Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.

Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat.

Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling, in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinities of ≤30% (wt/vol) in situ, at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed 2 days after reducing the porewater salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria, Bacteroidetes, and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria, which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this salt flat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. IMPORTANCE Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even the limitations imposed on microbial processes by saturation-level salinity found on Earth have rarely been studied in situ. While abundance and diversity of microbial life in salt-saturated environments are well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. In particular, oxygenic photosynthesis has barely been explored beyond 5 M NaCl (28% wt/vol). By applying a variety of biogeochemical and molecular methods, we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust-covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several-fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.

Marine heatwaves reveal coral reef zones susceptible to bleaching in the Red Sea.

As the Earth's temperature continues to rise, coral bleaching events become more frequent. Some of the most affected reef ecosystems are located in poorly monitored waters, and thus, the extent of the damage is unknown. We propose the use of marine heatwaves (MHWs) as a new approach for detecting coral reef zones susceptible to bleaching, using the Red Sea as a model system. Red Sea corals are exceptionally heat-resistant, yet bleaching events have increased in frequency. By applying a strict definition of MHWs on >30 year satellite-derived sea surface temperature observations (1985-2015), we provide an atlas of MHW hotspots over the Red Sea coral reef zones, which includes all MHWs that caused major coral bleaching. We found that: (a) if tuned to a specific set of conditions, MHWs identify all areas where coral bleaching has previously been reported; (b) those conditions extended farther and occurred more often than bleaching was reported; and (c) an emergent pattern of extreme warming events is evident in the northern Red Sea (since 1998), a region until now thought to be a thermal refuge for corals. We argue that bleaching in the Red Sea may be vastly underrepresented. Additionally, although northern Red Sea corals exhibit remarkably high thermal resistance, the rapidly rising incidence of MHWs of high intensity indicates this region may not remain a thermal refuge much longer. As our regionally tuned MHW algorithm was capable of isolating all extreme warming events that have led to documented coral bleaching in the Red Sea, we propose that this approach could be used to reveal bleaching-prone regions in other data-limited tropical regions. It may thus prove a highly valuable tool for policymakers to optimize the sustainable management of coastal economic zones.

Metabolites from the Marine-Facultative Aspergillus sp. MEXU 27854 and Gymnoascus hyalinosporus MEXU 29901 from Caleta Bay, Mexico.

During our ongoing research on fungal strains from unexplored sources, the reinvestigation of the CHCl3-MeOH extract of the marine-facultative Aspergillus sp. MEXU 27854 yielded a new N-methyl cyclic pentapeptide (1) along with known butyrolactone II and PF1233 A. In addition, from the marine-facultative Gymnoascus hyalinosporus MEXU 29901, a new alternariol glucoside, 10-O-[ß-D-(4-methoxyl-glucopyranosyl)]-4-O-methylalternariol (2) and known alternariol 4-O-methyl ether, alternariol and beauvericin, were isolated. The structures of 1 and 2 were established by detailed spectroscopic data, and their absolute configuration was ascertained by Marfey's analysis and HRESIMS-MS/MS data for 1, and by chemical degradation and optical rotation analysis for 2.

Sources for Leads: Natural Products and Libraries.

Natural products have traditionally been a major source of leads in the drug discovery process. However, the development of high-throughput screening led to an increased interest in synthetic methods that enabled the rapid construction of large libraries of molecules. This resulted in the termination or downscaling of many natural product research programs, but the chemical libraries did not necessarily produce a larger amount of drug leads. On one hand, this chapter explores the current state of natural product research within the drug discovery process. On the other hand it evaluates the efforts made to increase the amount of leads generated from chemical libraries and considers what role natural products could play here.

Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula.

A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC-MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).

Actinomycetes - The Repertoire of Diverse Bioactive Chemical Molecules: From Structures to Antibiotics.

The urgent need for novel antibiotics in the face of escalating global antimicrobial resistance necessitates innovative approaches to identify bioactive compounds. Actinomycetes, renowned for their prolific production of antimicrobial agents, stand as a cornerstone in this pursuit. Their diverse metabolites exhibit multifaceted bioactivities, including potent antituberculosis, anticancer, immunomodulatory, immuno-protective, antidiabetic, etc. Though terrestrial sources have been exploited significantly, contemporary developments in the field of antimicrobial drug discovery have put marine actinomycetes in a prominent light as a promising and relatively unexplored source of novel bioactive molecules. This is further boosted by post-genomic era advances like bioinformatics-based secretome analysis and reverse engineering that have totally revitalized actinomycetes antibiotic research. This review highlights actinomycetes-based chemically diverse scaffolds and clinically validated antibiotics along with the enduring significance of actinomycetes from untouched ecosystems, especially with recent advanced techniques in the quest for next-generation antimicrobials.

Postharvest quality and ripening behaviour of un-explored genotypes of Himalayan plain mango diversity.

India is renowned for its mango diversity, with more than 1000 genotypes reported. However, the Himalayan plains bear some elite genotypes which supposed to bear high postharvest value, the systemic postharvest study of which is yet to be attempted. The aim of present study is to evaluate the postharvest quality and ripening behviour of these important genotypes. Thus, 15 un-explored mango genotypes of this region were selected and evaluated for ripening behaviour and detailed postharvest profiling via internal (total phenolic and total flavonoid content), nutritional attributes (Brix: acid ratio, total carotenoid concentration, ascorbic acid content and antioxidant activity), sensory evaluation, fruit softening enzymes (polygalactouronase, pectin methylesterase and lipoxygenase), shelf life attributes (respiration rate, physiological loss in weight and storage life in days) external attributes (fruit weight, fruit firmness, peel thickness, fruit shape and dry seed weight) and mineral contents (Calcium, potassium and phosphorous) under ambient storage (25 ± 4 °C and 65 ± 5 % RH). The results revealed that the highest total flavonoid content (682.40 µg g-1), ascorbic acid (46.88 mg 100 g-1) and antioxidant activity (4.84 µmol TE g-1) exhibited by 'Sukul'. The total phenolic content was recorded as the highest in 'Safed Malda' (510.42 µg GAE g-1 FW), and total carotenoid concentration was recorded as the highest in 'Sipiya' (7.30 mg 100 g-1) 'Zardalu' (7.04 mg 100 g-1) and 'Mithua' (6.98 mg 100 g-1). Interestingly, genotypes such as 'Sukul', Sipiya' and 'Krishna Bhog 'exhibited a 4-5 days higher storage life than other selected genotypes. Screened genotypes exhibited a high diversity of nutritional and biochemical contents. The results of this study bear practical utility for research (quality improvement programme) and the processing industry.

Recent Advancements and Unexplored Biomedical Applications of Green Synthesized Ag and Au Nanoparticles: A Review.

Green synthesis of silver (Ag) and gold (Au) nanoparticles (NPs) has acquired huge popularity owing to their potential applications in various fields. A large number of research articles exist in the literature describing the green synthesis of Ag and Au NPs for biomedical applications. However, these findings are scattered, making it time-consuming for researchers to locate promising advancements in Ag and Au NPs synthesis and their unexplored biomedical applications. Unlike other review articles, this systematic study not only highlights recent advancements in the green synthesis of Ag and Au NPs but also explores their potential unexplored biomedical applications. The article discusses the various synthesis approaches for the green synthesis of Ag and Au NPs highlighting the emerging developments and novel strategies. Then, the article reviews the important biomedical applications of green synthesized Ag and Au NPs by critically evaluating the expected advantages. To expose future research direction in the field, the article describes the unexplored biomedical applications of the NPs. Finally, the articles discuss the challenges and limitations in the green synthesis of Ag and Au NPs and their biomedical applications. This article will serve as a valuable reference for researchers, working on green synthesis of Ag and Au NPs for biomedical applications.

Novel targets for potential therapeutic use in Diabetes mellitus.

Future targets are a promising prospect to overcome the limitation of conventional and current approaches by providing secure and effective treatment without compromising patient compliance. Diabetes mellitus is a fast-growing problem that has been raised worldwide, from 4% to 6.4% (around 285 million people) in past 30 years. This number may increase to 430 million people in the coming years if there is no better treatment or cure is available. Ageing, obesity and sedentary lifestyle are the key reasons for the worsening of this disease. It always had been a vital challenge, to explore new treatment which could safely and effectively manage diabetes mellitus without compromising patient compliance. Researchers are regularly trying to find out the permanent treatment of this chronic and life threatening disease. In this journey, there are various treatments available in market to manage diabetes mellitus such as insulin, GLP-1 agonist, biguanides, sulphonyl ureas, glinides, thiazolidinediones targeting the receptors which are discovered decade before. PPAR, GIP, FFA1, melatonin are the recent targets that already in the focus for developing new therapies in the treatment of diabetes. Inspite of numerous preclinical studies very few clinical data available due to which this process is in its initial phase. The review also focuses on the receptors like GPCR 119, GPER, Vaspin, Metrnl, Fetuin-A that have role in insulin regulation and have potential to become future targets in treatment for diabetes that may be effective and safer as compared to the conventional and current treatment approaches.

Evaluation of immunomodulatory and antioxidant properties of traditional Kwath, conventional extracts of plants Cocculus hirsutus and Cuscuta reflexa - in vitro &ex vivo studies.

INTRODUCTION: The consumption of 'Patalagarudi' (Cocculus hirsutus 'CHP') and 'Amarbel' (Cuscuta reflexa 'CRA') as ethnic plants for health promotions rarely validated. The limited literature reported these plants as antioxidant and immunomodulators. OBJECTIVE: To evaluate the biodynamic properties of CHP and CRA extracts. METHODOLOGY: The traditional formulation, 'Kwath' (K) and conventional extracts were prepared with CRA and CHP. The total phenolic content (TPC) was estimated. Various polyphenol compounds in the extracts were eluted on UHPLC. The biodynamic activities; i. Free radical scavenging (FRS-DPPH and ABTS), ii. Intracellular ROS scavenging activity in RAW 264.7 cell line iii. Spleenocytes proliferation assay for Th1/Th2 Immunomodulatory potential by flow-cytometer were assessed. RESULTS: The TPC in CRA (105-159 µg GAE/mg) and CHP (35-48 µg GAE/mg) recorded. The chromatographic peaks confirmed the presence of polyphenols in CRA and CHP extracts. UV spectra of the extracts to the extent possible have been correlated with certain polyphenols. The FRS (IC50) was significantly low in CRA-K (DPPH = 22.7; ABTS = 12.0 µg/ml) than CHP-K (DPPH = 70.4; ABTS = 50.2 µg/ml). Similarly, intracellular ROS scavenging activity with CRA-K (84%) showed the highest inhibitory potential compared to CHP-K (50%) and LPS control. The immunomodulatory activity of CRA-K significantly upregulated TH1 cytokines (TNFα and IFN-γ). The downregulation of Th2 cytokines (IL-4 and IL-10) was in all CRA and CHP extracts as compared to Con A. CONCLUSION: The current study confirms the immunomodulatory and antioxidant properties of CRA and CHP along with the presence of polyphenols.

[Novel angucycline/angucyclinone family of natural products discovered between 2010 and 2020].

Angucyclines/angucyclinones are a large group of polycyclic aromatic polyketides and their producers are widely distributed in nature. This family of natural products attracts great attention because of their diverse biological activities and unique chemical structures. With the development of synthetic biology and the exploitation of the actinomycetes from previously unexplored environments, angucyclines/angucyclinones-like natural products with new skeletons were continuously discovered, thus enriching the structural diversity of this family. In this review we summarize the new angucyclines/angucyclinones analogues discovered in the last decade (2010-2020) by using different strategies, such as changing cultivation conditions, genetic modification, genome mining, bioactivity-guided compound isolation, and fermentation of actinomycetes from underexplored environments. We also discuss the role of synthetic biology in the discovery and development of new compounds of the angucycline/angucyclinone family.

Antimicrobial, Antioxidant, and Antiproliferative Effects of Coronilla minima: An Unexplored Botanical Species.

Coronilla species, belonging to the Coronilla genus (Fabaceae), have long been used in traditional medicine for treating cold, diabetes, pain, and as cardiotonics. The goal of the present study was to explore the phytochemical composition and pharmaco-toxicological properties of C. minima. In this regard, phenolic content, scavenging/reducing properties and antimicrobial activity toward pathogen bacterial (Escherichia coli, Pseudomonas aeruginosa, Bacillus cereus, Staphylococcus aureus) and fungal strains (Candida albicans, C. tropicalis, Aspergillus tubigensis and A. minutus) were investigated. Extract effects on human colon cancer HCT116 cell viability were also assayed. Finally, a bioinformatics approach was conducted with the aim to identify putative microbial and human protein targets underlying antibacterial, antimycotic, and antiproliferative effects. Phytochemical investigation suggested that water extract is richer in terms of total flavonoid and phenol content, whereas the hydroalcoholic extract was revealed to be more potent as antioxidant agent. According to bioinformatics analysis, the antibacterial activity of the hydroalcoholic extract could be related to its content in resveratrol. The presence of resveratrol could also explain the hydroalcoholic extract efficacy in reducing HCT116 cell viability. In conclusion, the present study represents the first phytochemical and bio-pharmacological investigation about C. minima. Like other plants belonging to the Fabaceae family, C. minima revealed a good source of resveratrol, which could explain, albeit partially, the efficacy of the hydroalcoholic extract as antimicrobial, antioxidant, and antiproliferative agent.

Prevalence and Profile of Bullying Involvement among Students of Rural Schools of Anand, Gujarat, India.

BACKGROUND: Bullying can have short- and long-term implications on physical as well as mental health. The objective of this study was to assess the prevalence of bullying involvement (bully, victim, and bully-victim) and know profiles of bullying among students of rural schools of Anand, Gujarat, in Western India. MATERIALS AND METHODOLOGY: A questionnaire in the Gujarati language was administered to sixth to tenth graders of 12 rural schools (n = 2552) in the Anand district. The questionnaire included four questions each to screen for bullying behavior and victim experiences; Peer Interaction in Primary Schools Questionnaire (PIPSQ, a self-reported measure of individuals' levels of bullying behaviors and victimization experiences), and Strength and Difficulties Questionnaire (SDQ, to assess emotional, behavior, and interpersonal difficulties experienced), apart from demographic information. The analysis of variance (ANOVA)/Chi-square test was applied to determine associations. RESULTS: Prevalence of bullying involvement was 70% (n = 1529; 9.1% bullies, 18.6% victims, and 42.3% bully-victims). The prevalence of bullies was higher in boys (77.5%) compared with girls (58.3%). In addition, the prevalence of victims was higher in boys (67.2%) compared with girls (51%). No association was found between various categories and family type, birth order, number of friends, or grade. Bully-victim was the worst affected group as per the SDQ profile. CONCLUSIONS: There is a high prevalence of bullying-related involvement compared with earlier studies and a complete lack of bullying prevention policies at the school level. A simple screening strategy, using a few questions to identify bullying-related involvement, is valid and useful. Guidelines need to be devised to standardize future bullying-related research in India.

Antimicrobial and enzymatic activity of actinomycetes isolated from soils of coastal islands.

Microbiological investigation of unexplored ecosystems is crucial for discovering of antibiotic producing actinomycetes. The present study was conducted to determine antimicrobial activity and identify the most active strains. Actinomycetes were isolated using the spread plate technique following by serial dilution of samples on starch casein agar. The screening method consists of primary and secondary testing. The most active isolates were identified based on molecular and cultural methods. 42 out of 66 isolates displayed antimicrobial potential. 63% exhibited antibacterial activity, 16% antifungal activity, and 16% displayed both activities. Identified isolates, Streptomyces scabrisporus, Streptomyces sparsogenes, Streptomyces misakiensis, Streptomyces cirratus, Streptomyces lincolnensis, Streptomyces endophyticus, Streptomyces chartreusis, and Streptomyces alboniger showed a broad spectrum of enzymatic activities. The results indicated that these isolates may serve as antibiotic and enzyme-producing microbes.

Purification and characterization of an extracellular ß-xylosidase from Pseudozyma hubeiensis NCIM 3574 (PhXyl), an unexplored yeast.

This paper reports on the production of ß-xylosidase from an unexplored yeast, Pseudozyma hubeinsis. The expression of this enzyme could be induced by beech wood xylan when the yeast was grown at 27 °C. The enzyme was purified to homogeneity as a glycoprotein with 23 % glycosylation. The purification protocol involved ammonium sulphate precipitation, QAE-Sephadex A50 ion exchange chromatography and sephacryl-200 column chromatography which resulted in 8.3-fold purification with 53.12 % final recovery. The purified enzyme showed prominent single band on SDS-PAGE. It is a monomeric protein of 110 kDa molecular weight confirmed by SDS-PAGE followed by MALDI-TOF mass spectrometry (112.3 kDa). The enzyme was optimally active at 60 °C and pH 4.5 and stable at pH range (4-9) and at 50 °C for 4 h. Chemical modification studies revealed that active site of the purified enzyme comprised of carboxyl, tyrosine and tryptophan residues. The carboxyl residue is involved in catalysis and tryptophan residue is solely involved in substrate binding. The best match from the search of the NCBInr database was with gi|808364558 glycoside hydrolase of Pseudozyma hubeiensis SY62 with 26 % sequence coverage confirming that it is a glycoside hydrolase/beta-glucosidase. From the search of customized SWISSPROT database, it was revealed that SWISSPROT does not contain any entries that are similar to the purified enzyme.

Novel angucycline/angucyclinone family of natural products discovered between 2010 and 2020 / 生物工程学报

Angucyclines/angucyclinones are a large group of polycyclic aromatic polyketides and their producers are widely distributed in nature. This family of natural products attracts great attention because of their diverse biological activities and unique chemical structures. With the development of synthetic biology and the exploitation of the actinomycetes from previously unexplored environments, angucyclines/angucyclinones-like natural products with new skeletons were continuously discovered, thus enriching the structural diversity of this family. In this review we summarize the new angucyclines/angucyclinones analogues discovered in the last decade (2010-2020) by using different strategies, such as changing cultivation conditions, genetic modification, genome mining, bioactivity-guided compound isolation, and fermentation of actinomycetes from underexplored environments. We also discuss the role of synthetic biology in the discovery and development of new compounds of the angucycline/angucyclinone family.

Advances in the application of human embryonic stem cells in disease treatment / 基础医学与临床

The application of human embryonic stem cell(hES cell) contributes a lot to the disease treatment,and shows a great potentiality especially in organ transplantation and tissue engineering.Although hES cell therapy has not reached clinical application,some newly achieved results are encouraging.This review mainly presents results recently published in applying hES cell for disease treatment.