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Abstract The Himalayan mountain range in India is home to some of the most diverse ethnic communities and tribes, especially in the northwestern Himalayan range, which spans between the Indian provinces/states of Uttarakhand and Himachal Pradesh. The rich and diversity of the local flora offers nutritional diversity and ensures therapeutic certainty for the local communities (e.g., Garhwali, Kumaoni, Bhotiya, Jaunsari, Gaddi, and Kinnauri). The local varieties of millet, legumes, leafy vegetables, tubers, and ferns in different forms (fresh, sundried, flour, pickled, or fermented) are commonly used to prepare different dishes and locally produced beverages (e.g., soor/sur, pakhoi/paakuyi, chhang, jann/jan, jhol, lugdi/lugri, etc.). This centuries-old indigenous experience, the knowledge of local flora, and the traditional food preparation are key to meeting the dietary demands of local communities. In addition, these local delicacies are also rich in health-benefiting bioactive molecules and have functional food properties, which are not documented yet. Therefore, this review closely examines the functional food properties of the traditional food prepared in the Uttarakhand and Himachal Pradesh regions and provides the scientific evidence to preserve this rich dietary traditions.

Abstract Introduction Regdanvimab, a monoclonal antibody pharmaceutical, is the first Korean drug approved for treating coronavirus disease 2019 (COVID-19). We analyzed the therapeutic efficacy of regdanvimab in patients with the COVID-19 delta variant infection. Methods We retrospectively reviewed the electronic medical records of patients hospitalized at two Korean tertiary COVID-19 hospitals with COVID-19 delta variant infection between May 26, 2021, and January 30, 2022. To analyze the therapeutic efficacy of regdanvimab, the patients were divided into regdanvimab and non-regdanvimab groups and were 1:1 propensity-score (PS)-matched on age, severity at admission, and COVID-19 vaccination history. Results Of 492 patients, 262 (53.3%) and 230 (46.7%) were in the regdanvimab and non-regdanvimab groups, respectively. After PS matching the groups on age, severity at admission, and COVID-19 vaccination history, each group comprised 189 patients. The 30-day hospital mortality rates (0.0% vs. 1.6%, p = 0.030), proportions of patients with exacerbated conditions to severe/critical/died (9.5% vs. 16.4%, p = 0.047), proportions who received oxygen therapy because of pneumonia exacerbation (7.4% vs. 16.4%, p = 0.007), and proportions with a daily National Early Warning Score ≥ 5 from hospital day 2 were significantly lower in the regdanvimab group. Conclusions We showed that regdanvimab reduced the exacerbation rates of conditions and mortality in patients with the COVID-19 delta variant infection. Thus, it is recommended to streamline the drug approval system during epidemics of new variant viruses to improve the availability and usage of therapeutics for patients. To facilitate this, relevant institutional support is required.

Abstract Background Gastrodia elata Blume (GEB), a traditional medicinal herb, has been reported to have pharmacological effect including protection against liver, neuron and kidney toxicity. However, explanation of its underlying mechanisms remains a great challenge. This study investigated the protective effects of GEB extract on vancomycin (VAN)-induced nephrotoxicity in rats and underlying mechanisms with emphasis on the anti-oxidative stress, anti-inflammation and anti-apoptosis. The male Sprague-Dawley rats were randomly divided three groups: control (CON) group, VAN group and GEB group with duration of 14 days. Results The kidney weight and the serum levels of blood urea nitrogen and creatinine in the GEB group were lower than the VAN group. Histological analysis using hematoxylin & eosin and periodic acid Schiff staining revealed pathological changes of the VAN group. Immunohistochemical analysis revealed that the expression levels of N-acetyl-D-glucosaminidase, myeloperoxidase and tumor necrosis factor-alpha in the GEB group were decreased when compared with the VAN group. The number of terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling-positive cells, phosphohistone and malondialdehyde levels were lower in the GEB group than VAN group. The levels of total glutathione in the GEB group were higher than the VAN group. Conclusions The findings of this study suggested that GEB extract prevents VAN-induced renal tissue damage through anti-oxidation, anti-inflammation and anti-apoptosis.

AbstractA rapid decline of Abies koreana has been reported in most of the natural alpine habitats in Korea. It is generally accepted that this phenomenon is due to climate change even though no clear conclusions have been drawn. Most research has focused on abiotic environmental factors, but studies on the relationships between A. koreana and soil fungal microbiomes are scarce. In this study, the rhizoplane and rhizosphere fungal communities in the alive and dead Korean fir trees from its three major natural habitats including Mt. Deogyu, Mt. Halla, and Mt. Jiri in Korea were investigated to identify specific soil fungal groups closely associated with A. koreana. Soil fungal diversity in each study site was significantly different from another based on the beta diversity calculations. Heat tree analysis at the genus level showed that Clavulina, Beauveria, and Tomentella were most abundant in the healthy trees probably by forming ectomycorrhizae with Korean fir growth and controlling pests and diseases. However, Calocera, Dacrymyces, Gyoerffyella, Hydnotrya, Microdochium, Hyaloscypha, Mycosymbioces, and Podospora were abundant in the dead trees. Our findings suggested that Clavulina, Beauveria, and Tomentella are the major players that could be considered in future reforestation programs to establish ectomycorrhizal networks and promote growth. These genera may have played a significant role in the survival and growth of A. koreana in its natural habitats. In particular, the genus Gyoerffyella may account for the death of the seedlings. Our work presented exploratory research on the specific fungal taxa associated with the status of A. koreana.

Tomato is an economically and nutritionally important crop and is vulnerable to drought. Under drought, soil microbes provide beneficial effects to plants and alleviate stress. We suggest a reconstruction of the soil microbiome using biofumigation, an organic farming method, to protect tomatoes. In this study, we treated soil in four ways with varied concentrations: biofumigation (BF0.5, BF1.0, and BF1.5), green manure treatment (GM0.5, GM1.0, and GM1.5), autoclaving (AT), and non-treatment (NT). Tomatoes were grown in each treated soil, subjected to water shortages, and were rewatered. We investigated plant phenotypes and soil properties, focused on microbial communities using the Illumina MiSeq® System. Relative Water Content and malondialdehyde were measured as plant stress. The results showed that the 1% biofumigation treatment had 105% and 108.8% RWC during drought and after rewatering, compared to the non-treated soil. The highest concentration, the 1.5% treatment, lowered RWC due to an excess of NO3−, K+, Ca2+, and decreased alpha diversity. Through PLS-PM, bacterial alpha diversity was found to be the largest factor in the increase in RWC (coefficient = 0.3397), and both biofumigant and green manure significantly increased the Shannon index and observed species. In addition, biofumigation increased beneficial functional genes (purine metabolism, pyrimidine metabolism, carbon fixation pathways, and zeatin bio-synthesis) of soil microorganisms (p value < 0.05, 0.05, and Enterocarpus, Aspergillus, Leucothecium, Peniophora, and Wallemia) of the fungal network which might suppress the most dominant pathogen, Plectosphaerella. In conclusion, biofumigation-derived soil microbiome alterations have the potential to lower plant stress under drought.

Centella asiatica, a traditional herb, is widely recognized for its pharmacologically active components, such as asiaticoside, madecassoside, asiatic acid, and madecassic acid. These components render it a highly sought-after ingredient in various industries, including cosmetics and pharmaceuticals. This study aimed to enhance the production and activity of these pharmacological constituents of C. asiatica using the plant growth-promoting rhizobacterium Priestia megaterium HyangYak-01 during its cultivation. To achieve this goal, the researchers conducted field experiments, which revealed an increase in the production of pharmacologically active compounds in C. asiatica cultivated with a P. megaterium HyangYak-01 culture solution. Additionally, quadrupole time-of-flight mass spectrometry (Q-TOF MS) confirmed that the composition ratios of the C. asiatica extract treated with the P. megaterium HyangYak-01 culture solution differed from those of the untreated control and type strain-treated groups. Skin cell experiments indicated that the C. asiatica extract treated with the P. megaterium HyangYak-01 culture solution exhibited greater skin barrier improvement and less pronounced inflammatory responses than those from plants grown without the bacterial culture solution. This study demonstrates that microbial treatment during plant cultivation can beneficially influence the production of pharmacological constituents, suggesting a valuable approach toward enhancing the therapeutic properties of plants.

Odor emissions from animal manure present a significant environmental challenge in livestock farming, impacting air quality and farm sustainability. Traditional methods, such as chemical additives and manure treatment, can be costly, labor-intensive, and less eco-friendly. Therefore, this study investigated the effectiveness of microbial feed additives in reducing these odors. Conducted over three months in 2022 on a Korean beef cattle farm with 20 cattle, the experiment involved feeding a mixture of four microbial strains—Bacillus subtilis KNU-11, Lactobacillus acidophilus KNU-02, Lactobacillus casei KNU-12, and Saccharomyces cerevisiae KNU-06. Manure samples were collected from an experimental group (n = 9) and a control group (n = 11), with microbial community changes assessed through 16S ribosomal RNA gene amplicon sequencing. The results demonstrated significant reductions in specific odorous compounds in the experimental group compared to the control group: ammonia decreased by 64.1%, dimethyl sulfide by 81.3%, butyric acid by 84.6%, and isovaleric acid by 49.8%. Additionally, there was a notable shift in the microbiome, with an increase in the relative abundance of Ruminococcaceae and Prevotellaceae microbes associated with fiver degradation and fermentation, while the control group had higher levels of Bacteroidota and Spirochaetota, which are linked to pathogenicity. This study demonstrates that probiotics effectively alter intestinal microbiota to enhance microorganisms associated with odor mitigation, offering a promising and more sustainable approach to reducing odor emissions in livestock farming.

The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions and compared the microbiomes of wild long-tailed gorals and two types of captive long-tailed gorals. Our findings revealed that the gut microbiome diversity of wild long-tailed gorals is greatly reduced when they are reared in captivity. A comparison of the two types of captive long-tailed gorals confirmed that animals with a more diverse diet exhibit greater gut microbiome diversity. Redundancy analysis confirmed that wild long-tailed gorals are distributed throughout the highlands, midlands, and lowlands. For the first time, it was revealed that the long-tailed goral are divided into three groups depending on the height of their habitat, and that the gut bacterial community changes significantly when long-tailed gorals are raised through ex situ conservation. This provides for the first time a perspective on the diversity of food plants associated with mountain height that will be available to long-tailed goral in the future.

Summary: Although countless gut microbiome studies on colitis using mouse models have been carried out, experiments with small sample sizes have encountered reproducibility limitations because of batch effects and statistical errors. In this study, dextran-sodium-sulfate-induced microbial dysbiosis index (DiMDI) was introduced as a reliable dysbiosis index that can be used to assess the state of microbial dysbiosis in DSS-induced mouse models. Meta-analysis of 189 datasets from 11 independent studies was performed to construct the DiMDI. Microbial dysbiosis biomarkers, Muribaculaceae, Alistipes, Turicibacter, and Bacteroides, were selected through four different feature selection methods and used to construct the DiMDI. This index demonstrated a high accuracy of 82.3% and showed strong robustness (88.9%) in the independent cohort. Therefore, DiMDI may be used as a standard for assessing microbial imbalance in DSS-induced mouse models and may contribute to the development of reliable colitis microbiome studies in mouse experiments.

In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.

Abstract Spinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot −1) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH4 +, and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.

Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health concern. Additionally, the freshwater environment serves as a reservoir of antibiotic resistance genes (ARGs), which pose a risk of transmission during microbial dysbiosis, such as cyanoHABs. However, the interactions between potential synergistic pollutants, cyanoHABs, and ARGs remain poorly understood. During cyanoHABs, Microcystis and high microcystin levels were dominant in all the nine regions of the river sampled. The resistome, mobilome, and microbiome were interrelated and linked to the physicochemical properties of freshwater. Planktothrix and Pseudanabaena competed with Actinobacteriota and Proteobacteria during cyanoHABs. Forty two ARG carriers were identified, most of which belonged to Actinobacteriota and Proteobacteria. ARG carriers showed a strong correlation with ARGs density, which decreased with the severity of cyanoHAB. Although ARGs decreased due to a reduction of ARG carriers during cyanoHABs, mobile gene elements (MGEs) and virulence factors (VFs) genes increased. We explored the relationship between cyanoHABs and ARGs for potential synergistic interaction. Our findings demonstrated that cyanobacteria compete with freshwater commensal bacteria such as Actinobacteriota and Proteobacteria, which carry ARGs in freshwater, resulting in a reduction of ARGs levels. Moreover, cyanoHABs generate biotic and abiotic stress in the freshwater microbiome, which may lead to an increase in MGEs and VFs. Exploration of the intricate interplays between microbiome, resistome, mobilome, and pathobiome during cyanoHABs not only revealed that the mechanisms underlying the dynamics of microbial dysbiosis but also emphasizes the need to prioritize the prevention of microbial dysbiosis in the risk management of ARGs.

Abstract Background Biofumigation is a non-chemical sustainable approach that reshapes soil microbiota to overcome challenges in way of continuous cultivation. However, the type and quantity of substrate have a significant impact on microbiota shifts and the subsequent success of biofumigation. Moreover, studies on the effects of biofumigant concentration in combination with fumigation duration on soil microbiota dynamics are very rare. Research methods We performed microcosm experiments to investigate how a biofumigant (Korean canola cultivar, HanRa) at various concentrations (0.5%, 1%, 2–4% w/w: biofumigant/soil) and fumigation periods (2–4 weeks) affects the soil bacterial and fungal communities. Subsequently, pot experiments employing two Korean canola cultivars (HanRa and YongSan) at 1% (w/w) were carried out. Results Illumina MiSeq analysis revealed that 2–4% biofumigant, regardless of incubation period, had a significant negative impact on microbial diversity and network complexity. In contrast, 1% biofumigant transformed the bacterial, fungal, and inter-kingdom networks into a highly connected and complex network without affecting microbial diversity. Bacillus, Clostridium, and Pseudomonas were the most highly stimulated bacterial genera in the biofumigated soils, whereas the abundance of Acidobacteria members was greatly reduced. The 2–4% amendments had substantially and more differentially abundant Fusarium than the 1%. Soil nutrition (e.g., pH, nitrate, ammonium, and exchangeable potassium), fruit yield, and weed suppression were enhanced in subsequent pot experiments. Of the nine soil chemical properties, phosphate and exchangeable potassium were the main factors influencing the microbial community assembly. Conclusions Optimized biofumigation-mediated increase in nitrate, ammonium, and potassium availability in the soil without causing any negative effects on soil microbial diversity indicates its potential as a preplant to improve crop productivity. This study contributes significantly to our understanding of how an optimal biofumigant can help ameliorate obstacles in continuous cropping. Graphical Abstract

Background/Aims: Although fecal microbiota transplantation (FMT) has been proven as one of the promising treatments for patients with ulcerative colitis (UC), potential prognostic markers regarding the clinical outcomes of FMT remain elusive. Methods: We collected fecal samples of 10 participants undergoing FMT to treat UC and those from the corresponding donors. We categorized them into two groups: responders and nonresponders. Sequencing of the bacterial 16S rRNA gene was conducted on the samples to explore bacterial composition. Results: Analyzing the gut microbiota of patients who showed different outcomes in FMT presented a distinct microbial niche. Source tracking analysis showed the nonresponder group had a higher rate of preservation of donor microbiota, underscoring that engraftment degrees are not one of the major drivers for the success of FMT. At the phylum level, Bacteroidetes bacteria were significantly depleted (p

Toxic blooms of cyanobacteria, which can produce cyanotoxins, are prevalent in freshwater, especially in South Korea. Exposure to cyanotoxins via ingestion, inhalation, and dermal contact may cause severe diseases. Particularly, toxic cyanobacteria and their cyanotoxins can be aerosolized by a bubble-bursting process associated with a wind-driven wave mechanism. A fundamental question remains regarding the aerosolization of toxic cyanobacteria and cyanotoxins emitted from freshwater bodies during bloom seasons. To evaluate the potential health risk of the aerosolization of toxic cyanobacteria and cyanotoxins, the objectives of this study were as follows: 1) to quantify levels of microcystin in the water and air samples, and 2) to monitor microbial communities, including toxic cyanobacteria in the water and air samples. Water samples were collected from five sites in the Nakdong River, South Korea, from August to September 2022. Air samples were collected using an air pump with a mixed cellulose ester membrane filter. Concentrations of total microcystins were measured using enzyme-linked immunosorbent assay. Shotgun metagenomic sequencing was used to investigate microbial communities, including toxic cyanobacteria. Mean concentrations of microcystins were 960 μg/L ranging from 0.73 to 5,337 μg/L in the water samples and 2.48 ng/m3 ranging from 0.1 to 6.8 ng/m3 in the air samples. In addition, in both the water and air samples, predominant bacteria were Microcystis (PCC7914), which has a microcystin-producing gene, and Cyanobium. Particularly, abundance of Microcystis (PCC7914) comprised more than 1.5% of all bacteria in the air samples. This study demonstrates microbial communities with genes related with microcystin synthesis, antibiotic resistance gene, and virulence factors in aerosols generated from cyanobacterial bloom-affected freshwater body. In summary, aerosolization of toxic cyanobacteria and cyanotoxins is a critical concern as an emerging exposure route for potential risk to environmental and human health.

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

Abstract Ethiopian honey wine is one of the country's most popular spontaneously fermented traditional alcoholic beverages. However, the final product of this natural fermentation system is frequently of poor and inconsistent quality. Furthermore, it makes the process difficult to predict, control, and correct. Thus, the main aim of this study was to develop a direct fermentation system for Ethiopian honey wine, Tej. After isolating fermentative microbial strains from Tej samples, they were subjected to intensive screening to fit to its purpose. Later, phenotypic and genotypic characterization, and inoculation of isolates to honey-must were performed sequentially. Finally, microbial interaction and physicochemical analysis, including volatile compounds profiling, were done for the inoculated samples. The identified isolates were strains of Saccharomycetaceae and Lactobacillaceae families. These strains showed a good ability to tolerate osmotic stress and a lower pH environment. Tej sample produced by mixed culture inoculation of Saccharomyces and Lactobacillus species showed similar physicochemical, volatile compounds, and sensory attributes values with that of the control sample. Thus, a mixture of Saccharomyces and Lactobacillus strains could be used as a starter culture to produce Ethiopian honey, Tej, without scarifying of its major quality attributes.

Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO3−, total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.

Gut-microbial butyrate is a short-chain fatty acid (SCFA) of significant physiological importance than the other major SCFAs (acetate and propionate). Most butyrate producers belong to the Clostridium cluster of the phylum Firmicutes, such as Faecalibacterium, Roseburia, Eubacterium, Anaerostipes, Coprococcus, Subdoligranulum, and Anaerobutyricum. They metabolize carbohydrates via the butyryl-CoA: acetate CoA-transferase pathway and butyrate kinase terminal enzymes to produce most of butyrate. Although, in minor fractions, amino acids can also be utilized to generate butyrate via glutamate and lysine pathways. Butyrogenic microbes play a vital role in various gut-associated metabolisms. Butyrate is used by colonocytes to generate energy, stabilizes hypoxia-inducible factor to maintain the anaerobic environment in the gut, maintains gut barrier integrity by regulating Claudin-1 and synaptopodin expression, limits pro-inflammatory cytokines (IL-6, IL-12), and inhibits oncogenic pathways (Akt/ERK, Wnt, and TGF-β signaling). Colonic butyrate producers shape the gut microbial community by secreting various anti-microbial substances, such as cathelicidins, reuterin, and β-defensin-1, and maintain gut homeostasis by releasing anti-inflammatory molecules, such as IgA, vitamin B, and microbial anti-inflammatory molecules. Additionally, butyrate producers, such as Roseburia, produce anti-carcinogenic metabolites, such as shikimic acid and a precursor of conjugated linoleic acid. In this review, we summarized the significance of butyrate, critically examined the role and relevance of butyrate producers, and contextualized their importance as microbial therapeutics.

The population of the Korean fir, Abies koreana, is declining at an accelerating rate, and the average mortality rate in 2019 exceeded 36.43% on Mt. Hallasan in Jeju Island, Republic of Korea. Several prior studies have reported different reasons with various interpretations, indicating that additional data, such as data on microbial communities that promote plant growth and resistance to abiotic stresses, are required to understand the phenomenon further. This is the first investigation that documents the changes in the soil microbial and fungal community and soil physicochemical properties resulting from the death of the Korean fir. In our case, high throughput sequencing data have been provided for the soil microbiome and mycobiome of Korean fir trees, identifying the microbial composition differences before and after the decline in the health of Korean fir trees. The results showed that the soil fungal community was considerably shaped in response to the decline in the health of Korean fir rather than the soil bacterial community. The decline in health or the death of Korean fir trees contributed to the decrease in diversity and dominance of symbiotic fungi such as Russula, Sebacina, and Phenoliferia in the forest ecosystem. It also weakened the complexity and ecological competition of the fungal co-occurrence network. Structural equation modeling showed that the death of Korean fir was strongly associated with the concentrations of soil nutrients such as available phosphorus (P2O5) and potassium ion (K+) concentrations and low moisture content, adversely affecting the symbiotic relationship with ectomycorrhizal fungi. Our findings shed light on the critical taxa of mycobiome of live and dead A. koreana plants and their relationship with ecological edaphic factors, highlighting their potential role as biomarkers for the death of Korean fir.

Finger millet (Eleusine coracana) is a staple food in several parts of the world because of its high nutritional value. In addition to its high nutrient content, finger millet contains numerous bioactive compounds, including polyphenol (10.2 mg/g TAE), flavonoid (5.54 mg/g CE), phytic acid (0.48%), and dietary fiber (15–20%). Polyphenols are known for their anti-oxidant and anti-diabetic role. Phytic acid, previously considered an anti-nutritive substance, is now regarded as a nutraceutical as it reduces carbohydrate digestibility and thus controls post-prandial glucose levels and obesity. Thus, finger millet is an attractive diet for patients with diabetes. Recent findings have revealed that the anti-oxidant activity and bio-accessibility of finger millet polyphenols increased significantly (P < 0.05) in the colon, confirming the role of the gut microbiota. The prebiotic content of finger millet was also utilized by the gut microbiota, such as Faecalibacterium, Eubacterium, and Roseburia, to generate colonic short-chain fatty acids (SCFAs), and probiotic Bifidobacterium and Lactobacillus, which are known to be anti-diabetic in nature. Notably, finger millet-induced mucus-degrading Akkermansia muciniphila can also help in alleviate diabetes by releasing propionate and Amuc_1100 protein. Various millet bio-actives effectively controlled pathogenic gut microbiota, such as Shigella and Clostridium histolyticum, to lower gut inflammation and, thus, the risk of diabetes in the host. In the current review, we have meticulously examined the role of gut microbiota in the bio-accessibility of millet compounds and their impact on diabetes.

Androgenetic alopecia (AGA) is a non-scarring and progressive form of hair loss occurring in both men and women. Although genetic predisposition and sex steroid hormones are the main causes, many factors remain unknown, and various extrinsic factors can negatively affect the lifespan of hair. We investigated skin–gut axis microorganisms as potential exogenous factors causing AGA, through comparative analyses of the scalp and gut microbiome in individuals with and without AGA in a Korean cohort. Using 16S rRNA gene sequencing, we characterized the scalp and gut microbiomes of 141 individuals divided into groups by sex and presence of AGA. Alpha diversity indices in the scalp microbiome were generally higher in individuals with AGA than in healthy controls. These indices showed a strong negative correlation with scalp-inhabitant bacteria (Cutibacterium and Staphylococcus), indicating that the appearance of non-inhabitant bacteria increases as hair loss progresses. No significant differences in diversity were observed between the gut microbiomes. However, bacterial functional differences, such as bile acid synthesis and bacterial invasion of epithelial cells, which are related to intestinal homeostasis, were observed. The networks of the scalp and gut microbiome were more complex and denser with higher values of the network topology statistic coefficient values (i.e., transitivity, density, and degree centrality) and more unique associations in individuals with AGA than in healthy controls. Our findings reveal a link between skin–gut microorganisms and AGA, indicating the former’s potential involvement in the latter’s development. Additionally, these results provide evidence for the development of cosmetics and therapeutics using microorganisms and metabolites involved in AGA.

Abstract Background To identify disease-specific cytokine and growth factor profile differences in the aqueous humor between wet age-related macular degeneration (AMD) patients and age-matched controls and to correlate their levels with the optical coherence tomography (OCT) findings. Methods Aqueous humors were obtained from 13 wet AMD eyes and 10 control eyes. Twenty cytokines and growth factors were measured using a RayBio antibody microarray technology in wet AMD and control eyes. Results The samples obtained from wet AMD patients exhibited a significantly increased expression of MCP-1, MIP-1α, MIP-1β, and vascular endothelial growth factor (VEGF). Subretinal fluid (SRF) patients showed significantly lower levels of proinflammatory cytokines, such as IL-1α and GM-CSF, than those without SRF. Pigment epithelial detachments (PED) patients showed lower levels of inflammatory cytokines, such as GM-CSF, IFN-γ, and TNF-α, than those without PED. Subretinal tissue (SRT) patients showed a higher level of IFN-γ than those without SRT. Compared with the controls, type 1 macular neovascularization (MNV) patients showed increased levels of MCP-1, MIP-1α, and MIP-1β, but not VEGF (p = 0.083). However, type 2 MNV patients showed increased levels of MCP-1 and VEGF (p = 0.040 and p = 0.040). Conclusion Inflammatory cytokines varied according to the type of AMD- and OCT-based parameters. Our observation of low levels of VEGF in patients with type 1 MNV implies that the inhibition of VEGF alone appears to be insufficient treatment for these patients and that cytokines such as MCP-1, MIP-1α, and MIP-1β should be modulated. And the presence of SRF in MNV may be associated with a positive prognosis because we found relatively low levels of proinflammatory cytokines.

An intermittent fasting regimen is widely perceived to lead to various beneficial health effects, including weight loss, the alleviation of insulin resistance, and the restructuring of a healthy gut microbiome. Because it shares certain commonalities with this dietary intervention, Ramadan fasting is sometimes misinterpreted as intermittent fasting, even though there are clear distinctions between these two regimens. The main purpose of this study is to verify whether Ramadan fasting drives the same beneficial effects as intermittent fasting by monitoring alterations in the gut microbiota. We conducted a study involving 20 Muslim individuals who were practicing Ramadan rituals and assessed the composition of their gut microbiomes during the 4-week period of Ramadan and the subsequent 8-week period post-Ramadan. Fecal microbiome analysis was conducted, and short-chain fatty acids (SCFAs) were assessed using liquid-chromatography–mass spectrometry. The observed decrease in the levels of SCFAs and beneficial bacteria during Ramadan, along with the increased microbial diversity post-Ramadan, suggests that the daily diet during Ramadan may not provide adequate nutrients to maintain robust gut microbiota. Additionally, the notable disparities in the functional genes detected through the metagenomic analysis and the strong correlation between Lactobacillus and SCFAs provide further support for our hypothesis.

Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group.

This dataset contains raw and analyzed microbial data for the samples of spontaneously fermented Ethiopian honey wine, Tej, collected from three locations of Ethiopia. It was generated using culture independent amplicon sequencing technique. To gain a better understanding of microbial community variance and similarity across Tej samples from the same and different locations, the raw sequenced data obtained from the Illumina Miseq sequencer was subjected to a bioinformatics analysis. Lower diversity and richness of both bacterial and fungal communities were observed for all of the Tej samples. Besides, samples collected from Debre Markos area showed a significant discriminating tax for both bacterial and fungal communities. In nutshell, this amplicon sequencing dataset provides a useful collection of data for modernizing this spontaneous fermentation into a directed inoculated fermentation. Detail discussion on microbiome of Tej samples is given in [1].

Abstract The skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.

Abstract Background Pseudomyopia is caused by increased refractive power by ciliary muscle spasm. Most patients cannot overcome pseudomyopia spontaneously; therefore, treatment of pseudomyopia is fastidious and needs a multidisciplinary approach. We report a case of unusual pseudomyopia with paradoxical accommodation, straining eyes to induce emmetropia at far distance and relaxing eyes to focus at near objects, contrary to physiological accommodation. Case presentation A 33-year-old woman experienced intermittent distant vision discomfort. This occurred at least a few hundred times daily. She could see near objects clearly; however, distant objects could be seen clearly only when she strained her eyes. Uncorrected distance visual acuity was 20/20 and manifest refraction (MR) in both eyes in the relaxed state was approximately − 2.5 D. MR changed to approximately − 0.5 D when she grimaced and strained her eyes when attempting to focus on distant letters. Her response was contrary to the physiological accommodative response. Cycloplegic refraction was approximately 0.0 D. Binocular autorefractor/keratometer was used to objectively evaluate her refractive response and pupil reaction according to accommodative stimulation. The IOL Master was used to evaluate the anterior chamber depth (ACD), lens thickness (LT), and pupil diameter with relaxed and strained eyes. For stepwise static accommodative stimuli (1–5 D), the refractive responses were correspondingly stepwise, similar to those elicited by healthy individuals. However, contrary to physiological accommodation, she strained her eyes to see distant objects and relaxed them to see near objects. There was no change in pupil diameter despite the accommodative stimuli being maximum. Biometry results showed that ACD deepened and LT flattened with eye strain, which were contrary to those during physiological accommodation. Conclusions We report a rare case with reverse of physiological accommodative response. When patients complain of unusual distant visual discomfort, pseudomyopia with paradoxical accommodation should be considered.

Ex situ conservation is used to protect endangered wildlife. As captive and wild long-tailed gorals are known to be similar, individuals under ex situ conservation can be reintroduced into nature. However, there is no appropriate indicator to evaluate them. Here, we amplified the internal transcribed spacer 2 (ITS2) region and compared the gut ecological information (eco-information) of captive and wild long-tailed gorals. We validated the existing ITS86F and ITS4 universal primers using reference sequences of the National Center for Biotechnology Information (NCBI) and improved their matching rates. We compared the gut eco-information of captive and wild long-tailed gorals obtained through experiments using the improved primer pair and found that the gut ecological diversity of captive gorals was low. Based on this, we suggested that the gut eco-information can be used as an evaluation index before reintroducing captive long-tailed gorals. Furthermore, we identified four plant types from the gut eco-information of wild long-tailed gorals, which can be the additional food sources to enhance the reduced intestinal ecological diversity of the captive animals.

In the present study, we aimed to investigate age-, cryptorchidism-, and testicular tumor-related changes in miRNAs in the testis and epididymis of dogs. Twelve healthy male dogs were divided into two groups: young (3 years, n = 4). Five dogs with unilateral cryptorchidism, one with a Sertoli cell tumor, and one with seminoma were referred to a veterinary hospital. After surgery, the testes and epididymis tails were collected. A high-throughput miRNA array analysis was performed to identify miRNAs affected by age, cryptorchidism, and testicular tumors. The expression of only cfa-miR-503 was downregulated in the epididymis of younger dogs, whereas the expression of 64 miRNAs was upregulated. Among them, the top five miRNAs were cfa-miR-26a, cfa-miR-200c, cfa-let-7c, cfa-let-7b, and cfa-let-7a. The expression of cfa-miR-148a and cfa-miR-497 was considerably lower in cryptorchid testis than in healthy dog testis. In the epididymis, the cfa-miR-1841 level was significantly decreased. We observed a significant difference in the expression of 26 cfa-miRNAs between testicular tumors and normal tissues. This study demonstrated that aging and cryptorchidism have a causal relationship with miRNA expression. The identified miRNAs may be candidate genes for male reproductive traits and could be applied in molecular breeding programs.

Abstract Background Neuromuscular hamartoma is a very rare tumor; with only five cases reported in the orbit. It often occurs in infants and young children and involves large peripheral nerves, but there has been only few reports of occurrence in the orbit and adults. Case presentation This paper describes a 70-year-old man with an incidental orbital mass detected by an imaging test and who later developed associated symptoms. The mass was diagnosed as neuromuscular hamartoma. Superior rectus muscle recession and inferior rectus muscle resection were performed in the right eye for hypertropia secondary to postoperative inferior rectus muscle palsy. Hypertropia in the right eye and diplopia improved after surgery, and regular follow-up is underway. Conclusion This is the first case of an incidentally detected orbital mass diagnosed by histologic examination as a neuromuscular hamartoma in an older patient whose proptosis progressed after a long period of inactivity.

Background/Aims Stress is closely related to the deterioration of digestive disease. Melatonin has potent anti-inflammatory properties. The objective of this study was to determine the effect of water stress (WS) and sleep deprivation (SD) on intestinal microbiota and roles of melatonin in stressful condition. Methods We used C57BL/6 mice and specially designed water bath for stress and SD for 10 days. We measured melatonin concentrations in serum, feces, and colon tissues by high-performance liquid chromatography. Genomic DNA was extracted from feces and amplified using primers targeting V3 to V4 regions of bacterial 16S ribosomal RNA genes. Results Compared to the control, melatonin concentration was lower in the WS and SD. Fecal concentration was 0.132 pg/mL in control, 0.062 pg/mL in WS, and 0.068 pg/mL in SD. In colon tissue, it was 0.45 pg/mL in control, 0.007 pg/mL in WS, and 0.03 pg/mL in SD. After melatonin treatment, melatonin concentrations in feces and colon tissue were recovered to the level of control. Metagenomic analysis of microbiota showed abundance in colitogenic microbiota in WS and SD. Melatonin injection attenuated this harmful effect. WS and SD showed decreased Lactobacillales and increased Erysipelotrichales and Enterobacteriales. Melatonin treatment increased Akkermansia muciniphila and Lactobacillus and decreased Bacteroides massiliensis and Erysipelotrichaceae. Conclusions This study showed that stress and SD could affect intestinal dysbiosis and increase colitogenic microbiota, which could contribute to the aggravating digestive disease. Melatonin concentrations in feces and colon tissue decreased under WS and SD. Melatonin treatment brought recovery of melatonin concentration in colon tissue and modulating dysbiosis of intestinal microbiota.

Abstract Background Multifocal spherical nonstaining cavities and gram-positive, rod-shaped, and endospore-forming bacteria were found in the liver of a sow that died suddenly. Clostridium novyi type B was identified and isolated from the sudden death case, and the isolate was characterized by molecular analyses and bioassays in the current study. Results C. novyi was isolated from the liver of a sow that died suddenly and was confirmed as C. novyi type B by differential PCR. The C. novyi isolate fermented glucose and maltose and demonstrated lecithinase activity, and the cell-free culture supernatant of the C. novyi isolate exhibited cytotoxicity toward Vero cells, demonstrating that the isolate produces toxins. In addition, whole-genome sequencing of the C. novyi isolate was performed, and the complete sequences of the chromosome (2.29 Mbp) and two plasmids (134 and 68 kbp) were identified for the first time. Based on genome annotation, 7 genes were identified as glycosyltransferases, which are known as alpha toxins; 23 genes were found to be related to sporulation; 12 genes were found to be related to germination; and 20 genes were found to be related to chemotaxis. Conclusion C. novyi type B was isolated from a sow in a sudden death case and confirmed by biochemical and molecular characterization. Various virulence-associated genes were identified for the first time based on whole-genome sequencing.

Inflammatory bowel disease involves the breaking down of tight junctions and triggers leaky gut syndrome. In this study, we evaluated the effect of cinnamon subcritical water extract (CSE) on gut health improvement using a mouse colitis model induced by 5 % dextran sodium sulfate. The mice were treated with varying concentrations of CSE for 21 days and assessed. We examined histopathological changes, mRNA expression of cytokines and tight junction proteins, and alteration of the gut microbiome. CSE treatment improved clinical symptoms. Moreover, myeloperoxidase activity, interleukin (IL)-1β, IL-6, tumor necrosis factor-α protein, and mRNA expression were reduced in the CSE-treated groups. However, CSE increased the mRNA expression of tight junction proteins, such as ZO-1, occludin, mucin-1, mucin-2, and E-cadherin. In addition, CSE altered the microbiome to reduce inflammation. These results suggested that CSE could prevent dextran sodium sulfate sodium-induced colitis and disruption of the intestinal environment.

Downer cow can be caused by muscular paralysis, neurological damage, metabolic disorder, and/or the complication of microbial infection. However, downer cow with unknown etiology is issued because of the non-detection of its bacterial etiological agent. In this study, differences in the bacterial community in brain tissues between downer cattle with unknown etiology and healthy slaughtered cattle are investigated. Bacterial diversity and representative genera between downer and normal cattle were significantly different (p < 0.05). There are significant differences in representative genera of downer and normal cattle, especially the significance, fold change, and area under the receiver operating characteristic curve score (p < 0.05). Furthermore, the prediction of functional genes in brain microbiota between the downer and normal cattle revealed differences in the cluster of orthologous gene categories, such as lipid transport and metabolism, secondary metabolite biosynthesis, and signal transduction (p < 0.05). This study revealed a significant difference in microbiota between the downer and normal cattle. Thus, we demonstrate that representative genera from downer cattle through 16S rRNA gene amplicon sequencing and microbiota analysis have the potential as candidates for bacterial etiological agents for downer cow.

Overweight and obesity, associated with various health complications, refer to abnormal or excessive fat accumulation conditions that harm health. Like humans, obesity is a growing problem in dogs, which may increase the risk of serious diseases such as diabetes and cancer. Mulberry leaf has shown potential anti-obesity and anti-diabetes effects in several studies. Our research studied the impact of mulberry leaf supplements in healthy old overweight dogs for 12 weeks. Blood and fecal samples were collected from the dogs before and after treatment for different analyses, including whole transcriptome and gut microbiome analysis. The Body Condition Score (BCS) and blood glucose levels were significantly decreased in all mulberry treatment groups, which justifies the anti-obesity effect of mulberry leaf in dogs. Throughout the whole transcriptome study, the downregulation of PTX3 and upregulation of PDCD-1, TNFRSF1B, RUNX3, and TICAM1 genes in the high mulberry group were found, which have been associated with anti-inflammatory effects in the literature. It may be an essential gene expression mechanism responsible for the anti-inflammatory and, subsequently, anti-obesity effects associated with mulberry leaf treatment, as confirmed by real-time polymerase chain reaction analysis. In microbiome analysis, Papillibacter cinnamivorans, related to the Mediterranean diet, which may cause anti-inflammatory effects, were abundant in the same treatment group. Further studies may be required to establish the gene expression mechanism and role of abundant bacteria in the anti-obesity effect of mulberry supplements in dogs. Overall, we propose mulberry leaves as a portion of food supplements for improving blood glucose levels and the anti-inflammation of blood in companion dogs.

Paenibacillus sonchi LMG 24727T was acquired from the Belgian Coordinated Collections of Microorganisms (BCCM) isolated from Sonchus oleraceus rhizosphere soil. This strain is a gram-positive, aerobic, rod-shaped bacterium. The strain's genomic DNA was extracted using a Wizard® Genomic DNA Purification Kit, and whole-genome sequencing was performed using the Nanopore MinION platform. Whole-genome assembly was performed using Flye assembler, and a total 7,782,254 bp length of circular chromosome and two plasmids was assembled by using a 1,558,445,868 bp length of raw reads. Genome annotation by the Prokaryotic Genome Annotation Pipeline (PGAP) showed the complete genome to contain 50.6% G+C content; 6264 protein-coding genes; 27 rRNA genes; 89 tRNA genes; and 4 ncRNA genes. Additionally, multiple genes related to nitrogen metabolism were annotated from the Rapid Annotation using Subsystem Technology (RAST) server. The complete genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) and have been deposited at DDBJ/ENA/GenBank under the accession number CP068595.1, CP068596.1, and CP068597.1.

Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. Therefore, we analyzed the bacterial and fungal communities in the bark and rhizosphere soil of healthy peach trees and those with gummosis. Through high-throughput sequencing, we obtained unprecedented insights into the bacterial and fungal dynamics of each group, including their diversity and taxonomic classification, as well as network analyses. We found that the presence of gummosis drives a significantly higher alpha diversity in the bark bacterial community. Peach gummosis bark mycobiomes included greater numbers of opportunistic pathogens such as Ascochyta, Botryosphaeria, Saccharomyces, Nectriaceae_NA, Trametes, and Valsaceae_NA. However, the microbiome also included bacteria beneficial to plant growth and the production of polysaccharides—namely, 1174-901-12, Catenibacterium, Cutibacterium, Friedmanniella, Methylobacterium-Methylorubrum, Pseudomonas, Rhodobacter, and Sphingomonas. Furthermore, we confirmed that gummosis induced a more complex structure in the bark microbiome network. We conclude that the findings of this study provide a valuable aid in profiling the overall peach tree microbial ecosystem, which can be utilized to develop precise biomarkers for the early diagnosis of gummosis.

Owing to the emergence and improvement of high-throughput technology and the associated reduction in costs, next-generation sequencing (NGS) technology has made large-scale sampling and sequencing possible. With the large volume of data produced, the processing and downstream analysis of data are important for ensuring meaningful results and interpretation. Problems in data analysis may be encountered if researchers have little experience in using programming languages, especially if they are clinicians and beginners in the field. A strategy for solving this problem involves ensuring easy access to commercial software and tools. Here, we observed the current status of free web-based tools for microbiome analysis that can help users analyze and handle microbiome data effortlessly. We limited our search to freely available web-based tools and identified MicrobiomeAnalyst, Mian, gcMeta, VAMPS, and Microbiome Toolbox. We also highlighted the various analyses that each web tool offers, how users can analyze their data using each web tool, and noted some of their limitations. From the abovementioned list, gcMeta, VAMPS, and Microbiome Toolbox had several issues that made the analysis more difficult. Over time, as more data are generated and accessed, more users will analyze microbiome data. Thus, the availability of free and easily accessible web tools can enable the easy use and analysis of microbiome data, especially for those users with less experience in using command-line interfaces.

We use magnetotransport in dual-gated magnetic topological insulator heterostructures to map out a phase diagram of the topological Hall and quantum anomalous Hall effects as a function of the chemical potential (primarily determined by the back gate voltage) and the asymmetric potential (primarily determined by the top gate voltage). A theoretical model that includes both surface states and valence band quantum well states allows the evaluation of the variation of the Dzyaloshinskii-Moriya interaction and carrier density with gate voltages. The qualitative agreement between experiment and theory provides strong evidence for the existence of a topological Hall effect in the system studied, opening up a route for understanding and manipulating chiral magnetic spin textures in real space.

The purpose of the present study was to investigate the anti-inflammatory effects of a sugar isomer, leucrose (D-glucopyranosyl-α-(1–5)-D-fructopyranose) in a dextran sulfate sodium (DSS)-induced colitis mouse model and in RAW 264.7 macrophages. Colitis was induced in vivo with administration of two cycles of DSS (2.5%). Two groups of mice received an AIN-93G diet with 25% or 50% of the total sucrose content replaced with leucrose. This leucrose supplementation improved disease activity index (DAI) scores, colon length, histopathological damage, and myeloperoxidase (MPO) activity levels. In addition, the expression of pro-inflammatory mediators and cytokines decreased in the leucrose supplementation groups compared with the DSS alone treatment group. Furthermore, leucrose supplementation increased M2 macrophage polarization. Leucrose treatment suppressed IL-4-induced M2 polarization and increased JAK1/STAT6 phosphorylation in RAW264.7 cells. Taken together, these results indicate that leucrose exerts an anti-inflammatory effect by regulating M2 macrophage polarization via inflammatory cytokines and the JAK1/STAT6 signaling pathway.

Quorum sensing (QS) enables bacteria to organize gene expression programs, thereby coordinating collective behaviors. It involves the production, release, and population-wide detection of extracellular signaling molecules. The cellular processes regulated by QS in bacteria are diverse and may be used in mutualistic coordination or in response to changing environmental conditions. Here, we focused on the influence of the QS-dependent genes of our model bacterial strain Serratia fonticola GS2 on potential plant growth promoting (PGP) activities including indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and biofilm formation. Based on genomic and phenotypic experimental data we identified and investigated the function of QS genes in the genome of the model strain. Our gene deletion study confirmed the biological functionality of the QS auto-inducer (gloI) and receptor (gloR) on potential PGP activities of GS2. A transcriptomic approach was also undertaken to understand the role of QS genes in regulation of genes primarily involved in PGP activities (IAA, ACC deaminase activity, and biofilm formation). Both transcriptomic and phenotypic data revealed that the QS-deletion mutants had considerably less PGP activities, as compared to the wild type. In addition, in vivo plant experiments showed that plants treated with GS2 had significantly higher growth rates than plants treated with the QS-deletion mutants. Overall, our results showed how QS-dependent genes regulate the potential PGP activities of GS2. This information may be helpful in understanding the relationship between QS-dependent genes and the PGP activity of bacteria, which aid in the production of practical bio-fertilizers for plant growth promotion.

We identified an antimicrobial peptide (AMP) from Lactobacillus acidophilus that was antagonistic to Aeromonas hydrophila. In vitro studies such as well-diffusion and field trials revealed that the AMP was active against A. hydrophila. The field trials of AMP using A. hydrophila-infected Channa striatus with a mannone oligosaccharide (MOS) prebiotic, A. hydrophila antigens, A. hydrophila-infected fish serum, L. acidophilus, and Lactobacillus cell free-supernatant (LABS-CFS) on an indicator organism further revealed that the antimicrobial agent could protect C. striatus. Other than the AMP, none of the above were able to eliminate the infectious agent A. hydrophila, and were only able to delay the death rate for 3–4 days. Thus, we conclude that the AMP is antagonistic to A. hydrophila and may be used for treatment of A. hydrophila infections. Subsequent L. acidophilus whole-genome sequence analyses enabled an understanding of the (probable) gene arrangement and its location on the chromosome. This information may be useful in the generation of recombinant peptides to produce larger quantities for treatment.

The intestinal tract is one of the most sensitive organs following irradiation. The protective effect of specific indigenous microbiota on irradiation-induced damage to intestinal epithelial cells has not been reported. Mice were irradiated with a single dose of 6 Gy of gamma rays. The intestinal damage was analyzed by histopathology. Intestinal stemness and differentiation were determined by intestinal organoid culture. Microbiota community was observed by high-throughput 16S rRNA gene sequencing and oligotyping analysis. We showed that distal small intestine was damaged by sublethal dose of gamma irradiation. Intestinal organoids derived from the irradiated mice showed defects in budding and mucin expression, suggesting the detrimental effect of irradiation on the intestinal stemness and differentiation. In addition, irradiation reduced intestinal immunoglobulin A level, concomitant with decreased microbiota diversity based on our high-throughput 16S rRNA gene sequencing data. Especially, the relative abundance of Lactobacillus was reduced at early time point post-irradiation; however, it was recovered at late time point. Oligotyping analysis within the Lactobacillus genus indicated that Lactobacillus-related oligotype 1 (OT1) including Lactobacillus acidophilus might drive recovery after irradiation as it was associated with increased long-term numbers post-exposure. We showed that treatment with heat-killed L. acidophilus rescued the budding-impaired organoids and induced sufficient differentiation in epithelial cells, and particularly mucin-producing cells, in intestinal organoids. This study provides the first evidence that the indigenous gut bacteria L. acidophilus enhance intestinal epithelial function with respect to irradiation-induced intestinal damage by improving intestinal stem cell function and cell differentiation.

The prevalence of inflammatory bowel disease (IBD) is increasing worldwide, and the key risk factor is high sugar diet. The objective of this study was to investigate anti-inflammatory effects of turanose on IBD in a dextran sulfate sodium (DSS)-induced colitis mouse model. An amylosucrase from Neisseria sicca (NsiAS) was newly identified and successfully expressed. This enzyme exhibited optimal activity at 45 °C and pH 8.5. By utilizing this recombinant enzyme expressed in the E. coli host, turanose yield maximally reached 47% from 2.0 M sucrose. Colitis was induced with two 5-d cycles of 2.5% DSS in drinking water with a 10-d inter-cycle interval. Mice were fed AIN93G diet with 25% and 50% turanose replacement. Improved disease activity index scores, colon length, histopathological features, and myeloperoxidase activity were observed in the turanose supplemented group. Meanwhile, decreases in micro RNA (miR)-21 expression, histone acetylation, expression of pro-inflammatory cytokines, and phosphorylated ERK and STAT3 were observed in colon tissues. Notably, miR-21 and histone acetylation levels were found to positively correlated with expression of tumor necrosis factor α. In conclusion, turanose can attenuate colitis via regulatory effects on miRNA-21 expression and histone acetylation-related proinflammatory mediators. These findings also support further exploration of turanose as a potential therapeutic sugar substitute for patients with IBD.

Phyllodulcin, an isocoumarin derivatives and well-known natural sweetener derived from Hydrangea macrophylla var, was evaluated for its roles in diabetes-related metabolic and genetic changes by regulating glucose homeostasis in the liver. C57BL/KsJ-db/db mice received 20 mg/kg body weight (b.w.) stevioside (SVS 20), 10 mg/kg b.w. phyllodulcin (P 10), or 20 mg/kg b.w. phyllodulcin (P 20) for four weeks. Water and food intake were significantly lower in the phyllodulcin supplemented group compared with the diabetic group. Phyllodulcin supplementation suppressed the levels of fasting blood glucose, HbA1c, and plasma and hepatic triglyceride level. Phyllodulcin improved hepatic lipogenesis, while also suppressing inflammation and oxidative stress. Phyllodulcin inhibited hepatic fibrosis and regulated liver glucose homeostasis. Thus, these results indicate the potential of phyllodulcin to serve as a therapeutic agent to improve global hepatic function and metabolic abnormalities of diabetic conditions and the necessity to be better explored.

Abstract Biliary atresia (BA) results in severe bile blockage and is caused by the absence of extrahepatic ducts. Even after successful hepatic portoenterostomy, a considerable number of patients are likely to show progressive deterioration in liver function. Recent studies show that mutations in protein-coding mitochondrial DNA (mtDNA) genes and/or mitochondrial genes in nuclear DNA (nDNA) are associated with hepatocellular dysfunction. This observation led us to investigate whether hepatic dysfunctions in BA is genetically associated with mtDNA mutations. We sequenced the mtDNA protein-coding genes in 14 liver specimens from 14 patients with BA and 5 liver specimens from 5 patients with choledochal cyst using next-generation sequencing. We found 34 common non-synonymous variations in mtDNA protein-coding genes in all patients examined. A systematic 3D structural analysis revealed the presence of several single nucleotide polymorphism-like mutations in critical regions of complexes I to V, that are involved in subunit assembly, proton-pumping activity, and/or supercomplex formation. The parameters of chronic hepatic injury and liver dysfunction in BA patients were also significantly correlated with the extent of hepatic failure, suggesting that the mtDNA mutations may aggravate hepatopathy. Therefore, mitochondrial mutations may underlie the pathological mechanisms associated with BA.

Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community.

The long-tailed goral (Naemorhedus caudatus) is an endangered species found in the mountains of eastern and northern Asia. Its populations have declined for various reasons, and this species has been designated as legally protected in South Korea. Although various ecological studies have been conducted on long-tailed gorals, none have investigated the gut microbiome until now. In the present study, we compared the diversity and composition of the gut microbiome of seven populations of Korean long-tailed gorals. By analyzing the gut microbiome composition for each regional population, it was found that four phyla—Firmicutes, Actinobacteriota, Bacteroidota, and Proteobacteria—were the most dominant in all regions on average. The alpha diversity of the gut microbiome of the goral population in the northern regions was high, while that in the southern regions was low. Through the analysis of beta diversity, the seven long-tailed goral populations have been divided into three groups: the Seoraksan population, the Samcheock population, and the Wangpicheon population. It was possible to confirm the regional migration of the animals using the gut microbiome based on the site-relational network analysis. It was found that the most stable population of long-tailed gorals in Korea was the Seoraksan population, and the closely related groups were the Samcheok and Wangpicheon populations, respectively. Wangpicheon appeared to be a major point of dispersal in the migration route of Korean long-tailed gorals.

Livestock odors are unavoidable problems in modern industrial society. We foresaw a role for fermented organic wastes in controlling odorous gases. In this study, we applied fermented coffee grounds to the floor area of a dairy cow barn and assessed alterations in odor compounds and a microbial shift over a period of three weeks. The treatment dramatically reduced ten odor compounds (more than 50%), highlighting the utility of fermented coffee grounds as an excellent product to reduce odors derived from cow manure. By the end of the treatment, the microbial consortium showed increases in rare families whose prevalence and abundance before the treatment had been low. Network analysis manifested 23 bacterial families dominant in fermented coffee grounds, negatively connected with odorous compounds, indicating potential odor-reducing bacterial families. This study provides an insight into using bacteria at the community level as a treatment to solve an environmental issue; simultaneously, it suggests proper usage of organic wastes by recycling them as fermenters for beneficial bacteria.