Taxonomic Markers Research Articles

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling

BackgroundUnderstanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers. Furthermore, the availability of genome sequences for various microbial organisms has prompted the integration of genome-scale metabolic modelling that provides insights into the metabolic interactions influencing host health. However, the analysis from a single study may not be consistent, necessitating a meta-analysis.ResultsWe conducted a meta-analysis and integrated with constraint-based metabolic modelling approach, focusing on the microbiome of pacific white shrimp Penaeus vannamei, an extensively cultured marine candidate species. Meta-analysis revealed that Acinetobacter and Alteromonas are significant indicators of "health" and "disease" specific taxonomic biomarkers, respectively. Further, we enumerated metabolic interactions among the taxonomic biomarkers by applying a constraint-based approach to the community metabolic models (4416 pairs). Under different nutrient environments, a constraint-based flux simulation identified five beneficial species: Acinetobacter spWCHA55, Acinetobacter tandoii SE63, Bifidobacterium pseudolongum 49 D6, Brevundimonas pondensis LVF1, and Lutibacter profundi LP1 mediating parasitic interactions majorly under sucrose environment in the pairwise community. The study also reports the healthy biomarkers that can co-exist and have functionally dependent relationships to maintain a healthy state in the host.ConclusionsToward this, we collected and re-analysed the amplicon sequence data of P. vannamei (encompassing 117 healthy and 142 disease datasets). By capturing the taxonomic biomarkers and modelling the metabolic interaction between them, our study provides a valuable resource, a first-of-its-kind analysis in aquaculture scenario toward a sustainable shrimp farming.

The use of the intergenic spacer region psbA-trnH of the chloroplast genome for the analysis of the taxonomic position and genetic polymorphism of the Ukrainian populations of Tulipa quercetorum Klokov et Zoz

Aim. Tulipa quercetorum is included in the Red Data Book of Ukraine as a vulnerable species. The International Botanical Taxonomy considers T. quercetorum synonymous with T. sylvestris, a wide-ranging polymorphic species. The necessity and type of conservation measures aimed at preserving Ukrainian populations of T. quercetorum depend on its taxonomic interpretation. Accordingly, we used the chloroplast marker psbA-trnH to analyze the taxonomic status of the Ukrainian populations of T. quercetorum. Methods. PCR amplification, sequencing of the psbA-trnH spacer region, and bioinformatic analysis. Results. We have sequenced psbA-trnH of four accessions of T. quercetorum representing different regions of its distribution area in Ukraine. Comparison with the sequences of T. sylvestris s. l. showed that the differences in the psbA-trnH spacer are mainly represented by with oligonucleotide indels. Three out of four samples of T. quercetorum from Ukrainian populations contain a specific variant of inversion in the loop region of the 3' UTR of psbA mRNA, which is not characteristic for samples of T. sylvestris s. l. Conclusions. The data obtained indicate the genetic uniqueness of Ukrainian populations of T. quercetorum, however, for the accurate determination of its taxonomic status additional molecular markers, preferably of nuclear localization, are required.

Phytochemical and chemotaxonomic studies on four plants from genus of Urtica L. (Urticaceae)

The study aims to conduct phytochemical investigation on four different species of Urtica L., collected in China. The main components of different types of plants in this genus are flavonoids, coumarins, lignans and so on, which are compatible with this study. Eight substances were isolated from Urtica laetevirens Maxim., Urtica mairei Levl., Urtica fissa E. Pritz. and Urtica triangularis Hand-Mass.: one terpenoid (1), one coumarin (2), four lignans (3–6) and two flavonoids (7 and 8). Among them, compound 2 was isolated from all four plants, compounds 1 and 8 were first discovered from Urtica L. In addition, secolignans could be regarded as taxonomic markers for the genus of Urtica L., and its accumulation may be related to its location and altitude. All the above results of the research contributed to consolidating the chemotaxonomic knowledge of Urtica L..

Chemical Profile and Antioxidant Capacity of Propolis from Tetragonula, Lepidotrigona, Lisotrigona and Homotrigona Stingless Bee Species in Vietnam.

The present study aimed to analyze and compare the chemical profile and antioxidant capacity of propolis from different bee species and different regions. The chemical profiles of propolis from six stingless bee species (Tetragonula iridipennis, T. laeviceps, Lepidotrigona terminata, L. ventralis, Lisotrigona carpenteri and Homotrigona apicalis) collected from a total of eight locations in Vietnam were investigated by gas chromatography-mass spectrometry (GC-MS). More than 70 compounds were identified, amongst which phenolic lipids (cardanols, resorcinols and anacardic acids), aromatic acids, triterpenes and xanthones. Taxonomic markers for Mangifera indica (phenolic lipids and cycloartane triterpenes) were detected in propolis from bees of the genera Tetragonula and Lepidotrigona, although in different amounts, whereas propolis from H. apicalis was characterized by triterpenes of the amyrine type, typical of dipterocarp trees. A clear discrimination between both groups was observed by principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). Propolis from Tetragonula and Lepidotrigona spp. and from Lisotrigona carpenteri, which is rich in xanthones, possesses higher radical scavenging and ferric-reducing capacity than that from H. apicalis. Propolis produced by all six stingless bee species in Vietnam was analyzed for the first time. In addition, this is the first report on L. carpenteri propolis.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane—whose role in its health and growth is crucial—remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3–V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments—especially in fungi—and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Leidynema bestium sp. n. (Oxyuridomorpha: Thelastomatidae) an intestinal parasite of blaberid cockroaches from Yaroslavl Zoo, Russia

A new species of thelastomatid Leidynema bestium sp. n. is described from the hind gut lumen of the cockroaches Diploptera punctata (Eschscholtz, 1922) and Elliptorhina chopardi (Lefeuvre, 1966). The new species is characterized by a combination of morphological features: presence of lateral alae in both sexes with posterior margin of alae in females not ending in the shape of a spike; longitudinal striation of the anteriormost annuli in males; four male genital papillae, equatorial position of vulva. In the cladogram inferred from analysis of D2-D3 segment of LSU rDNA L. bestium sp. n. demonstrates a position independent of the Leidynema species with known sequences of this taxonomic marker near the basal node for this genus.

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes.

We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.

Ancient marine sediment DNA reveals diatom transition in Antarctica

Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.

Multilocus sequence typing of diverse phytoplasmas using hybridization probe-based sequence capture provides high resolution strain differentiation.

Phytoplasmas are insect-vectored, difficult-to-culture bacterial pathogens that infect a wide variety of crop and non-crop plants, and are associated with diseases that can lead to significant yield losses in agricultural production worldwide. Phytoplasmas are currently grouped in the provisional genus ‘Candidatus Phytoplasma’, which includes 49 ‘Candidatus’ species. Further differentiation of phytoplasmas into ribosomal groups is based on the restriction fragment length polymorphism (RFLP) pattern of the 16S rRNA-encoding operon, with more than 36 ribosomal groups (16Sr) and over 100 subgroups reported. Since disease symptoms on plants are not associated with phytoplasma identity, accurate diagnostics is of critical importance to manage disease associated with these microorganisms. Phytoplasmas are typically detected from plant and insect tissue using PCR-based methods targeting universal taxonomic markers. Although these methods are relatively sensitive, specific and are widely used, they have limitations, since they provide limited resolution of phytoplasma strains, thus necessitating further assessment of biological properties and delaying implementation of mitigation measures. Moreover, the design of PCR primers that can target multiple loci from phytoplasmas that differ at the sequence level can be a significant challenge. To overcome these limitations, a PCR-independent, multilocus sequence typing (MLST) assay to characterize an array of phytoplasmas was developed. Hybridization probe s targeting cpn60, tuf, secA, secY, and nusA genes, as well as 16S and rp operons, were designed and used to enrich DNA extracts from phytoplasma-infected samples for DNA fragments corresponding to these markers prior to Illumina sequencing. This method was tested using different phytoplasmas including ‘Ca. P. asteris’ (16SrI-B), ‘Ca. P. pruni’ (16SrIII-A),‘Ca. P. prunorum’ (16SrX-B), ‘Ca. P. pyri’ (16SrX-C), ‘Ca. P. mali’ (16SrX-A), and ‘Ca. P. solani’ (16SrXII-A). Thousands of reads were obtained for each gene with multiple overlapping fragments, which were assembled to generate full-length (typically >2 kb), high-quality sequences. Phytoplasma groups and subgroups were accurately determined based on 16S ribosomal RNA and cpn60 gene sequences. Hybridization-based MLST facilitates the enrichment of target genes of phytoplasmas and allows the simultaneous determination of sequences corresponding to seven different markers. In this proof-of-concept study, hybridization-based MLST was demonstrated to be an efficient way to generate data regarding ‘Ca. Phytoplasma’ species/strain differentiation.

Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria.

Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM(1)-trnL(1)-trnA-trnF-trnK-trnL(2)-trnQ-trnH-trnM(2)-nad2-nad3-atp9-cox2-trnR(1)-nad4L-nad5-cob-trnC-cox1-trnR(2)-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM(3)) was first processed from the mitogenome and was subsequently processed into smaller mono-, di-, or tricistronic RNAs.

Chemotaxonomic Significance and Environmental Implications of the Phytochemical Constituents of four Mussaenda L. (Rubiaceae) taxa in Nigeria

This work investigated the phytoconstituents of some Mussaenda taxa (Rubiaceae) collected from Nsukka (Derived Savanna) and Uyo (Tropical Rainforest) ecological zones of Nigeria to establish their contribution as possible taxonomic and environmental monitoring markers. Fresh leaf samples used in this study were collected from plants of the same age, air-dried, and made into powder for further use. Histochemical and phytochemical tests were carried out by following the standard procedures. Results of the comparative phytochemical screening revealed the presence of flavonoids, alkaloids, glycosides, phenols, hydrogen cyanide, reducing sugars, soluble carbohydrates, saponins, steroids, terpenoids, and tannins in varying proportions. Results of the phytochemical constitute analysis revealed the presence of the cystoliths from the M. elegans (MEL) and M. erythrophylla (MER) which were absent in Mussaenda “ Doña Aurora” (MDA) and Mussaenda “Doña Luz”(MDL). Further, the presence of the Raphides was unique to MEL while Gum and mucilage were reported only in MDA. Quantitatively, MEL had the highest value of terpenoids (650.88 mg/100g) while MDA had the highest values of phenols (899.27 mg/100g), alkaloids (311.01 mg/100g), reducing sugars (967.35 mg/100g), steroids (2.89 mg/100g), soluble carbohydrates (27.68 mg/100g) and tannins (393.16 mg/100g), and MDL was richest in glucosides (339.64 mg/100g), flavonoids (69.34 mg/100g) and hydrogen cyanides (1.34 mg/100g). The cluster analysis based on obtained phytochemical data revealed three (3) distinct clusters with MEL in cluster 1; MDA and MDL in cluster 2 while cluster 3 had MER. The evolutionary closeness of the two infraspecific and exotic species (MDA and MDL) were confirmed and their taxonomic relationship with the indigenous infrageneric taxa (MEL and MER) was established. The results also highlight the opportunity of employing plant metabolomics in ecological studies and environmental monitoring.

One-step PCR amplicon sequencing libraries perform better than two-step when assessing soil microbial diversity and community profiles.

Despite adoption of high-throughput sequencing of PCR-amplified microbial taxonomic markers for ecological analyses, distinct approaches for preparing amplicon libraries exist. One approach utilises long fusion primers and a single PCR (one-step) while another utilises shorter primers in a first reaction, before transferring diluted amplicons to a second reaction for barcode index incorporation (two-step). We investigated whether transferring diluted amplicons risked creating artificially simplified, poorly diverse communities. In soils from three sites with paired cropland and forest, one-step yielded higher alpha-diversity indices, including detection of two-four times more unique taxa. Modelling expected taxa per sequence observation predicted that one-step reaches full coverage by 104 sequences per sample while two-step needs 105-109. Comparisons of rank abundance demonstrated that two-step covered only 38%-69% of distributions. Beta-diversity showed better separation of communities in response to land use change under one-step, although both approaches showed a significant effect. Driving differences was underestimation of relatively minor taxa with the two-step procedure. These taxa were low in abundance, yet play important roles in carbon cycling, secondary metabolite production, anaerobic metabolism, and bacterial predation. We conclude that one-step amplicon libraries are advisable for studies focussed on diversity or relatively minor yet functionally important taxa.

Phylogenetic, Allometric, and Ecological Factors Affecting Morphological Variation in the Scapula and Humerus of Spiny Rats (Rodentia: Echimyidae)

Locomotion, as a fundamental function in mammals directly associated with the use of ecological resources, is expected to have anatomical structures functionally committed that evolved under intense selective pressure, possibly carrying specializations for different locomotor habits. Among caviomorph rodents, the family Echimyidae stands out for having the greatest species richness, with relatively well-resolved phylogenetic relationships, wide variation in body mass, and remarkable diversity of locomotor habits, including arboreal, scansorial, semi-aquatic, semifossorial, and terrestrial forms. Thus, Echimyidae constitutes a promising model for understanding how phylogenetic, allometric, and ecological factors affect the evolution of postcranial structures directly linked to locomotor function. We investigated the influence of these three factors on scapular and humeral morphological variation in 38 echimyid species using two-dimensional geometric morphometry and phylogenetically informed comparative methods. Scapular and humeral shape variation had a low correlation with body mass and structure size, conveying a small or negligible allometric effect. Conversely, a significant moderate to strong phylogenetic signal was detected in both structures, suggesting that an important part of their morphometric variation results from shared evolutionary history. Notably, morphological variation of the scapula was extensively structured by phylogeny, without the marked influence of locomotor habits, suggesting that its shape may be a suitable taxonomic marker. Finally, locomotor habits were important in structuring the morphological variation of the humerus. Our results suggest that the morphologies of the scapula and humerus, despite being anatomically and functionally interconnected, were differentially shaped by ecological factors associated with locomotor habits.

Investigation of memory-enhancing effects of Streptococcus thermophilus EG007 in mice and elucidating molecular and metagenomic characteristics using nanopore sequencing

Over the past decades, accumulating evidences have highlighted the gut microbiota as a key player in the brain functioning via microbiota–gut–brain axis, and accordingly, the beneficial role of several probiotic strains in cognitive ability also have been actively investigated. However, the majority of the research have demonstrated the effects against age-related cognitive decline or neurological disease. To this end, we aimed to investigate lactic acid bacteria strains having beneficial effects on the cognitive function of healthy young mice and elucidate underlying characteristics by carrying out nanopore sequencing-based genomics and metagenomics analysis. 8-week consumption of Streptococcus thermophilus EG007 demonstrated marked enhancements in behavior tests assessing short-term spatial and non-spatial learning and memory. It was revealed that EG007 possessed genes encoding various metabolites beneficial for a health condition in many aspects, including gamma-aminobutyric acid producing system, a neurotransmitter associated with mood and stress response. Also, by utilizing 16S–23S rRNA operon as a taxonomic marker, we identified more accurate species-level compositional changes in gut microbiota, which was increase of certain species, previously reported to have associations with mental health or down-regulation of inflammation or infection-related species. Moreover, correlation analysis revealed that the EG007-mediated altered microbiota had a significant correlation with the memory traits.

A rapid, simple, and reliable assay to authenticate Peruvian kiwicha (A. caudatus) for food applications

Amaranth has acquired great economic impact as functional food, with species originating from Mexico dominating global trade. In contrast, the Peruvian A. caudatus (kiwicha) has been vastly neglected, although it is endowed with very promising nutritive traits. Morphological plasticity and taxonomic ambiguities render authentication of Amaranth difficult, such that the identity of commercial samples is often unclear. To safeguard the authenticity of kiwicha and, thus, consumer safety, we characterised a germplasm collection of 84 Amaranth accessions on both, the morphological and the genetic level. We show that kiwicha can be delineated phenotypically from other species by its late flowering, taller posture, and lower grain yields. Instead, flower and seed color, often used as proxy for identity, do not qualify as taxonomic markers. Using the plastidic barcoding marker psbA-trnH igs we were able to identify a specific Single Nucleotide Polymorphism (SNP) that separated kiwicha from all other species of Amaranth. This allowed us to develop a sequencing-free authentication assay using an Amplified Refractory Mutation System (ARMS) strategy. As a result kiwicha in commercial samples can be authenticated by a single duplex-PCR yielding a diagnostic side band reporting A. caudatus against all other species of Amaranthus. This fingerprinting assay will help to develop the nutritive potential of kiwicha and to safeguard seed material for A. caudatus against adulteration by the far more prevalent species from Mexico.

Bacterial Diversity and Dynamics during Spontaneous Cheese Whey Fermentation at Different Temperatures

The effect of temperature (32–50 °C) on bacterial dynamics and taxonomic structure was evaluated during spontaneous whey fermentation for lactic acid production. Bacterial plate count in fresh whey (5 log CFU/mL) increased in two orders of magnitude after 60 h of fermentation (7 log CFU/mL), followed by one log reduction after 120 h (6 log CFU/mL) at 37 and 42 °C. Streptococcus and Lactobacillus counts ranged between 5–9 and 5–8 log CFU/mL, respectively. High-throughput sequencing of the 16S rRNA gene (V3-V4 region) used as a taxonomic marker revealed thirteen different bacterial phyla. Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were detected in all fermentation treatments (32–50 °C, 0–120 h), where Firmicutes was the predominant phylum. Bacterial diversity included more than 150 bacterial genera with predominant lactic acid bacteria (belonging to Firmicutes) such as Lactobacillus, Lactococcus, Streptococcus, and Tetragenococcus. At the species level, fresh whey presented 61 predominant species (relative abundance &gt; 0.05%); however, only 57.4% of these resisted the fermentation conditions (most of them belonging to lactic acid bacteria genera). Tetragenococcus halophilus, Lactococcus lactis, and Enterococcus casseliflavus were the predominant bacteria found in all treatments. Temperatures between 37–42 °C were more favorable for lactic acid production and could be considered appropriate conditions for fermented whey production and for the standardization of some artisanal cheese-making processes requiring acid whey addition for milk coagulation. The diversity of native beneficial bacteria found in fresh whey offers attractive technological characteristics, and their fermentative capacity would represent a biotechnological option to add value to cheese whey.

Dimeric phenanthrenoids: possible biogenetic pathway and missing compounds

Secondary metabolites extracted from plants have historically been critical for drug discovery, but their isolation involves expensive and complicated procedures in terms of time and labor resources. Thus, the biogenetic pathway offers the possibility of identifying specific compounds that have not yet been isolated and predicting their isolation from specific natural sources. In plants, biphenanthrenes represent a relatively small group of aromatic secondary metabolites that are considered as important taxonomic markers with promising biological activities. To date, 38 mixed phenanthrenoid dimers have been identified, the biosynthesis of which involves the radical coupling of the two subunits, namely, a phenanthrene and a dihydrophenanthrene. For each of the compounds, it is possible to identify the single phenanthrenic and dihydrophenanthrenic units constituting the considered dimer. Based on the biogenetic pathway, it is possible to identify 19 phenanthrenes and 17 dihydrophenanthrenes, and to distinguish those already known from those not yet isolated. By comparing the results of the possible biosynthetic pathway for each compound with the data in the literature, it is possible to identify three known phenanthrenes and seven known dihydrophenanthrenes, as well as eleven new phenanthrenes and five new dihydrophenanthrenes, and to identify from which plant it is possible to isolate them. This could direct the work of researchers seeking to identify known or new molecules useful for their possible biological properties, and ultimately, to confirm the veracity of the proposed and generally accepted biosynthetic pathway.

Are short-read amplicons suitable for the prediction of microbiome functional potential? A critical perspective.

Taxonomic marker gene analysis allows uncovering taxonomic profiles of microbial communities at low cost, making it omnipresent in microbiome research. There is an ever-expanding set of tools to extract further biological information from this kind of data. In this perspective, we enunciate several concerns regarding the biological validity of predicting functional potential from taxonomic profiles, especially when they are generated by short-read sequencing. The taxonomic resolution of marker genes, intragenomic variability of marker genes, and the compositional nature of microbiome data are discussed. Combining actual measurements of microbiome functions with predicted functional potentials is proposed as a powerful approach to better understand microbiome functioning. In this context, the significance of predicted functional potentials for generating and testing hypotheses is highlighted. We argue that functions of microbiomes predicted from microbiome DNA read count data generated by short-read amplicon sequencing should not serve as the only basis to draw biological inferences.

The Role of Ingenane Diterpenes in Cancer Therapy: From Bioactive Secondary Compounds to Small Molecules

Diterpenes are a class of critical taxonomic markers of the Euphorbiaceae family, representing small compounds (eg, molecules) with a wide range of biological activities and multi-target therapeutic potential. Diterpenes can exert different activities, including antitumor and multi-drug resistance-reversing activities, and antiviral, immunomodulatory, and anti-inflammatory effects, mainly due to their great structural diversity. In particular, one polycyclic skeleton has been highlighted: ingenane. Besides this natural diterpene, promising polycyclic skeletons may be submitted to chemical modification—by in silico approaches, chemical reactions, or biotransformation—putatively providing more active analogs (eg, ingenol derivatives), which are currently under pre-clinical investigation. This review outlines the current mechanisms of action and potential therapeutic implications of ingenol diterpenes as small cancer molecules.

Micromorphological leaf epidermal traits as potential taxonomic markers for infrageneric classification of Oxytropis (Fabaceae).

The characteristics of the leaf epidermis have proven to be useful criteria to support taxonomic studies within Fabaceae. However, there are few systematic studies on the taxonomic significance of leaf epidermis of Oxytropis DC. Here, we used light and scanning electron microscopy to investigate leaf epidermal characteristics of 18 species of genus Oxytropis from the Northeastern Margin of Qinghai-Tibet Plateau. Our examination showed two main types of leaf epidermal cells: polygonal and irregular, and four different patterns of anticlinal walls: straight-arched, sinuolate, undulate, and sinuate. All species studied possess anomocytic stomata. Two trichome shapes were identified: strip-like trichomes, that were present only in O.ciliata, and cylindrical trichomes, present in all other species. Epidermal cell shape and anticlinal wall pattern were constant within species and are useful for species delimitation within genus Oxytropis, when combined with other macroscopic traits. The shape of trichomes can be useful for distinguishing O.ciliata from the other investigated species. Stomatal type was the same within the genus and may be used to elaborate the phylogenetic relationships between genera in combination with data on stomata from other genera. Cluster analysis results were largely consistent with the classification of species and sections based on macro morphological data, indicating that foliar epidermis characteristics of Oxytropis can be used as markers for taxonomic identification at the infrageneric classification level. Lastly, our results support the delineation of the section Leucopodia as an independent section but do not support the merging of section Gobicola into section Baicalia.