Exploring the biological diversity and source species of medicinal horseflies through metabarcoding.

Horseflies from the Tabanidae family play a significant role in traditional Chinese medicine to treat various health conditions, including coronary heart disease, stroke, headaches, liver cirrhosis, psoriasis, and hepatic carcinoma. There are 27 species of Tabaninae (Tabanidae) used as medicine, and they showed high morphological similarities with those for which medicinal properties have not been reported. Nonetheless, there have been reports suggesting that medicinal crude drugs sometimes contain irrelevant or false species, impacting the drug's efficacy. In this current study, we collected 14 batches, totaling 13,528 individuals, from various provinces in China. Instead of "classic" DNA barcoding strategy, we employed a high-throughput metabarcoding approach to assess the biological composition of crude drug mixtures derived from horseflies. Our analysis identified 40 Amplicon Sequence Variants (ASVs) with similarity percentages ranging from 92% to 100% with 12 previously reported species. Species delimitation methods revealed the presence of 11 Molecular Operational Taxonomic Units (MOTUs), with ten belonging to the Tabanus genus and one to Hybomitra. Tabanus sp6 displayed the highest relative abundance, and its ASVs showed close resemblance to Tabanus pleski. Our investigations revealed that the medicinal batches were biologically composed of 6 to 12 species. Some batches contained ASVs that closely resembled species previously associated with false Tabanus species. In conclusion, our findings offer valuable insights into the biological composition of crude drugs derived from horseflies and have the potential to enhance the quality of these traditional medicines.

The metabarcoding of Grubs: Traditional herbal medicine of Scarabaeidae larvae.

Grubs, called Qicao in China, have a long tradition as herbal medicine in East Asia. These larvae belong to the diverse family Scarabaeidae and are typically harvested from the wild during their immature stage based on morphological characteristics. However, rapid and accurate identification becomes challenging when relying solely on external morphological features, as the lack of clarity on biological sources raises safety concerns for clinical applications. The application of DNA metabarcoding provides a solution by enabling the determination of the biological source of a large sample. In the current study, we collected 19 batches of Grubs, consisting of 11,539 individuals, from the market and analyzed their biological composition through metabarcoding. We identified 49 Amplicon Sequence Variants (ASVs), 21 of which were Grubs. The 21 ASVs were classified into seven Molecular Operational Taxonomic Units (MOTUs) through species delimitation, which revealed that commercially available Grubs are predominantly sourced from Protaetia brevitarsis seulensis, while species of Rutelinae, Anomala, and Holotrichia were also abundant in some commercial batches. Among the identified ASVs, 28 belonged to non-Grub species and indicated adulteration from different animal families; high abundances of these ASVs were detected for Bombycidae, Tabanidae, and Viviparidae. Our findings underscore the complexity of Grubs' species composition and advocate for a deeper understanding of the wildlife sources contributing to herbal products. This research contributes valuable insights into the molecular identification of Grubs, paving the way for enhanced quality assurance in traditional medicine applications to provide safe and effective medicines for humanity.

WITHDRAWN: Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding.

After consultation with external experts, the authors acknowledged discrepancies in the classification of certain Berberis samples discussed in the article. Berberis is one of the most complex plant genera, and identifications are very hard, limited to only a handful of experts due to rampant hybridizations and other issues of reticulate evolution. This article has therefore been withdrawn at the request of the authors and with the consent of the editor until the species identification issue has been resolved. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.

Increasing trends in the use of the Precivia® intravitreal injection assist device across the UK.

BACKGROUND: Intravitreal anti-VEGF injections are the most frequently performed outpatient procedure in the UK, the need for which continues to rise. To meet this demand, injection assist devices such as Precivia® are increasingly adopted to aid in their prompt and safe delivery. We present data on the usage of Precivia® intravitreal injection assist device across two district general hospitals and its distribution across the UK over five years. METHODS: A retrospective review was undertaken of all Precivia® assisted intravitreal injections delivered at Great Western Hospitals NHS Trust (GWH), and Gloucestershire and Cheltenham Hospitals NHS Trust (GCH) between 2015-2020. Data were also obtained from the Precivia® device UK distributor; Veni Vidi Medical. RESULTS: In GCH, 47,968 intravitreal injections were administered with Precivia®: 5947 in year 1; 7058 in year 2; 9893 in year 3; 11,503 in year 4 and 13,567 injections in year 5, observing a 128.13% increase in the use of Precivia® over the five-year-period. In GWH, 26,923 injections were administered with Precivia®: 4232 in year 1; 5117 in year 2; 5437 in year 3; 5878 in year 4 and 6259 in year 5, observing a 47.89% increase in Precivia® injections over a five-year study period. The number of Precivia® devices distributed across the UK similarly increased including 42,150 devices sold in 2015; 68,125 in 2016; 72,575 in 2017; 88,325 in 2018; 112,850 in 2019 and 115,125 in 2020 observing a 173.31% increase in five years. CONCLUSION: An increasing trend in the use of the Precivia® intravitreal injection assist device was observed across the UK.

Chimeric vaccine design against the conserved TonB-dependent receptor-like ß-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330.

Kingella kingae is a Gram-negative bacterium that primarily causes pediatric infections such as septicemia, endocarditis, and osteoarticular infections. Its virulence is attributed to the outer membrane proteins having implications in bacterial adhesion, invasion, nutrition, and host tissue damage. TonB-dependent receptors (TBDRs) play an important role in nutrition and were previously implicated as vaccine targets in other bacteria. Therefore, we targeted the conserved ß-barrel TBDR domain of these proteins for designing a vaccine construct that could elicit humoral and cellular immune responses. We used bioinformatic tools to mine TBDR-containing proteins from K. kingae ATCC 23330 and then predict B- and T-cell epitopes from their conserved ß-barrel TDR domain. A chimeric vaccine construct was designed using three antigenic epitopes, covering >98% of the world population and capable of inciting humoral and adaptive immune responses. The final construct elicited a robust immune response. Docking and dynamics simulation showed good binding affinity of the vaccine construct to various receptors of the immune system. Additionally, the vaccine was predicted to be safe and non-allergenic, making it a promising candidate for further development. In conclusion, our study demonstrates the potential of immunoinformatics approaches in designing chimeric vaccines against K. kingae infections. The chimeric vaccine we designed can serve as a blueprint for future experimental studies to develop an effective vaccine against this pathogen, which can serve as a potential strategy to prevent K. kingae infections.

Lateral tarsal strip procedure: comparison of absorbable sutures and non-absorbable polypropylene suture. Does the suture type matter?

BACKGROUND/OBJECTIVES: To determine whether the success and complication rates of the Lateral Tarsal Strip (LTS) Procedure, when treating involutional ectropion/entropion, is influenced by the use of suture when attaching the tarsal strip to the periosteum. SUBJECTS/METHODS: Multi-centre retrospective comparative study of re-operation and complication rates (Recurrence, Dehiscence, Suture Infection, Granuloma, Haemorrhage, Residual-Lid Laxity, Suture Extrusion and Repeat Procedure) in LTS, between 01/01/2017 and 01/01/2022 who met the inclusion/exclusion criteria, for involutional ectropion/entropion using an absorbable polyglactin (vicryl) and non-absorbable polypropylene suture (prolene). RESULTS: 1079 operations in 891 patients (36% female, average age 81.4 years) were performed with an average follow-up of 1.785 years. 588 operations in 475 patients were performed using prolene whilst 491 procedures in 416 patients were performed using vicryl sutures. Of these, 61% were performed by a consultant surgeon in the prolene group compared to 49.7% in the vicryl group. Overall complication rates between prolene and vicryl were 24.7% and 29.7% (p = 0.061) respectively. Higher complication rates for post-operative residual lid laxity, granuloma and suture infection were greater in the vicryl group versus prolene (2.65% and 0.51% p = 0.004, 2.24% and 0.68% p = 0.03, 1.83% and 0.17% p = 0.007 respectively). Non-significant results for dehiscence or repeat procedures (2.24% and 2.21% p = 0.974, 6.72% and 9.01% p = 0.166 respectively). CONCLUSIONS: Both sutures are effective for the correction of involutional ectropion/entropion with LTS. Dehiscence and redo rates were not statistically significant. Nevertheless, the use of vicryl suture was found to be associated with a higher complication rate for: post-operative residual lid laxity, granuloma and suture infection.

Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential.

Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.

Malnutrition among patients with Type-2 Diabetes Mellitus.

Objectives: The present study aims to evaluate the nutritional status of diabetic patients using Subjective Global Assessment (SGA) tool. Methods: A prospective cross-sectional study was conducted at Endocrine and Medicine Department of Lady Reading Hospital from September 2019 to March 2020. A total of 359 patients diagnosed with Type-2 Diabetes Mellitus (T2DM) were included in the study. The malnutrition status was assessed using SGA, and clinical parameters including albumin and total leukocyte count (TLC). Results: We have observed mild to moderate malnutrition among 48.2% patients, and severe malnutrition in 10.6% patients as per the SGA scoring. Among the factors associated with nutritional status were BMI (p<0.01), and presence of CAD (DM complication) (p=0.015). As per the correlation analysis, BMI had a significant negative correlation with nutritional status (r=-0.351; p<0.01). Conclusion: It is concluded from the study results that there is a high prevalence of malnutrition among the enrolled diabetic patients.

Safety and efficacy of Empagliflozin in Pakistani Muslim patients with type 2 diabetes (SAFE-PAK); a randomized clinical trial.

BACKGROUND: Sodium-Glucose-Co-Transporter 2 (SGLT2) inhibitor (Empagliflozin) is an effective drug in controlling blood glucose through predominantly glycosuria. Glycosuria increases the risk of genitourinary infections in diabetes. This study was aimed to establish the safety and efficacy of Empagliflozin (Group-A) versus standard care (Group-B) in Pakistani Muslim individuals with type 2 diabetes. METHODS: A multicenter, randomized clinical trial was conducted in five cities across Pakistan from July 2019 to August 2020. Patients of both genders aged 18-75 years, body mass index (BMI) ≤ 45 kg/m2, glycosylated hemoglobin (HbA1c) 7-10% (53 mmol/mol to 86 mmol/mol) and treatment-naive to Empagliflozin were included. Treatment was given for 24 weeks, and allocation was done through randomization. RESULTS: Out of 745 screened patients, 333 met the eligibility criteria, and a total of 244 (73.3%) patients were enrolled. More hypoglycemic events were reported in the standard care group, whereas positive urine culture, fungal infection, dehydration, and hypotension occurrence were comparable between the two groups. The 6 months mean HbA1c reduction was significant in both groups; (Group-A: 0.91 ± 0.15; p < 0.001 vs. Group-B2: 0.79 ± 0.14; p < 0.001). Efficacy comparison at 6 months revealed a significant reduction in weight and systolic blood pressure (SBP) in Group A only (Group-A: 1.4 ± 0.4 kg; p < 0.002 vs. Group-B: 0.01 ± 0.5 kg; p < 1.00), (Group-A: 5.1 ± 1.7 mmHg; p < 0.012 vs. Group-B: 2.3 ± 1.7 mmHg; p < 0.526). CONCLUSIONS: Empagliflozin was a safe drug compared to standard care in Pakistani Muslim patients with diabetes. It was as effective as standard care in the clinical setting but achieved glycemic control by reducing weight and SBP in type 2 diabetes patients. TRIAL REGISTRATION: This study was registered in the NIH US National Library of Medicine clinical trials registry at Clinicaltrials.gov with the registration number: NCT04665284 on 11/12/2020.

Efficacy and safety of combination of empagliflozin and metformin with combination of sitagliptin and metformin during Ramadan: an observational study.

BACKGROUND: Management of diabetes during fasting is a clinical challenge. Sodium glucose co-transporter -2 inhibitors (SGLT2i) are considered safe with a low risk of hypoglycemia. However, studies on SGLT2i are scarce. This study was designed to compare the efficacy, safety, and tolerability of empagliflozin with metformin during Ramadan in comparison with sitagliptin and metformin. METHODS: It was a prospective, observational study, conducted at 11 different sites all across Pakistan on an outpatient basis during Ramadan (May 2021-June 2021). including 132 patients, 88 who received metformin and sitagliptin, and 44 patients who received metformin and empagliflozin. RESULTS: Patients of the SGLT-2i group experienced similar symptomatic hypoglycemic episodes (15.9%) as the sitagliptin group. There was an improvement in blood sugar levels after the use of SGLT-2i (RBS 181 ± 64 before Ramadan vs 162 ± 53 after Ramadan). HbA1c also improved after the use of SGLT-2i before and after Ramadan (7.2 ± 0.8 vs 6.9 ± 0.9 for Metformin + Empagliflozin and 7.8 ± 1.5 vs 7.6 ± 1.6 for Metformin and sitagliptin). Weight and BMI improved after the use of SGLT-2i (BMI 36.5 ± 4.8 before Ramadan and 33.7 ± 2.4 after Ramadan). There were no reported cases of urinary tract infection in the empagliflozin group. CONCLUSION: SGLT-2 inhibitors combined with metformin for patients with diabetes during Ramadan fasting is as effective, safe and well tolerated as DPP4 combined with metformin.

Use of Camelina sativa and By-Products in Diets for Dairy Cows: A Review.

Camelina sativa, belonging to the Brassicaceae family, has been grown since 4000 B.C. as an oilseed crop that is more drought- and cold-resistant. Increased demand for its oil, meal, and other derivatives has increased researchers' interest in this crop. Its anti-nutritional factors can be reduced by solvent, enzyme and heat treatments, and genetic engineering. Inclusion of camelina by-products increases branched-chain volatile fatty acids, decreases neutral detergent fiber digestibility, has no effect on acid detergent fiber digestibility, and lowers acetate levels in dairy cows. Feeding camelina meal reduces ruminal methane, an environmental benefit of using camelina by-products in ruminant diets. The addition of camelina to dairy cow diets decreases ruminal cellulolytic bacteria and bio-hydrogenation. This reduced bio-hydrogenation results in an increase in desirable fatty acids and a decrease in saturated fatty acids in milk obtained from cows fed diets with camelina seeds or its by-products. Studies suggest that by-products of C. sativa can be used safely in dairy cows at appropriate inclusion levels. However, suppression in fat milk percentage and an increase in trans fatty acid isomers should be considered when increasing the inclusion rate of camelina by-products, due to health concerns.

Phenotypic characterization and genome analysis of a novel Salmonella Typhimurium phage having unique tail fiber genes.

Salmonella enterica serovar Typhimurium is a foodborne pathogen causing occasional outbreaks of enteric infections in humans. Salmonella has one of the largest pools of temperate phages in its genome that possess evolutionary significance for pathogen. In this study, we characterized a novel temperate phage Salmonella phage BIS20 (BIS20) with unique tail fiber genes. It belongs to the subfamily Peduovirinae genus Eganvirus and infects Salmonella Typhimurium strain (SE-BS17; Acc. NO MZ503545) of poultry origin. Phage BIS20 was viable only at biological pH and temperature ranges (pH7 and 37 °C). Despite being temperate BIS20 significantly slowed down the growth of host strain for 24 h as compared to control (P < 0.009). Phage BIS20 features 29,477-base pair (bp) linear DNA genome with 53% GC content and encodes for 37 putative ORFs. These ORFs have mosaic arrangement as indicated by its ORF similarity to various phages and prophages in NCBI. Genome analysis indicates its similarity to Salmonella enterica serovar Senftenberg prophage (SEStP) sequence (Nucleotide similarity 87.7%) and Escherichia virus 186 (~ 82.4% nucleotide similarity). Capsid genes were conserved however those associated with tail fiber formation and assembly were unique to all members of genus Eganvirus. We found strong evidence of recombination hotspot in tail fiber gene. Our study identifies BIS20 as a new species of genus Eganvirus temperate phages as its maximum nucleotide similarity is 82.4% with any phage in NCBI. Our findings may contribute to understanding of origin of new temperate phages.

Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae.

Salmonella Typhimurium, a foodborne pathogen, is a major concern for food safety. Its MDR serovars of animal origin pose a serious threat to the human population. Phage therapy can be an alternative for the treatment of such MDR Salmonella serovars. In this study, we report on detailed genome analyses of a novel Salmonella phage (Salmonella-Phage-SSBI34) and evaluate its therapeutic potential. The phage was evaluated for latent time, burst size, host range, and bacterial growth reduction in liquid cultures. The phage stability was examined at various pH levels and temperatures. The genome analysis (141.095 Kb) indicated that its nucleotide sequence is novel, as it exhibited only 1-7% DNA coverage. The phage genome features 44% GC content, and 234 putative open reading frames were predicted. The genome was predicted to encode for 28 structural proteins and 40 enzymes related to nucleotide metabolism, DNA modification, and protein synthesis. Further, the genome features 11 tRNA genes for 10 different amino acids, indicating alternate codon usage, and hosts a unique hydrolase for bacterial lysis. This study provides new insights into the subfamily Vequintavirinae, of which SSBI34 may represent a new genus.

Safety and efficacy of nurse led intravitreal injection service with Precivia® injection assist device.

INTRODUCTION: Intravitreal anti-VEGF injections are the most frequently performed outpatient procedure in the UK. Ophthalmic allied healthcare professionals are replacing medical professionals in delivering injections nationwide. The use of injection assist devices such as Precivia® has been well established and increasingly adopted to aid in their safe delivery. We present outcomes of nurse-led intravitreal injections using the Precivia® injection assist device over a five-year period in the UK. METHODS: A retrospective review was completed of all anti-VEGF intravitreal injections delivered at the Great Western Hospital between May 2015 and May 2020. RESULTS: Over the five-year study period, 2318 patients underwent a total of 26,923 intravitreal injections; 20,421 (75.8%) of which were delivered by appropriately trained ophthalmic nurses. The annual number of injections increased year-on-year from 2112 injections in 2015-2016 to 5410 injections in 2019-2020. The mean age of patients was 75.7±12.2 years with a female-to-male ratio was 1.17:1. Wet age-related macular degeneration represented the major indication for injections followed by retinal vein occlusion and diabetic maculopathy respectively. Three cases of post-injection endophthalmitis out of 20,421 (0.015%) injections in nurse injection group were identified during the study period. There were no cases of lens touch, retinal detachment or systemic thromboembolic events. CONCLUSION: Use of the Precivia® intravitreal injection assist device by trained ophthalmic allied health professionals is a safe and cost-effective way to deliver intravitreal injections service.

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification.

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 - 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens (a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

Balancing Complex Signals for Robust Predictive Modeling.

Robust predictive modeling is the process of creating, validating, and testing models to obtain better prediction outcomes. Datasets usually contain outliers whose trend deviates from the most data points. Conventionally, outliers are removed from the training dataset during preprocessing before building predictive models. Such models, however, may have poor predictive performance on the unseen testing data involving outliers. In modern machine learning, outliers are regarded as complex signals because of their significant role and are not suggested for removal from the training dataset. Models trained in modern regimes are interpolated (over trained) by increasing their complexity to treat outliers locally. However, such models become inefficient as they require more training due to the inclusion of outliers, and this also compromises the models' accuracy. This work proposes a novel complex signal balancing technique that may be used during preprocessing to incorporate the maximum number of complex signals (outliers) in the training dataset. The proposed approach determines the optimal value for maximum possible inclusion of complex signals for training with the highest performance of the model in terms of accuracy, time, and complexity. The experimental results show that models trained after preprocessing with the proposed technique achieve higher predictive accuracy with improved execution time and low complexity as compared to traditional predictive modeling.

Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae).

The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the chloroplast threonine (trnT-GGU) gene was previously reported in Cryptomeria japonica (Cupressaceae), Pelargonium × hortorum (Geraniaceae), and Anaphalis sinica and Leontopodium leiolepis of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of 13 subfamilies of Asteraceae and found this gene as a pseudogene in core Asteraceae (Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae), which was linked to an insertion event within the 5' acceptor stem and is not associated with ecological factors such as habit, habitat, and geographical distribution of the species. The pseudogenization of trnT-GGU was not predicted in codon usage, indicating that the superwobbling phenomenon occurs in core Asteraceae in which a single transfer RNA (trnT-UGU) decodes all four codons of threonine. To the best of our knowledge, this is the first evidence of a complete clade of a plant species using the superwobbling phenomenon for translation.

Comparative analysis of the serum microbiome of HIV infected individuals.

HIV infects the CD4 cells which marks the suppression of our immune system. DNA from serum of healthy, treated and untreated HIV infected individuals was extracted. The DNA was subjected to 16S metagenomic sequencing and analyzed using QIIME2 pipeline. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota and Actinobacteria. Treated HIV infection showed highest abundance of Firmicutes (66.40%) significantly higher than untreated HIV infection (35.88%) and control (41.89%). Bacilli was most abundant class in treated (63.59%) and second most abundant in untreated (34.53%) while control group showed highest abundance of class Gamma-proteobacteria (45.86%). Untreated HIV infection group showed Enterococcus (10.72%) and Streptococcus (6.599%) as the most abundant species. Untreated HIV infection showed significantly higher (p = 0.0039) species richness than treated and control groups. An altered serum microbiome of treated HIV infection and higher microbial abundance in serum of untreated HIV infection was observed.

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae.

The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between "Senecioneae and Anthemideae" and "Astereae and Gnaphalieae" or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.