, including those of the recently described species S. tibetica. Furthermore, a critical discussion (based on morphoanatomical findings) is made on the key features that could be used to distinguish S. lenis from S. vulgaris.

Obeticholic acid attenuates the intestinal barrier disruption in a rat model of short bowel syndrome

BackgroundShort bowel syndrome (SBS) features nutrients malabsorption and impaired intestinal barrier. Patients with SBS are prone to sepsis, intestinal flora dysbiosis and intestinal failure associated liver disease. Protecting intestinal barrier and preventing complications are potential strategies for SBS treatment. This study aims to investigate the effects of farnesoid X receptor (FXR) agonist, obeticholic acid (OCA), have on intestinal barrier and ecological environment in SBS. Methods and resultsThrough testing the small intestine and serum samples of patients with SBS, impaired intestinal barrier was verified, as evidenced by reduced expressions of intestinal tight junction proteins (TJPs), increased levels of apoptosis and epithelial cell damage. The intestinal expressions of FXR and related downstream molecules were decreased in SBS patients. Then, global FXR activator OCA was used to further dissect the potential role of the FXR in a rat model of SBS. Low expressions of FXR-related molecules were observed on the small intestine of SBS rats, along with increased proinflammatory factors and damaged barrier function. Furthermore, SBS rats possessed significantly decreased body weight and elevated death rate. Supplementation with OCA mitigated the damaged intestinal barrier and increased proinflammatory factors in SBS rats, accompanied by activated FXR-related molecules. Using 16S rDNA sequencing, the regulatory role of OCA on gut microbiota in SBS rats was witnessed. LPS stimulation to Caco-2 cells induced apoptosis and overexpression of proinflammatory factors in vitro. OCA incubation of LPS-pretreated Caco-2 cells activated FXR-related molecules, increased the expressions of TJPs, ameliorated apoptosis and inhibited overexpression of proinflammatory factors. ConclusionsOCA supplementation could effectively ameliorate the intestinal barrier disruption and inhibit overexpression of proinflammatory factors in a rat model of SBS and LPS-pretreated Caco-2 cells. As a selective activator of FXR, OCA might realize its protective function through FXR activation.

Effects of baculovirus infection on intestinal microflora of BmNPV resistant and susceptible strain silkworm.

Bombyx moriL. (Lepidoptera: Bombycidae) nucleopolyhedrovirus (BmNPV) is a serious pathogen causing huge economic losses to sericulture. There is growing evidence that the gut microbiota of silkworms plays a critical role in shaping host responses and interactions with viral infection. However, little is known about the differences in the composition and diversity of intestinal microflora, especially with respect to silkworm strain differences and BmNPV infection-induced changes. Here, we aim to explore the differences between BmNPV-resistant strain A35 and susceptible strain P50 silkworm and the impact of BmNPV infection on intestinal microflora in different strains. The 16S rDNA sequencing analysis revealed that the fecal microbial populations were distinct between A35 and P50 and were significantly changed post BmNPV infection in both strains. Further analysis showed that the BmNPV-resistant strain silkworm possessed higher bacterial diversity than the susceptible strain, and BmNPV infection reduced the diversity of intestinal flora assessed by feces in both silkworm strains. In response to BmNPV infection, the abundance of Muribaculaceae increased in P50 and decreased in A35, while the abundance of Enterobacteriaceae decreased in P50 and increased in A35. These results indicated that BmNPV infection had various effects on the abundance of fecal microflora in different silkworm strains. Our findings not only broadened the understanding of host-pathogen interactions but also provided theoretical help for the breeding of resistant strains and healthy rearing of silkworms based on symbiotic bacteria.

Deep Learning-enhanced Hyperspectral Imaging for the Rapid Identification and Classification of Foodborne Pathogens

Background: Bacterial cellulose (BC) is a versatile biomaterial with numerous applications, and the identification of bacterial strains that produce it is of great importance. This study explores the effectiveness of a Stacked Autoencoder (SAE)-based deep learning method for the classification of bacterial cellulose-producing bacteria. Objective: The primary objective of this research is to assess the potential of SAE-based classification models in accurately identifying and classifying bacterial cellulose-producing bacteria, with a particular focus on strain GZ-01. objective: The primary objective of this research is to assess the potential of SAE-based classification models in accurately identifying and classifying bacterial cellulose-producing bacteria, with a particular focus on strain GZ-01. Methods: Strain GZ-01 was isolated and subjected to a comprehensive characterization process, including morphological observations, physiological and biochemical analysis, and 16S rDNA sequencing. These methods were employed to determine the identity of strain GZ-01, ultimately recognized as Acetobacter Okinawa. The study compares the performance of SAE-based classification models to traditional methods like Principal Component Analysis (PCA). Results: The SAE-based classifier exhibits outstanding performance, achieving an impressive accuracy of 94.9% in the recognition and classification of bacterial cellulose-producing bacteria. This approach surpasses the efficacy of conventional PCA in handling the complexities of this classification task. Conclusion: The findings from this research highlight the immense potential of utilizing nanotechnology- driven data analysis methods, such as Stacked Autoencoders, in the realm of bacterial cellulose research. These advanced techniques offer a promising avenue for enhancing the efficiency and accuracy of bacterial cellulose-producing bacteria classification, which has significant implications for various applications in biotechnology and materials science.

Molecular and SEM studies on Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae)

Presenting new molecular and scanning electron microscope (SEM) features, this study gives additional data to the better knowledge of Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae), a parasite of the European catfish Silurus glanis Linnaeus, 1758 (Siluriformes, Siluridae) cultured in a commercial fish farm in Hungary. In addition, notes on the early development of sclerotized anchors are also provided. The main morphological difference of T. vistulensis compared to other congeneric species is associated with the male copulatory organ, which exhibits 5–7 loops in the middle of the penis length and a long open V-shaped sclerotized accessory piece, dividing terminally into two parts, securing the terminal part of the penis tube. The present study provides for the first time molecular characterization data based on the 2694 bp long nucleotide sequence of rDNA (ITS1, 5.8S, ITS2, and flanked with partial 18S and partial 28S) submitted in GenBank with the accession number OR916383. A phylogenetic tree based on ITS1 sequences supports a well-defined clade including T. vistulensis, forming a sister group with T. siluri, a species-specific monopisthocotylan parasite to S. glanis. The morphological characterization of T. vistulensis, especially for the male copulatory organ, together with the molecular data in the present study, extends knowledge about this monopisthocotylan species and provides new information for future phylogeny studies.

Synopsis of the species of OrtholineaShulman, 1962 (Cnidaria: Myxosporea: Ortholineidae)

A synopsis of Ortholinea Shulman, 1962 (Cnidaria: Myxosporea: Ortholineidae) is presented and identifies 26 nominal species presently allocated within this genus. Species morphological and morphometric features, tissue tropism, type-host, and type-locality are provided from original descriptions. Data from subsequent redescriptions and reports is also given. Accession numbers to sequences deposited in GenBank are indicated when available, and the myxospores were redrawn based on original descriptions. The information gathered shows that Ortholinea infect a wide taxonomic variety of freshwater and marine fish. Nonetheless, the broad host specificity reported for several species is not fully supported by morphological descriptions and requires molecular corroboration. The members of this genus are coelozoic and mainly parasitize the urinary system, with few species occurring in the gallbladder. Ortholinea visakhapatnamensis is the only exception, being histozoic in the visceral peritoneum. Molecular data of the small subunit ribosomal RNA gene (SSU rDNA) is available for about one third of Ortholinea species, with genetic interspecific variation ranging between 1.65% and 29.1%. Phylogenetic analyses reveal Ortholinea to be polyphyletic, with available SSU rDNA sequences clustering within the subclades of the highly heterogenous freshwater urinary clade of the oligochaete-infecting lineage. The life cycles of two Ortholinea species have been clarified based on molecular inferences and identify triactinomyxon actinospores as counterparts, and marine oligochaetes of the family Naididae as permissive hosts to this genus.

DIAZOTROPHIC ENDOPHYTE Klebsiella sp. N5 FROM SORGHUM SHOWS CROSS-COLONIZATION AND PLANT GROWTH PROMOTION IN RICE

Rice necessitates the highest levels of N fertilizers during its cultivation increasing demand for nitrogen fertilizers as well as negatively affecting the environment. Endophytic diazotrophic bacteria were isolated from sorghum, out of 35 isolates Klebsiella sp. N5 showed maximum potential for biological nitrogen fixation. Primary screening of strain N5 was done with acetylene reduction assay indicating dry root activity of 638.55 nmol C2H4 h-1 g-1. That was further confirmed by nifH gene amplification. The strain was identified morphologically, biochemically and 16S rDNA sequencing analysis and identified as Klebsiella sp. strain N5. This strain exhibited other plant growth-promoting (PGP) traits, such as phosphate solubilization, production of indole acetic acid, siderophore activity, ACC deaminase activity, and anti-fungal activity. PGP endophyte N5 was inoculated into rice seedlings to investigate its interaction under axenic conditions and to characterize its ability to colonize non-native host plant rice. Extensive colonization of rice roots was corroborated by Scanning electron microscopy. In-planta experiments with rice seeds inoculated with Klebsiella sp. N5 showed significant improvements in various agronomic traits such as increase in shoot length, root length, fresh and dry weight of root and shoot, chlorophyll content, and nitrogen content of the plant and soil compared to the untreated plants. Klebsiella sp. N5, a cross colonizer from sorghum (C4 plant) to rice (C3 plant) plays a crucial role in facilitating the acquisition of essential resources such as nitrogen, phosphorus, and iron through direct mechanisms. This study expands the horizon for its potential as a valuable bioinoculant for sustainable agricultural practices, particularly in non-native host rice, paving the way for future field trials.

Of sea, rivers and symbiosis: Diversity, systematics, biogeography and evolution of the deeply diverging florideophycean order Hildenbrandiales (Rhodophyta)

The Hildenbrandiales, a typically saxicolous red algal order, is an early diverging florideophycean group with global significance in marine and freshwater ecosystems across diverse temperature zones. To comprehensively elucidate the diversity, phylogeny, biogeography, and evolution of this order, we conducted a thorough re-examination employing molecular data derived from nearly 700 specimens. Employing a species delimitation method, we identified Evolutionary Species Units (ESUs) within the Hildenbrandiales aiming to enhance our understanding of species diversity and generate the first time-calibrated tree and ancestral area reconstruction for this order. Mitochondrial cox1 and chloroplast rbcL markers were used to infer species boundaries, and subsequent phylogenetic reconstructions involved concatenated sequences of cox1, rbcL, and 18S rDNA. Time calibration of the resulting phylogenetic tree used a fossil record from a Triassic purportedly freshwater Hildenbrandia species and three secondary time points from the literature. Our species delimitation analysis revealed an astounding 97 distinct ESUs, quintupling the known diversity within this order. Our time-calibration analysis placed the origin of Hildenbrandiales (crown age) in the Ediacaran period, with freshwater species emerging as a monophyletic group during the later Permian to early Triassic. Phylogenetic reconstructions identified seven major clades, experiencing early diversification during the Silurian to Carboniferous period. Two major evolutionary events—colonization of freshwater habitats and obligate systemic symbiosis with a marine fungus—marked this order, leading to significant morphological alterations without a commensurate increase in species diversification. Despite the remarkable newly discovered diversity, the extant taxon diversity appears relatively constrained when viewed against an evolutionary timeline spanning over 800 million years. This limitation may stem from restricted geographic sampling or the prevalence of asexual reproduction. However, species richness estimation and rarefaction analyses suggest a substantially larger diversity yet to be uncovered—potentially four times greater. These findings drastically reshape our understanding of the deeply diverging florideophycean order Hildenbrandiales species diversity, and contribute valuable insights into this order evolutionary history and ecological adaptations. Supported by phylogenetic, ecological and morphological evidence, we established the genus Riverina gen. nov. to accommodate freshwater species of Hildenbrandiales, which form a monophyletic clade in our analyses. This marks the first step toward refining the taxonomy of the Hildenbrandiales order, a task demanding thorough revisions, notably the creation of several genera to address the polyphyletic status of Hildenbrandia. However, the limited diagnostic features pose a challenge, necessitating a fresh approach to defining genera. A potential solution lies in embracing a molecular systematic perspective, which can offer precise delineations of taxonomic boundaries.

Therapeutic Mechanism of Cornus Officinalis Fruit Coreon on ALI by AKT/Nrf2 Pathway and Gut Microbiota

BackgroundAcute liver injury (ALI) often precipitates severe liver function impairment and is associated with high mortality rates. Traditional Chinese Medicine (TCM) has demonstrated efficacy in mitigating hepatic damage by exhibiting anti-inflammatory effects, enhancing antioxidant activity, and modulating gut microbiota (GM). Numerous studies have identified similar or identical bioactive compounds within the Cornus Officinalis Fruit Coreon(COFO) and its flesh. Notably, Cornus Officinalis has been shown to possess potent hepatoprotective properties. However, studies on the pharmacological effects and mechanism of action of COFO for hepatoprotection have received little attention. PurposeTo elucidate the mechanisms underlying the COFO effect in ALI by integrating GM gene sequencing, quantifying Short-Chain Fatty Acids (SCFAs), and examining relevant signaling pathways. Materials and MethodsA rat model for carbon tetrachloride (CCl4)-induced ALI was established, and the best liver protective components of COFO were selected by pathological observation and biochemical determination. The therapeutic efficacy of COFO in mitigating liver injury was elucidated through an integrated approach that included network pharmacology, biochemical indexes, 16S rDNA sequencing analyses, short-chain fatty acids, Western blotting analysis of protein levels, and immunohistochemical evaluations. ResultsPharmacological evaluation established that the n-butanol fraction (CNBP) provided optimal hepatoprotective effects. Firstly, the chemical constituents of CNBP were characterized, and its principal anti-ALI targets, such as ALI, AKT1, TNF, and IL-6, were identified through network pharmacology analysis. Secondly, experimental validation revealed that CNBP may enhance the genetic diversity of the GM, augmenting the diversity of the microbial community, increasing the levels of three SCFAs, and activating key proteins in the AKT/Nrf2 signaling pathway (AKT1, TNF-α, IL-6, NF-κB p65, Nrf2, and HO-1). Consequently, CNBP exhibited hepatoprotective effects, with antioxidative and anti-inflammatory properties. ConclusionCNBP may mitigate GM-induced disturbances, augment the levels of three SCFAs, activate the AKT/Nrf2 signaling pathway, and exhibit antioxidant and anti-inflammatory effects, thereby conferring hepatoprotective benefits.

Characterization of gut microbiota in patients with stage 3-4 chronic kidney disease: a retrospective cohort study.

Multiple factors, such as dietary patterns, pharmaceutical interventions, and exposure to harmful substances, possess the capacity to influence gut microbiota composition. Gut microbiota dysbiosis has emerged as a significant contributor to the progression of chronic kidney disease (CKD) and its associated complications. By comprehending the intricacies of the intestinal microbiota, this research endeavor holds the potential to offer novel perspectives on potential strategies for mitigating CKD progression. In this retrospective analysis, we assessed gut microbiota composition in CKD patients. Fecal samples were collected from a cohort of 44 patients with stage 3-4 CKD, alongside a control group consisting of 132 healthy volunteers. Subsequently, 16s rDNA sequencing was conducted to examine the composition of the gut microbiota. Our findings revealed significant alterations in the diversity of intestinal microbiota in fecal samples between patients with stage 3-4 CKD and healthy subjects. Among the 475 bacterial genera, 164 were shared, while 242 dominant genera were exclusive to healthy subjects and 69 to CKD stages 3-4 samples. Notably, healthy volunteers exhibited a prevalence of intestinal Firmicutes and Bacteroidetes, whereas stage 3-4 CKD patients displayed higher abundance of Proteobacteria and Actinobacteria. The presence of uncultured Coprobacillus sp. notably contributed to distinguishing between the two groups. ROC curve analysis identified distinct microbiota with superior diagnostic efficacy for discriminating stage 3-4 CKD patients from healthy individuals. Metabolic pathway analysis revealed differing dominant pathways between the two groups-the NADH dehydrogenase pathway in healthy individuals and the phosphate acetyltransferase pathway in stage 3-4 CKD patients. Moreover, the CKD cohort displayed a higher proportion of Gram-negative bacteria and facultative anaerobes. In conclusion, our study underscores the profound influence of gut microbiota dysbiosis on CKD progression. The distinct microbial profiles observed in CKD patients highlight the potential efficacy of microbiota-based interventions in mitigating CKD advancement.

Milling degree affects the fermentation properties of rice: perspectives from the composition of nutrients and gut microbiota via in vitro fermentation

Fermentation substrates of rice with different milling degrees (MDs) were prepared and fermented with human feces to compare their fermentation properties and effects on gut microbiota. MD 0s, MD 5s and MD 60s represented brown rice, moderately-milled rice and white rice, respectively. After in vitro fermentation, the MD 5s group showed higher starch utilization, compared with the MD 0s and 60s groups evaluated by Fourier transform infrared spectrometer, and confocal laser scanning microscope. Effects of fermentation substrates of rice with different MDs on gut microbiota were evaluated by 16S rDNA sequencing. All the sample groups reduced the pH and produced short-chain fatty acids (SCFAs) and branched-chain fatty acids. The MD 5s group exhibited higher α-diversity than the MD 0s and 60s groups. Abundances of Phascolarctobacterium, Blautia and norank_f_Ruminococcaceae were higher in the MD 0s and 5s groups, compared with the MD 60s group. These bacteria were also positively correlated with the SCFAs production via Spearman correlation analysis. In vitro culture assay revealed that fermentation substrates of MD 0s and 5s promoted the growth of two probiotics (Akkermansia muciniphila and Bifidobacterium adolescentis). Our results showed that moderate milling might be an appropriate way to produce rice products with richer nutrients and better fermentation properties.

Production of γ–aminobutyric acid–enriched sourdough bread using an isolated Pediococcus pentosaceus strain JC30

A γ–aminobutyric acid (GABA)–producing strain JC30 was isolated from traditional kimchi, which was identified as Pediococcus pentosaceus by 16S rDNA sequencing. P. pentosaceus JC30 was highly tolerant to acid, bile salt, and high temperatures. The survival rate of JC30 in MRS medium (pH 2.5) for 3 h was 60.96%. Furthermore, the survival rate of JC30 in MRS medium with 3 mg/mL bile salt for 24 h was 86.62%. The survival rate of JC30 in MRS medium at 56°C and 58°C for 10 min was 97.17% and 78.20%, respectively. When 2% v/v JC30 (8.0 log10 CFU/mL) was added to prepare sourdough and the sourdough was then used to make bread, the bread had a higher specific volume (5.13 ± 0.12 mL/g) and GABA content (3.32 ± 0.04 mg/g DW) than the control.