Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies

Banxia Xiexin decoction modulates gut microbiota and gut microbiota metabolism to alleviate DSS-induced ulcerative colitis

ETHNOPHARMACOLOGICAL RELEVANCE

Banxia Xiexin decoction (BXD) is a classic traditional Chinese medicine prescription for treating ulcerative colitis (UC). However, its potential mechanism of action is still unclear.

AIM OF THE STUDY

Reveal the correlation between the beneficial impacts of BXD on UC and the composition of the gut microbiota.

MATERIALS AND METHODS

The major constituents of BXD were identified using the HPLC-DAD technique. An experimental model of UC was induced in male C57BL/6 mice by administering dextran sodium sulfate (DSS). A total of 48 mice were divided into different groups, including control, model, high-dose BXD treatment, medium-dose BXD treatment, low-dose BXD treatment, and a group treated with 5-amino acid salicylic acid (5-ASA). Body weight changes and disease activity index (DAI) scores were documented; colon length, colon index, spleen index, and thymus index scores were determined; myeloperoxidase (MPO) and tumor necrosis factor-α (TNF-α) activities were assessed; and histological staining with hematoxylin-eosin and alcian blue/phosphate Schiff was performed. The immunofluorescence technique was employed to examine the presence of ZO-1 and occludin in the colon tissue. 16S rRNA sequencing was employed to assess the gut microbiota's diversity and metabolomics was utilized to examine alterations in metabolites within the gut microbiota. The impact of BXD on the gut microbiota was confirmed through fecal microbiota transplantation (FMT).

RESULTS

BXD exhibited a positive impact on UC mice, particularly in the high-dose BXD treatment group. The BXD group experienced weight recovery, decreased DAI scores, improved colon length, and restored of spleen and thymus index scores compared to the DSS group. Additionally, BXD alleviated colon damage and the inflammatory response while restoring intestinal barrier function. FMT in BXD-treated mice also showed therapeutic effects in UC mice. At the phylum level, the relative abundance of Desulfobacterota, Deferribacterota and Actinobacteriota increased; at the genus level, g__norank__f__Muribaculaceae, Dubosiella, Akkermansia, and Lactobacillus increased, whereas Faecalibaculum, Alloprevotella, Turicibacter, and g_Paraprevotella decreased. g__norank_f__Muribaculaceae was positively correlated with body weight and colon length and negatively with colon index scores, splenic index scores, and MPO levels; Alloprevotella was positively correlated with splenic index scores, histological scores, and TNF-α levels and negatively with thymus index scores and thymus index scores. Faecalibaculum was positively correlated with colon index scores and MPO levels. Metabolic investigations revealed 58 potential indicators, primarily associated with the metabolism of amino acids, purines, and lipids. Alloprevotella, g_Paraprevotella, and Bifidobacterium were strongly associated with metabolic pathways.

CONCLUSION

BXD showed beneficial therapeutic effects in UC mice. The mechanism may be by promoting the balance and variety of gut microbiota, as well as regulating the metabolism of amino acids, purines, and lipids.

Ecological Insights, and Fin Fish Diversity in Carps Spawning Grounds: Case Studies from the Surma River and Tanguar Haor, Bangladesh

This study aims to provide a thorough ecological understanding of fin fish diversity within carp spawning grounds in the Surma River and Tanguar haor. Over two spawning seasons, this research investigates ecological factors impacting fin fish diversity and abundance in carp spawning grounds of the Surma River and Tanguar haor, emphasizing water quality, habitat features, spawn availability, and environmental influences. Fish spawn samples were collected with eight "Savar nets" at chosen sites and reared in a fiberglass tank at the mini hatchery for species identification. The representative spawn samples were examined under a microscope for preliminary species identification before rearing. The study found that both the Surma River and Tanguar haor offer ideal conditions for carp spawning due to factors such as water quality, natural food availability, habitat suitability, and favorable climatic conditions. The study identified 39 fish species under the 10 fish groups from both locations, with a higher percentage of carp species (31.42%) in the Surma River in 2021 compared to 2022 (22.50%). In Tanguar haor, the percentage of carp species was 7.55% and 6.50% in 2021 and 2022, respectively. The Surma River's ecological indices (2021-2022) indicated decreased diversity, likely due to environmental degradation, while Tanguar haor showed lower diversity possibly attributable to multiple environmental stressors. The dominant carp species, Labeo calbasu, Labeo bata, and Labeo gonius, were identified in both the Surma River and Tanguar haor. The spawning distribution varied among different locations, with some sites showing a presence of carp species, such as Hajipur (T1) in the Surma River and Alam Duar (T2) in Tanguar haor. The findings highlight the importance of hydrological and environmental parameters in shaping carp spawning habitat distribution and abundance, contributing to aquatic biodiversity conservation and resource management.

Dynamics of soil biota and nutrients at varied depths in a Tamarix ramosissima-dominated natural desert ecosystem: Implications for nutrient cycling and desertification management

The underground community of soil organisms, known as soil biota, plays a critical role in terrestrial ecosystems. Different ecosystems exhibit varied responses of soil organisms to soil physical and chemical properties (SPCPs). However, our understanding of how soil biota react to different soil depths in naturally established population of salinity tolerant Tamarix ramosissima in desert ecosystems, remains limited. To address this, we employed High-Throughput Illumina HiSeq Sequencing to examine the population dynamics of soil bacteria, fungi, archaea, protists, and metazoa at six different soil depths (0-100 cm) in the naturally occurring T. ramosissima dominant zone within the Taklimakan desert of China. Our observations reveal that the alpha diversity of bacteria, fungi, metazoa, and protists displayed a linear decrease with the increase of soil depth, whereas archaea exhibited an inverse pattern. The beta diversity of soil biota, particularly metazoa, bacteria, and protists, demonstrated noteworthy associations with soil depths through Non-Metric Dimensional Scaling analysis. Among the most abundant classes of soil organisms, we observed Actinobacteria, Sordariomycetes, Halobacteria, Spirotrichea, and Nematoda for bacteria, fungi, archaea, protists, and metazoa, respectively. Additionally, we identified associations between the vertical distribution of dominant biotic communities and SPCPs. Bacterial changes were mainly influenced by total potassium, available phosphorus (AP), and soil water content (SWC), while fungi were impacted by nitrate (NO3-) and available potassium (AK). Archaea showed correlations with total carbon (TC) and AK thus suggesting their role in methanogenesis and methane oxidation, protists with AP and SWC, and metazoa with AP and pH. These correlations underscore potential connections to nutrient cycling and the production and consumption of greenhouse gases (GhGs). This insight establishes a solid foundation for devising strategies to mitigate nutrient cycling and GHG emissions in desert soils, thereby playing a pivotal role in the advancement of comprehensive approaches to sustainable desert ecosystem management.

A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach

Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune responses, the gut microbiome generates Treg cells, mediating the allergic response to environmental factors and exposure to allergens. Because of the complexity of asthma, microbiome analysis and other precision medicine methods are now widely regarded as essential elements of efficient disease therapy. An in-silico pipeline enables the comparative taxonomic profiling of 16S rRNA metagenomic profiles of 20 asthmatic patients and 15 healthy controls utilizing QIIME2. Further, PICRUSt supports downstream gene enrichment and pathway analysis, inferring the enriched pathways in a diseased state. A significant abundance of the phylum Proteobacteria, Sutterella, and Megamonas is identified in asthma patients and a diminished genus Akkermansia. Nasal samples reveal a high relative abundance of Mycoplasma in the nasal samples. Further, differential functional profiling identifies the metabolic pathways related to cofactors and amino acids, secondary metabolism, and signaling pathways. These findings support that a combination of bacterial communities is involved in mediating the responses involved in chronic respiratory conditions like asthma by exerting their influence on various metabolic pathways.

Ferrous Sulfate-Mediated Control of Phytophthora capsici Pathogenesis and Its Impact on Pepper Plant

Phytophthora capsici, a destructive fungal pathogen, poses a severe threat to pepper (Capsicum annuum L.) crops worldwide, causing blights that can result in substantial yield losses. Traditional control methods often come with environmental concerns or entail substantial time investments. In this research, we investigate an alternative approach involving ferrous sulfate (FeSO4) application to combat P. capsici and promote pepper growth. We found that FeSO4 effectively inhibits the growth of P. capsici in a dose-dependent manner, disrupting mycelial development and diminishing pathogenicity. Importantly, FeSO4 treatment enhances the biomass and resistance of pepper plants, mitigating P. capsici-induced damage. Microbiome analysis demonstrates that FeSO4 significantly influences soil microbial communities, particularly fungi, within the pepper root. Metabolomics data reveal extensive alterations in the redox metabolic processes of P. capsici under FeSO4 treatment, leading to compromised cell membrane permeability and oxidative stress in the pathogen. Our study presents FeSO4 as a promising and cost-effective solution for controlling P. capsici in pepper cultivation while simultaneously promoting plant growth. These findings contribute to a deeper understanding of the intricate interactions between iron, pathogen control, and plant health, offering a potential tool for sustainable pepper production.

The variation in the beta-casein genotypes and its effect on milk yield and genomic values in Holstein-Friesian cows

The A2 milk marker is gaining popularity worldwide; thus, many farms plan to convert their dairy cattle herds to the A2A2 genotype. Variation in beta-casein genotypes needs to be monitored in large dairy cattle populations. Therefore we aimed to evaluate the genotypic distributions, population genetics, and diversity parameters in Holstein-Friesian cows. A total of 1200 cattle were genotyped using the Affymetrix® Axiom® array system. We performed an association analysis regarding the CSN2 genotypes and phenotypic traits, including lactation and test-day milk yield. We next evaluated the effects of the genotypes considering the genetic merit of the animals. Animals were grouped based on their PTAs for milk production, fat, protein, and daughter pregnancy rate. Thus, we tested the genotype × genetic merit interaction for significance. The A2 allele frequency is remarkably high (0.68), and the heterozygous genotype is predominant (46.25%). The marker showed intermediate variability and diversity levels, indicating a considerable frequency of the A1A1 genotype (9.33%) remains in the population. ANOVA results showed no significant association between the CSN2 genotypes and milk yield traits. A similar finding is valid for the genotype × genetic merit regarding the genomic test results. The data presented here may be helpful for further investigations and applications on A2 milk production.

Exploring the bacterial genetic diversity and community structure of crude oil contaminated soils using microbiomics

The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.

Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection

To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03785-8.

Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle

Human health is strongly mediated by the gut microbiota ecosystem, which, in turn, depends not only on its state but also on its dynamics and how it responds to perturbations. Healthy microbiota ecosystems tend to be in criticality and antifragile dynamics corresponding to a maximum complexity configuration, which may be assessed with information and network theory analysis. Under this complex system perspective, we used a new analysis of published data to show that a children's population with an industrialized urban lifestyle from Mexico City exhibits informational and network characteristics similar to parasitized children from a rural indigenous population in the remote mountainous region of Guerrero, México. We propose then, that in this critical age for gut microbiota maturation, the industrialized urban lifestyle could be thought of as an external perturbation to the gut microbiota ecosystem, and we show that it produces a similar loss in criticality/antifragility as the one observed by internal perturbation due to parasitosis by the helminth A. lumbricoides. Finally, several general complexity-based guidelines to prevent or restore gut ecosystem antifragility are discussed.

Microbiota present in combined endodontic-periodontal diseases and its risks for endocarditis

INTRODUCTION

Infective endocarditis (IE) is an inflammatory disease usually caused by bacteria that enter the bloodstream and establish infections in the inner linings or valves of the heart, including blood vessels. Despite the availability of modern antimicrobial and surgical treatments, IE continues to cause substantial morbidity and mortality. Oral microbiota is considered one of the most significant risk factors for IE. The objective of this study was to evaluate the microbiota present in root canal (RC) and periodontal pocket (PP) clinical samples in cases with combined endo-periodontal lesions (EPL) to detect species related to IE using NGS.

METHODS

Microbial samples were collected from 15 RCs and their associated PPs, also from 05 RCs with vital pulp tissues (negative control, NC). Genomic studies associated with bioinformatics, combined with structuring of a database (genetic sequences of bacteria reported for infective endocarditis), allowed for the assessment of the microbial community at both sites. Functional prediction was conducted using PICRUSt2.

RESULTS

Parvimonas, Streptococcus, and Enterococcus were the major genera detected in the RCs and PPs. A total of 79, 96, and 11 species were identified in the RCs, PPs, and NCs, respectively. From them, a total of 34 species from RCs, 53 from PPs, and 2 from NCs were related to IE. Functional inference demonstrated that CR and PP microbiological profiles may not be the only risk factors for IE but may also be associated with systemic diseases, including myocarditis, human cytomegalovirus infection, bacterial invasion of epithelial cells, Huntington's disease, amyotrophic lateral sclerosis, and hypertrophic cardiomyopathy. Additionally, it was possible to predict antimicrobial resistance variants for broad-spectrum drugs, including ampicillin, tetracycline, and macrolides.

CONCLUSION

Microorganisms present in the combined EPL may not be the only risk factor for IE but also for systemic diseases. Antimicrobial resistance variants for broad-spectrum drugs were inferred based on PICRUSt-2. State-of-the-art sequencing combined with bioinformatics has proven to be a powerful tool for conducting studies on microbial communities and could considerably assist in the diagnosis of serious infections.

CLINICAL RELEVANCE

Few studies have investigated the microbiota in teeth compromised by combined endo-periodontal lesions (EPL), but none have correlated the microbiological findings to any systemic condition, particularly IE, using NGS techniques. In such cases, the presence of apical periodontitis and periodontal disease can increase IE risk in susceptible patients.

IL-10-dependent Effect of Chinese Medicine Abelmoschus manihot on Alleviating Intestinal Inflammation and Modulating Gut Microbiota

Inflammatory bowel disease (IBD) is a recurrent disease associated with a potential risk of colorectal cancer. Abelmoschus manihot (AM), a Chinese herbal medicine, is known to alleviate IBD. However, its mechanism of action requires further clarification. Here, we focused on the role of IL-10 and the gut microbiota in the mechanism of action of AM. The effects of AM on intestinal inflammation, mucus production, and gut microbes were evaluated in dextran sodium sulfate (DSS)-induced acute and chronic IBD models and in IL-10-deficient mice (IL-10[Formula: see text]). AM exhibited protective effects on acute and chronic models of IBD in wild-type mice by restoring body weight and colon length, promoting IL-10 secretion, and decreasing TNF-[Formula: see text] levels. Moreover, AM alleviated inflammatory infiltration, increased mucin 2 transcription, and increased the number of goblet cells in the colon. On the contrary, these effects were diminished in IL-10[Formula: see text] mice, which implied that the effect of AM on intestinal inflammation is IL-10-dependent. A gut microbial sequencing analysis showed that gut microbial dysbiosis was modulated by AM intervention. The regulatory effects of AM on Eggerthellaceae, Sutterellaceae, Erysipelotrichaceae, Burkholderiaceae, Desulfovibrionaceae, and Enterococcaceae were dependent on IL-10. These results revealed that AM ameliorated IBD and modulated gut microbes by promoting IL-10 secretion, indicating that AM has the potential to improve IBD and that AM is IL-10-dependent.

Association between vaginal microbiomes and neonatal septicemia in pregnant women with preterm premature rupture of membranes based on metagenome sequencing

BACKGROUND

Preterm premature rupture of membranes (PPROM) is closely associated with pathogenic microbiomes in the female reproductive tract, and can lead to neonatal septicemia. The current study aimed to investigate potential pathogenic microbiomes associated with neonatal septicemia based on DNA metagenome sequencing.

METHODS

In this study, a total of 7 pregnant women with PPROM presenting neonatal septicemia (experimental group) and 3 pregnant women with normal newborns (control group) were enrolled. Vaginal secretions at admission and before parturition as well as placental tissues after parturition were collected for DNA metagenome sequencing using whole genome shotgun method on the Illumina NovaSeq/HiSeq platform. Raw data were processed by BioBakery workflow, and MetaPhlAn4 was implemented for qualitative and quantitative analyses of microbiome. Lactobacillus crispatus, Gardneralla vaginalis, Fannyhessea vaginae and Streptococcus suis were specifically detected from the experimental group. The two groups were compared using Student's t-tests.

RESULTS

The indexes of Chao1 (P=0.00028/P=0.00072), abundance-based coverage estimator (ACE, P=0.00059/P=0.00026), Shannon (P=0.036/P=0.0065) and Simpson (P=0.007/P=0.041) in the experimental group were increased at admission and before parturition as compared with the control group. Several microbiomes, such as Lactobacillus crispatus, Gardneralla vaginalis, Fannyhessea vaginae and Streptococcus suis, were specifically detected in the experimental group. Notably, Gardnerella vaginalis and Streptococcus gallolyticus were identified from the vaginal secretions and placenta tissues of women with neonatal septicemia. Moreover, nucleic acid synthesis and carbohydrate metabolism-related pathways were enriched in the experimental group.

CONCLUSION

This study enhanced the current understanding of the mechanisms underlying pathogenic microbiomes in PPROM-induced neonatal septicemia. The trial registry number is ChiCTR2300070666 (URL: https://www.chictr.org.cn/showproj.html?proj=195648).

Oral microbiome of the inner surface of face masks and whole saliva during the COVID-19 pandemic

Wearing a face mask was strongly recommended during the COVID-19 pandemic. The purpose of this study was to investigate the diversity of the oral microbiome, the abundance of each bacterium on the inner surface of the mask, and the effects of xerostomia on the microbiota. The study was conducted on 55 generally healthy adults (45 women and 10 men, mean age 38.18 ± 12.49 years). Unstimulated flow rate (UFR) and stimulated flow rate (SFR) were measured in whole saliva samples collected for each condition. The 14 major oral bacterial species, including Porphyromonas gingivalis (P. gingivalis), Lactobacillus casei (L. casei), Tannerella forsythia (T. forsythia), and Treponema denticola (T. denticola) on the inner surface of the mask and in the UFR and SFR samples, were analyzed by real-time PCR. We found that the total DNA copy number of oral bacteria was significantly higher in UFR and SFR than in the mask (p < 0.001). On the inner surface of the mask, P. gingivalis and L. casei were the most abundant Gram-negative and Gram-positive species, respectively. The oral microbiome profile of the mask differed from that of the UFR and SFR samples. Shannon's diversity index was also significantly higher in the UFR and SFR than in the mask (2.64 ± 0.78, 2.66 ± 0.76, and 1.26 ± 1.51, respectively, p < 0.001). Shannon's diversity index of UFR and SFR had a significant positive correlation with each other (r = 0.828, p < 0.001), but there was no significant relationship with Shannon's diversity index of mask. Red complex abundance, including P. gingivalis, T. forsythia, and T. denticola, was significantly higher in UFR than in the mask. Interestingly, the DNA copy number of each of the 14 bacteria, the total bacterial amount, and Shannon's diversity index did not differ in the absence or presence of xerostomia (p > 0.05). In summary, oral bacteria migrated to and existed on the inside of the mask, and the presence of xerostomia did not affect the bacterial profiles. The inner surface of the mask had an independent oral microbiome profile, although this showed lower quantity and diversity than the UFR and SFR samples.

The Impact of a Very-Low-Calorie Ketogenic Diet in the Gut Microbiota Composition in Obesity

The very-low-calorie KD (VLCKD) is characterized by a caloric intake of under 800 kcal/day divided into less than 50 g/day of carbohydrate (13%) and 1 to 1.5 g of protein/kg of body weight (44%) and 43% of fat. This low carbohydrate intake changes the energy source from glucose to ketone bodies. Moreover, clinical trials have consistently shown a beneficial effect of VLCKD in several diseases, such as heart failure, schizophrenia, multiple sclerosis, Parkinson's, and obesity, among others. The gut microbiota has been associated with the metabolic conditions of a person and is regulated by diet interactions; furthermore, it has been shown that the microbiota has a role in body weight homeostasis by regulating metabolism, appetite, and energy. Currently, there is increasing evidence of an association between gut microbiota dysbiosis and the pathophysiology of obesity. In addition, the molecular pathways, the role of metabolites, and how microbiota modulation could be beneficial remain unclear, and more research is needed. The objective of the present article is to contribute with an overview of the impact that VLCKD has on the intestinal microbiota composition of individuals with obesity through a literature review describing the latest research regarding the topic and highlighting which bacteria phyla are associated with obesity and VLCKD.

Clonal Kinetics and Single-Cell Transcriptional Profiles of T Cells Mobilized to Blood by Acute Exercise

PURPOSE

Acute exercise redistributes large numbers of memory T cells, which may contribute to enhanced immune surveillance in regular exercisers. It is not known, however, if acute exercise promotes a broad or oligoclonal T-cell receptor (TCR) repertoire or evokes transcriptomic changes in "exercise-responsive" T-cell clones.

METHODS

Healthy volunteers completed a graded bout of cycling exercise up to 80% V̇O 2max . DNA was extracted from peripheral blood mononuclear cells collected at rest, during exercise (EX), and 1 h after (+1H) exercise, and processed for deep TCR-β chain sequencing and tandem single-cell RNA sequencing.

RESULTS

The number of unique clones and unique rearrangements was decreased at EX compared with rest ( P < 0.01) and +1H ( P < 0.01). Productive clonality was increased compared with rest ( P < 0.05) and +1H ( P < 0.05), whereas Shannon's Index was decreased compared with rest ( P < 0.05) and +1H ( P < 0.05). The top 10 rearrangements in the repertoire were increased at EX compared with rest ( P < 0.05) and +1H ( P < 0.05). Cross-referencing TCR-β sequences with a public database (VDJdb) revealed that exercise increased the number of clones specific for the most prevalent motifs, including Epstein-Barr virus, cytomegalovirus, and influenza A. We identified 633 unique exercise-responsive T-cell clones that were mobilized and/or egressed in response to exercise. Among these clones, there was an upregulation in genes related to cell death, cytotoxicity, and activation ( P < 0.05).

CONCLUSIONS

Acute exercise promotes an oligoclonal T-cell repertoire by preferentially mobilizing the most dominant clones, several of which are specific to known viral antigens and display differentially expressed genes indicative of cytotoxicity, activation, and apoptosis.

Bacterial Skin Microbiota of Seabass from Aegean Fish Farms and Antibiotic Susceptibility of Psychrotrophic Pseudomonas

Farming seabass (Dicentrarchus labrax) is an essential activity in the Mediterranean basin including the Aegean Sea. The main seabass producer is Turkey accounting for 155,151 tons of production in 2021. In this study, skin swabs of seabass farmed in the Aegean Sea were analysed with regard to the isolation and identification of Pseudomonas. Bacterial microbiota of skin samples (n = 96) from 12 fish farms were investigated using next-generation sequencing (NGS) and metabarcoding analysis. The results demonstrated that Proteobacteria was the dominant bacterial phylum in all samples. At the species level, Pseudomonas lundensis was identified in all samples. Pseudomonas, Shewanella, and Flavobacterium were identified using conventional methods and a total of 46 viable (48% of all NGS+) Pseudomonas were isolated in seabass swab samples. Additionally, antibiotic susceptibility was determined according to standards of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) in psychrotrophic Pseudomonas. Pseudomonas strains were tested for susceptibility to 11 antibiotics (piperacillin-tazobactam, gentamicin, tobramycin, amikacin, doripenem, meropenem, imipenem, levofloxacin, ciprofloxacin, norfloxacin, and tetracycline) from five different groups of antibiotics (penicillins, aminoglycosides, carbapenems, fluoroquinolones, and tetracyclines). The antibiotics chosen were not specifically linked to usage by the aquaculture industry. According to the EUCAST and CLSI, three and two Pseudomonas strains were found to be resistant to doripenem and imipenem (E-test), respectively. All strains were susceptible to piperacillin-tazobactam, amikacin, levofloxacin, and tetracycline. Our data provide insight into different bacteria that are prevalent in the skin microbiota of seabass sampled from the Aegean Sea in Turkey, and into the antibiotic resistance of psychrotrophic Pseudomonas spp.

Oroxin B improves metabolic-associated fatty liver disease by alleviating gut microbiota dysbiosis in a high-fat diet-induced rat model

Metabolic-associated fatty liver disease (MAFLD) has become a common chronic liver disease, but there is no FDA-approved drug for MAFLD treatment. Numerous studies have revealed that gut microbiota dysbiosis exerts a crucial effect on MAFLD progression. Oroxin B is a constituent of the traditional Chinese medicine Oroxylum indicum (L.) Kurz. (O. indicum), which has the characteristics of low oral bioavailability but high bioactivity. However, the mechanism through which oroxin B improves MAFLD by restoring the gut microbiota balance remains unclear. To this end, we assessed the anti-MAFLD effect of oroxin B in HFD-fed rats and investigated the underlying mechanism. Our results indicated that oroxin B administration reduced the lipid levels in the plasma and liver and lowered the lipopolysaccharide (LPS), interleukin 6 (IL-6), and tumor necrosis factor-α (TNF-α) levels in the plasma. Moreover, oroxin B alleviated hepatic inflammation and fibrosis. Mechanistically, oroxin B modulated the gut microbiota structure in HFD-fed rats by increasing the levels of Lactobacillus, Staphylococcus, and Eubacterium and decreasing the levels of Tomitella, Bilophila, Acetanaerobacterium, and Faecalibaculum. Furthermore, oroxin B not only suppressed Toll-like receptor 4-inhibitor kappa B-nuclear factor kappa-B-interleukin 6/tumor necrosis factor-α (TLR4-IκB-NF-κB-IL-6/TNF-α) signal transduction but also strengthened the intestinal barrier by elevating the expression of zonula occludens 1 (ZO-1) and zonula occludens 2 (ZO-2). In summary, these results demonstrate that oroxin B could alleviate hepatic inflammation and MAFLD progression by regulating the gut microbiota balance and strengthening the intestinal barrier. Hence, our study suggests that oroxin B is a promising effective compound for MAFLD treatment.

Investigating Visual Aesthetic Fatigue in Urban Green Spaces

Life experience suggests that visual aesthetic fatigue (VAF) is quite common. However, few academic works have focussed on VAF in landscapes, thus our understanding of this issue is very poor, not to mention what measures can be taken to mitigate it. To address these gaps, this study investigated VAF using 16 photographs taken in urban green spaces in Xuzhou (local landscapes) and Hong Kong (non-local landscapes) as stimuli. The visual aesthetic quality (VAQ) of 16 photographs was evaluated four times by the same college students at an interval of one week. Statistical analysis demonstrated that VAF occurred in urban green spaces. Male respondents had a higher VAF than females. There were no significant differences in VAQ and VAF between local and non-local landscapes. No landscape characteristic significantly correlated to or predicted VAF, implying that it is very difficult to mitigate VAF through designing and managing static landscapes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s41742-023-00517-x.

Correlations between Gut Microbial Composition, Pathophysiological and Surgical Aspects in Endometriosis: A Review of the Literature

Background and Objectives: Endometriosis is an estrogen-dependent, inflammatory, gynecological disorder represented by the migration of endometrial tissue outside the uterus. It can manifest through gynecological and gastrointestinal (GI) signs. Given the hormonal imbalances in endometriosis and the effect of microbiota on immune dysfunction, it has been thought that the human microbiome may play a role in its pathogenesis, acting differently before and after laparotomy. The aim of this review is to establish whether there is an interaction between endometriosis and gut microbial composition. Materials and Methods: We aimed to review available literature by systematically searching five databases: PubMed, EMBASE, Scopus, Cochrane Library, and ScienceDirect. We included records describing gut microbiota in the context of endometriosis-observing PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines-to recognize the presence of disease by the expression of bacterial taxa-based on 16S ribosomal RNA gene sequencing analysis. Results: Among 10 studies selected, there were four review articles and six clinical trials. The latter identified significant differences at a genus level in increased Prevotella, Blautia, and Bifidobacterium and decreased Paraprevotella, Ruminococcus, and Lachnospira (p < 0.05). In patients undergoing abdominal hysterectomy, Proteobacteria phylum increased from 34.36% before surgery to 54.04% after surgery (p < 0.05). Conclusions: Although scientific literature reports different characterizations of intestinal microbiota in endometriotic patients, further evidence is needed to develop new diagnostic-therapeutic strategies, for example, administration with probiotics before surgery.

Average weighted nucleotide diversity is more precise than pixy in estimating the true value of π from sequence sets containing missing data

Nucleotide diversity remains an important statistic in population genetic/genomic studies. Although recent advances in massive sequencing make generating sequence data sets cheaper and faster, currently used technologies often introduce substantial amounts of missing nucleotides in their output. A novel method of estimating π from data sets containing missing data - pixy - has also recently been proposed. In this study, the pixy estimator, π_pixy , was compared to average weighted nucleotide diversity, π_W . The estimators were tested both on sequences simulated in fastsimcoal and real sequence sets. Both sets were modified by random insertion of missing nucleotides. Weighted nucleotide diversity performed better in all pairwise comparisons. It was characterized by a smaller error and a narrower distribution of the results. π_pixy tends to overestimate the nucleotide diversity when both the proportion of missing data and the level of variation is low. Of the two estimators, only π_W estimated the true nucleotide diversity in a part of the simulations. A simple formula for estimating π_W allows for easy integration of the estimator in packages such as pixy, which would allow obtaining more precise estimates of nucleotide diversity either in a sliding window or for discrete genomic regions.

Response of dung beetle diversity to remediation of soil ecosystems in the Ecuadorian Amazon

Background

Efforts to alleviate the negative effects of oil spills in the Ecuadorian Amazon include remediation activities such as cleaning, reshaping, and revegetation of polluted areas. However, studies of the diversity of biological communities in these hydrocarbon-degraded ecosystems have never been carried out. Here, we evaluated the diversity of dung beetles on remediated soil ecosystems (Agricultural Soils and Sensitive Ecosystems) and on non-contaminated soils (Natural Forests and Palm Plantations).

Methodology

The study was conducted in Sucumbíos and Orellana provinces, in the Ecuadorian Amazon at four sampling sites per ecosystem type (a total of 16 sites). At each sampling site, six pitfall traps remained active for 120 consecutive h per month for 1 year.

Results

We collected 37 species and 7,506 individuals of dung beetles. We observed significant differences in mean species abundance, richness, and diversity between non-contaminated soil ecosystems and remediated soil ecosystems, with Natural Forests presenting the highest values, and Agricultural Soils the lowest values. Regarding sampling month, we also found significant differences among ecosystems, which were also higher in Natural Forests.

Discussion

The results suggest that hydrocarbon-degraded ecosystems tend to conserve lower beetle diversity one year after remediation highlighting the importance of Natural Forests for the conservation of tropical biodiversity. Therefore, dung beetle diversity could be used for future landscape management of these hydrocarbon-degraded ecosystems.

Alopecia Areata: Burden of Disease, Approach to Treatment, and Current Unmet Needs

Alopecia areata is an autoimmune hair loss disorder with variations in distribution, duration, and severity. The disease is chronic and often follows an unpredictable course, frequently leading to stress and anxiety for those who suffer from it. Throughout the years more knowledge has been gained regarding pathogenesis, diagnostic tools, impact on quality of life, as well as treatment strategies for alopecia areata. However, challenges in treating and alleviating the burden of disease remain. In this article, we discuss updates regarding the pathogenesis and treatment of alopecia areata and highlight unmet needs of the condition, including a review of limitations of current treatments, accessibility to management strategies, and the need for disease awareness and advocacy.

Valorization as a biofertilizer of an agricultural residue leachate: Metagenomic characterization and growth promotion test by PGPB in the forage plant Medicago sativa (alfalfa)

The abuse of chemical fertilizers in intensive agriculture has turned out in the contamination of ground and the soil on which they are applied. Likewise, the generation, storage, and destruction of plant residues from the agri-food industry poses a threat to the environment and human health. The current situation of growing demand for food implies the urgent need to find sustainable alternatives to chemical fertilizers and the management of agricultural waste. Valorization of this plant residue to produce natural biofertilizers using microbiological treatments is presented as a sustainable alternative. The microbial activity allows the transformation into simple molecules that are easily absorbed by plants, as well as the stimulation of plant growth. This double direct and indirect action induced significant increases against the variables of germination, viability, and biomass (dry weight). To guarantee biosafety, it is necessary to use new bio-technological tools, such as metagenomics, which allow the taxonomic analysis of microbial communities, detecting the absence of pathogens. In the present paper, a physicochemical and metagenomic characterization of a fertilizer obtained from agricultural plant waste valorization is carried out. Likewise, fertigation treatments were tested to which the Plant Growth Promoting Bacteria (PGPB) Pseudomonas agronomica and Bacillus pretiosus were added, both independently and in consortium. Metagenomic analysis has identified taxa belonging to the kingdoms Bacteria and Archaea; 10 phyla, 25 families, 32 genera and 34 species, none of them previously described as pathogenic. A 1/512 dilution of the fertilizer increased the germination rate of Medicago sativa (alfalfa) by 16% at 144 h, compared to the treatment without fertilizer. Both the fertilizer and the addition of PGPB in a double direct and indirect action induced significant increases against the variables of germination, viability, and biomass (dry weight). Therefore, the use of an agricultural residue is proposed, which after the addition of two new species is transformed into a biofertilizer that significantly induces plant growth in Mendicago sativa plants.

Exploring market-based wildlife trade dynamics in Bangladesh

Wildlife markets are hotspots for illegal wildlife trade, with traders operating as a result of weak monitoring and law enforcement. Knowledge of species traded, sources, and routes used for transport is needed to identify illegal wildlife trade markets and intervene to stem trade. We conducted surveys in 13 wildlife markets across Bangladesh every month during January-December 2019 to assess the abundance and diversity of wildlife taxa traded and the factors driving this trade. Passeriformes, Columbiformes, Psittaciformes, Artiodactyla, Carnivora and Testudines were the most traded orders. Wildlife markets were also centres of trade for high-value species, including the tiger Panthera tigris, crocodile Crocodylus porosus and tortoises. In hill markets and peri-urban markets the most commonly sold species originated from nearby forests, whereas urban markets included both native species and exotic species sourced internationally. Market type, road links to the market, the presence of law enforcement agencies, proximity to a port and form of sale (live animals or byproducts) all significantly influenced what is being traded. Trade of mammals, reptiles, high-value wildlife species and threatened species was less common in markets proximal to law enforcement agencies. Markets close to seaports or airports were more likely to sell mammals, threatened species and high-value wildlife. Based on our results, we recommend a set of interventions to help reduce market-based wildlife trade in Bangladesh.

Cftr deletion in mouse epithelial and immune cells differentially influence the intestinal microbiota

Cystic fibrosis (CF) is a life-threatening genetic disorder, caused by mutations in the CF transmembrane-conductance regulator gene (cftr) that encodes CFTR, a cAMP-activated chloride and bicarbonate channel. Clinically, CF lung disease dominates the adult patient population. However, its gastrointestinal illness claims the early morbidity and mortality, manifesting as intestinal dysbiosis, inflammation and obstruction. As CF is widely accepted as a disease of epithelial dysfunction, it is unknown whether CFTR loss-of-function in immune cells contributes to these clinical outcomes. Using cftr genetic knockout and bone marrow transplantation mouse models, we performed 16S rRNA gene sequencing of the intestinal microbes. Here we show that cftr deletion in both epithelial and immune cells collectively influence the intestinal microbiota. However, the immune defect is a major factor determining the dysbiosis in the small intestine, while the epithelial defect largely influences that in the large intestine. This finding revises the current concept by suggesting that CF epithelial defect and immune defect play differential roles in CF intestinal disease.

The cystic fibrosis transmembrane-conductance regulator (cftr) gene function in epithelial and immune cells affect gut microbiome in mice differently.

The Impact of the Anticoagulant Type in Blood Collection Tubes on Circulating Extracellular Plasma MicroRNA Profiles Revealed by Small RNA Sequencing

Pre-analytical factors have a significant influence on circulating microRNA (miRNA) profiling. The aim of this study was a comprehensive assessment of the impact of the anticoagulant type in blood collection tubes on circulating plasma miRNA profiles using small RNA sequencing. Blood from ten healthy participants (five males and five females from 25 to 40 years old) was taken in collection tubes with four different anticoagulants: acid citrate dextrose (ACD-B), sodium citrate, citrate-theophylline-adenosine-dipyridamole (CTAD) and dipotassium-ethylenediaminetetraacetic acid (K2 EDTA). Platelet-free plasma samples were obtained by double centrifugation. EDTA plasma samples had elevated levels of hemolysis compared to samples obtained using other anticoagulants. Small RNA was extracted from plasma samples and small RNA sequencing was performed on the Illumina NextSeq 500 system. A total of 30 samples had been successfully sequenced starting from ~1 M reads mapped to miRNAs, allowing us to analyze their diversity and isoform content. The principal component analysis showed that the EDTA samples have distinct circulating plasma miRNA profiles compared to samples obtained using other anticoagulants. We selected 50 miRNA species that were differentially expressed between the sample groups based on the type of anticoagulant. We found that the EDTA samples had elevated levels of miRNAs which are abundant in red blood cells (RBC) and associated with hemolysis, while the levels of some platelet-specific miRNAs in these samples were lowered. The ratio between RBC-derived and platelet-derived miRNAs differed between the EDTA samples and other sample groups, which was validated by quantitative PCR. This study provides full plasma miRNA profiles of 10 healthy adults, compares them with previous studies and shows that the profile of circulating miRNAs in the EDTA plasma samples is altered primarily due to an increased level of hemolysis.

Deconvolution of tumor composition using partially available DNA methylation data

Background

Deciphering proportions of constitutional cell types in tumor tissues is a crucial step for the analysis of tumor heterogeneity and the prediction of response to immunotherapy. In the process of measuring cell population proportions, traditional experimental methods have been greatly hampered by the cost and extensive dropout events. At present, the public availability of large amounts of DNA methylation data makes it possible to use computational methods to predict proportions.

Results

In this paper, we proposed PRMeth, a method to deconvolve tumor mixtures using partially available DNA methylation data. By adopting an iteratively optimized non-negative matrix factorization framework, PRMeth took DNA methylation profiles of a portion of the cell types in the tissue mixtures (including blood and solid tumors) as input to estimate the proportions of all cell types as well as the methylation profiles of unknown cell types simultaneously. We compared PRMeth with five different methods through three benchmark datasets and the results show that PRMeth could infer the proportions of all cell types and recover the methylation profiles of unknown cell types effectively. Then, applying PRMeth to four types of tumors from The Cancer Genome Atlas (TCGA) database, we found that the immune cell proportions estimated by PRMeth were largely consistent with previous studies and met biological significance.

Conclusions

Our method can circumvent the difficulty of obtaining complete DNA methylation reference data and obtain satisfactory deconvolution accuracy, which will be conducive to exploring the new directions of cancer immunotherapy. PRMeth is implemented in R and is freely available from GitHub (https://github.com/hedingqin/PRMeth).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04893-7.

Inhaled Corticosteroids Selectively Alter the Microbiome and Host Transcriptome in the Small Airways of Patients with Chronic Obstructive Pulmonary Disease

Background: Patients with chronic obstructive pulmonary disease (COPD) are commonly treated with inhaled corticosteroid/long-acting ß2-agonist combination therapy. While previous studies have investigated the host–microbiome interactions in COPD, the effects of specific steroid formulations on this complex cross-talk remain obscure. Methods: We collected and evaluated data from the Study to Investigate the Differential Effects of Inhaled Symbicort and Advair on Lung Microbiota (DISARM), a randomized controlled trial. Bronchoscopy was performed on COPD patients before and after treatment with salmeterol/fluticasone, formoterol/budesonide or formoterol-only. Bronchial brush samples were processed for microbial 16S rRNA gene sequencing and host mRNA sequencing. Longitudinal changes in the microbiome at a community, phylum and genus level were correlated with changes in host gene expression using a Spearman’s rank correlation test. Findings: In COPD patients treated with salmeterol/fluticasone, the expression levels of 676 host genes were significantly correlated to changes in the alpha diversity of the small airways. At a genus level, the expression levels of 122 host genes were significantly related to changes in the relative abundance of Haemophilus. Gene enrichment analyses revealed the enrichment of pathways and biological processes related to innate and adaptive immunity and inflammation. None of these changes were evident in patients treated with formoterol/budesonide or formoterol alone. Interpretation: Changes in the microbiome following salmeterol/fluticasone treatment are related to alterations in the host transcriptome in the small airways of patients with COPD. These data may provide insights into why some COPD patients treated with inhaled corticosteroids may be at an increased risk for airway infection, including pneumonia. Funding: The Canadian Institute of Health Research, the British Columbia Lung Association, and an investigator-initiated grant from AstraZeneca.

Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation

BACKGROUNDGut decontamination (GD) can decrease the incidence and severity of acute graft-versus-host disease (aGVHD) in murine models of allogeneic hematopoietic cell transplantation (HCT). In this pilot study, we examined the impact of GD on gut microbiome composition and the incidence of aGVHD in HCT patients.METHODSWe randomized 20 patients undergoing allogeneic HCT to receive (GD) or not receive (no-GD) oral vancomycin-polymyxin B from day -5 through neutrophil engraftment. We evaluated shotgun metagenomic sequencing of serial stool samples to compare the composition and diversity of the gut microbiome between study arms. We assessed clinical outcomes in the 2 arms and performed strain-specific analyses of pathogens that caused bloodstream infections (BSI).RESULTSThe 2 arms did not differ in the predefined primary outcome of Shannon diversity of the gut microbiome at 2 weeks post-HCT (genus, P = 0.8; species, P = 0.44) or aGVHD incidence (P = 0.58). Immune reconstitution of T cell and B cell subsets was similar between groups. Five patients in the no-GD arm had 8 BSI episodes versus 1 episode in the GD arm (P = 0.09). The BSI-causing pathogens were traceable to the gut in 7 of 8 BSI episodes in the no-GD arm, including Staphylococcus species.CONCLUSIONWhile GD did not differentially affect Shannon diversity or clinical outcomes, our findings suggest that GD may protect against gut-derived BSI in HCT patients by decreasing the prevalence or abundance of gut pathogens.TRIAL REGISTRATIONClinicalTrials.gov NCT02641236.FUNDINGNIH, Damon Runyon Cancer Research Foundation, V Foundation, Sloan Foundation, Emerson Collective, and Stanford Maternal & Child Health Research Institute.

Detecting steps in spatial genetic data: Which diversity measures are best?

Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, G_ST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, G_ST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (G_ST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.

Population Analysis of Diospyros lotus in the Northwestern Caucasus Based on Leaf Morphology and Multilocus DNA Markers

Diospyros lotus is the one of the most frost-tolerant species in the Diospyros genera, used as a rootstock for colder regions. Natural populations of D. lotus have a fragmented character of distribution in the Northwestern Caucasus, one of the coldest regions of Diospyros cultivation. To predict the behavior of D. lotus populations in an extreme environment, it is necessary to investigate the intraspecific genetic diversity and phenotypic variability of populations in the colder regions. In this study, we analyzed five geographically distant populations of D. lotus according to 33 morphological leaf traits, and the most informative traits were established, namely, leaf length, leaf width, leaf index (leaf to length ratio) and the length of the fourth veins. Additionally, we evaluated the intraspecific genetic diversity of D. lotus using ISSR and SCoT markers and proposed a new parameter for the evaluation of genetic polymorphism among populations, in order to eliminate the effect of sample number. This new parameter is the relative genetic polymorphism, which is the ratio of polymorphism to the number of samples. Based on morphological and genetic data, the northernmost population from Shkhafit was phenotypically and genetically distant from the other populations. The correspondence between several morphological traits (leaf width, leaf length and first to fifth right vein angles) and several marker bands (SCoT5, SCoT7, SCoT30: 800–1500 bp; ISSR13, ISSR14, ISSR880: 500–1000 bp) were observed for the Shkhafit population. Unique SCoT and ISSR fragments can be used as markers for breeding purposes. The results provide a better understanding of adaptive mechanisms in D. lotus in extreme environments and will be important for the further expansion of the cultivation area for persimmon in colder regions.

Tangnaikang Alleviates Hyperglycemia and Improves Gut Microbiota in Diabetic Mice

Dysregulation of gut microbiota contributes to the development of type 2 diabetes. To investigate the antidiabetic effect of Tangnaikang and its regulation of gut microbiota in diabetic KKAy mice, a type 2 diabetes mouse model was established by feeding KKAy mice with a high-fat diet (HFD) for 2 weeks. The diabetic KKAy mice were treated with vehicle, Acarbose, or different doses of Tangnaikang once a day for 8 weeks. The fasting plasma glucose (FPG) levels and bodyweights were measured weekly. The fecal and blood samples were collected 8 weeks after treatment. The 16s rRNA sequencing and bioinformatics analysis were conducted to explore the effects of Tangnaikang treatment on the richness, diversity, and relative abundance of gut microbiota. Compared with other treatments, high-dose Tangnaikang (4.68 g/kg) significantly reduced FPG levels while elevating bodyweights in model mice. Compared with saline treatment, different doses of Tangnaikang significantly increased gut microbial species richness and diversity. Linear discriminant analysis effect size identified potential bacterial biomarkers associated with Tangnaikang treatment. Relative abundance analysis revealed that Tangnaikang treatment modulated the abundance of gut bacteria at the class and genus levels, such as Bacilli, Lactobacillus, and Alistipes. The principal component analysis demonstrated that, compared with the samples of the high-dose group, the samples of medium-dose and low-dose groups were closer to those of the model group. Tangnaikang alleviated hyperglycemia and improved the composition and abundance of gut microbiota in diabetic KKAy mice.

Radish sprout alleviates DSS-induced colitis via regulation of NF-kB signaling pathway and modifying gut microbiota

In this study, we investigated the effects of radish sprout ethanol extract (RSE) on inflammatory responses in the macrophages and a mouse model of colitis. RSE administration was found to effectively inhibit the phosphorylation of IκB and, in turn, the production of pro-inflammatory enzymes and cytokines in lipopolysaccharide-stimulated macrophages. In dextran sulfate sodium (DSS)-colitis mice, RSE administration prevented body weight and colon length reduction, while decreasing inflammation and mucosal necrosis. The diversity of the fecal microbiota was significantly increased in the group treated with RSE. In addition, RSE administration decreased the relative abundance of the phylum Proteobacteria, which includes many pathogens, and increased the abundance of the genus Akkermansia. Beta diversity analyses showed that RSE administration restored the gut microbiota composition close to that of healthy mice. For the first time, we identified glycosides of sinapic acid as part of hydroxycinnamic acids in RSE with colitis-alleviating effects. Notably, 1,2-O-disinapoyl glucoside substantially decreased nitric oxide generation in LPS-stimulated macrophages.

A Meta-Analytical Investigation of the Gap between Measured and Predicted Inter-Population Genetic Diversity in Species of High Conservation Concern-The Case of the Critically Endangered European Mink Mustela lutreola L., 1761

Although properly designed sampling in population genetic studies is of key importance for planning evidence-informed conservation measures, sampling strategies are rarely discussed. This is the case for the European mink Mustela lutreola, a critically endangered species. In order to address this problem, a meta-analysis aiming to examine the completeness of mtDNA haplotype sampling in recent studies of M. lutreola inter-population genetic diversity was conducted. The analysis was performed using the sample-size-based rarefaction and extrapolation sampling curve method for three populations—the Northeastern (Russia, Belarus and Estonia), the Western (France and Spain), and the Southeastern (Romania). The extrapolated values of the Shannon–Wiener index were determined, assuming full sample coverage. The gap between the measured and predicted inter-population genetic diversity was estimated, indicating that the identified level of sample coverage was the lowest for the NE population (87%), followed by the SE population (96%) and the W population (99%). A guide for sampling design and accounting for sampling uncertainty in future population genetic studies on European mink is provided. The relatively low sample coverage for the Russian population clearly indicates an urgent need to take conservation measures for European mink in this country.

Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars

Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20-50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization.

Implementation of fecal microbiota transplantation in a medical center for recurrent or refractory Clostridioides difficile infection and report of preliminary outcome

Background

Fecal microbiota transplantation (FMT) has been shown to highly effective in the treatment of recurrent or refractory Clostridioides difficile infection (rCDI) in many countries of the world. Not until 2018, Ministry of Health and Welfare, Taiwan approved the application of FMT for rCDI under a special law. The study reported the first implementation of the technology in the medical center in Taiwan and the preliminary outcome.

Methods

FMT was used to treat patients with rCDI in Chang Gung Memorial Hospital. FMT was delivered by gastroenterologists using colonoscope. Strict donor screening was performed according to the guidelines. We followed up the clinical course of patients after FMT. 16S rRNA sequencing of fecal samples for donor, and also recipient before and after FMT was carried out.

Results

From September 2018 to June 2020, 39 patients with rCDI received FMT, with a successful rate of 89.7%. Two patients died due to causes unrelated to FMT, and two other cases showed no clinical improvement after the procedure. High school and college students showed the best pass rate during donor screening. The presence of multi-drug resistant pathogen was the most common cause for screening failure. We demonstrated in a case the use of rRNA sequencing as a biomarker indicating for the improvement of dysbiosis in a patient after FMT.

Conclusions

FMT was successfully implemented in a medical center in Taiwan and showed a comparable successful rate in treating rCDI, compared to other countries. Safety remains the most important issue when applying FMT in the clinical setting.

16S rRNA gene profiling of rhizospheric microbial community of Eichhornia crassipes

The rhizosphere of a plant is an important interface for the plant-microbe interaction that plays a significant role in the uptake and removal of heavy metal from contaminated sites. Eichhornia crassipes is a free-floating macrophyte and a well-known metal hyperaccumulator. It is a promising plant, which harbors a diverse microbial community in its rhizosphere. Therefore it is hypothesized that it can be a good habitat for microorganisms that supports plant growth and increases its phytoremediation potential. The rhizospheric DNA was extracted from the procured plant samples. The library was prepared and sequenced using the Illumina platform. 16S rRNA data from the Next Generation Sequencing (NGS) platform was analyzed using the QIIME software package. Alpha diversity was estimated from statistical indices i.e. Shannon index, Chao1 index, and observed species. The rarefaction plots, rank abundance curve, krona graph, and heat map were generated to study the rhizospheric community in detail. Metagenome consisted of 225,408 flash reads, 185,008 non-chimeric sequences with 17,578 Operational Taxonomic Units (OTU's), and 4622 OTU's without singletons. The data of present study are available at NCBI Bioproject (PRJNA631882). The taxonomic analysis of OTU's showed that the sequences belonged to major Phyla revealing the dominance of Proteobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia. The most abundant Genera in the sampled rhizosphere recorded were Thiothrix and Flavobacterium.