A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution

Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal pathways and evolution of compound production in sponges. This benefits the discovery rate and yield of bioprospecting for novel marine natural products by identifying lineages with high potential of being new sources of valuable sponge compounds. In this review, we summarize the current biochemical data on sponges and compare the metabolite distribution against a sponge phylogeny. We assess compound specificity to lineages, potential convergences, and suitability as diagnostic phylogenetic markers. Our study finds compound distribution corroborating current (molecular) phylogenetic hypotheses, which include yet unaccepted polyphyly of several demosponge orders and families. Likewise, several compounds and compound groups display a high degree of lineage specificity, which suggests homologous biosynthetic pathways among their taxa, which identifies yet unstudied species of this lineage as promising bioprospecting targets.

Intraspecific variability of floral and ornamental plants of Onagraceae family and mechanisms of their variety formation

The present review is devoted to intraspecific variability of floral and ornamental plants of the genus Clarkia purch. Family Onagraceae and clarification of the systematic status of the Godetia species introduced into Novosibirsk. Clarkia species from the Godetia and Rhodantos sections are noted for their particular beauty and duration of flowering. A comprehensive study of the influence of environmental conditions on genetic features of populations, ornamental qualities, flowering biology, morphogenesis, organogenesis, seed production and seed quality, agrotechnology’s of growing the above species of Clarkia, for selecting suitable forms and creating local varieties included in the basic assortment of flower crops for climatic conditions of Western Siberia as well as their introduction into urban gardening is necessary. The article discusses taxonomic markers important for determining the systematic position of Clarkia species from Godetia and Rhodantos sections in the family Onagraceae. Experimental data of genetic and cytological analyses carried out by foreign scientists for the last 100 years are presented, which give an idea of morphological, karyological characteristics and genetic variability in various species in the Godetia section. The mechanisms of inheritance of the flower colour trait and numerous variations in the position of the spot on the petals of different clarkia species have been established. Formation of the list of genes responsible for the Clarkia pigmentation system, location and size of the carmine spot will allow targeted selection for qualitative traits. The study of the pattern of multifactorial inheritance of habitus and flower shape traits among C. amoena subspecies contributes to the passage of the most decorative hybrid forms (varieties) as the starting material. In conclusion, a brief overview of promising species of the genus Clarkia from the Godetia and Rhodantos sections for ornamental plant breeding and selection is given.

Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

Graves’ Disease is the most common organ-specific autoimmune disease and has been linked in small pilot studies to taxonomic markers within the gut microbiome. Important limitations of this work include small sample sizes and low-resolution taxonomic markers. Accordingly, we studied 162 gut microbiomes of mild and severe Graves’ disease (GD) patients and healthy controls. Taxonomic and functional analyses based on metagenome-assembled genomes (MAGs) and MAG-annotated genes, together with predicted metabolic functions and metabolite profiles, revealed a well-defined network of MAGs, genes and clinical indexes separating healthy from GD subjects. A supervised classification model identified a combination of biomarkers including microbial species, MAGs, genes and SNPs, with predictive power superior to models from any single biomarker type (AUC = 0.98). Global, cross-disease multi-cohort analysis of gut microbiomes revealed high specificity of these GD biomarkers, notably discriminating against Parkinson’s Disease, and suggesting that non-invasive stool-based diagnostics will be useful for these diseases.

Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments

The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as ‘Amplicon Sequence Variants’ (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.

Efficient and stable metabarcoding sequencing data using a DNBSEQ-G400 sequencer validated by comprehensive community analyses

Metabarcoding is a widely used method for fast characterization of microbial communities in complex environmental samples. However, the selction of sequencing platform can have a noticeable effect on the estimated community composition. Here, we evaluated the metabarcoding performance of a DNBSEQ-G400 sequencer developed by MGI Tech using 16S and internal transcribed spacer (ITS) markers to investigate bacterial and fungal mock communities, as well as the ITS2 marker to investigate the fungal community of 1144 soil samples, with additional technical replicates. We show that highly accurate sequencing of bacterial and fungal communities is achievable using DNBSEQ-G400. Measures of diversity and correlation from soil metabarcoding showed that the results correlated highly with those of different machines of the same model, as well as between different sequencing modes (single-end 400 bp and paired-end 200 bp). Moderate, but significant differences were observed between results produced with different sequencing platforms (DNBSEQ-G400 and MiSeq); however, the highest differences can be caused by selecting different primer pairs for PCR amplification of taxonomic markers. These differences suggested that care is needed while jointly analyzing metabarcoding data from differenet experiments. This study demonstrated the high performance and accuracy of DNBSEQ-G400 for short-read metabarcoding of microbial communities. Our study also produced datasets to allow further investigation of microbial diversity.

Homoplasy as an Auxiliary Criterion for Species Delimitation

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking

The relationship between microbiota and health has been widely reported in humans and animals. We established a link between teat cistern microbiota composition and bovine mastitis, an inflammatory disease often due to bacterial infections. To further decipher the relationships between teat cistern microbiota and immune and microbial responses, a switch from twice- to once-daily milking (ODM) in 31 initially healthy quarters of dairy cows was used to trigger an udder perturbation. In this study, a temporal relationship was reported between initial teat cistern microbiota composition and richness, the immune response to ODM, and mastitis development. Quarters with a low initial microbiota richness and taxonomic markers such as Bacteroidetes and Proteobacteria were associated with a higher rate of mastitis during ODM. Quarters with a higher richness and taxonomic markers such as Firmicutes, including the Lachnospiraceae family, and genera such as Bifidobacterium and Corynebacterium displayed early inflammation following transition to ODM but without developing mastitis (no infection). Short-term compositional shifts of microbiota indicates that microbiotas with a higher initial richness were more strongly altered by transition to ODM, with notably the disappearance of rare OTUs. Microbiota modifications were associated with an early innate immune system stimulation, which, in turn, may have contributed to the prevention of mastitis development.

Leaf architecture and petiole anatomy of Philippine Dipterocarpus species (Dipterocarpaceae)

The study investigated the leaf architecture and petiole anatomy of eight Dipterocarpus (Dipterocarpaceae) species growing in Mount Makiling Forest Reserve (MMFR) in the Philippines to delineate the species, especially during their non-flowering phase. Leaf and petiole samples from MMFR were examined following the manual on leaf architecture studies. Freehand technique was used to examine the stomata and petiole characters. A UPGMA phenogram was then generated to determine the relationships among Dipterocarpus species using 26 leaf and petiole characters. The most useful characters to delineate Dipterocarpus species are the presence of trichomes, the arrangement of vascular bundles (medullary and outer vascular bundles), areolation, fimbrial vein, and leaf size. Other characters viz., the laminar ratio, blade class, laminar shape, base shape, margin type, and intersecondary, and layers and shape of parenchyma and collenchyma cells were useful as unifying characters. Therefore, certain characters of the leaf architecture and petiole anatomy may be used as taxonomic markers to delineate and correlate the Dipterocarpus species in the Philippines particularly during the nonflowering phase of the species. However, further investigations using samples from the wild populations of the species and molecular techniques may be done to elucidate the taxonomic use of the characters presented in this study. Bangladesh J. Plant Taxon. 27(1): 1-14, 2020 (June)

The use of CRISPR-Cas Selective Amplicon Sequencing (CCSAS) to reveal the eukaryotic microbiome of metazoans

Characterization of the eukaryotic microbiome is required to understand the role of microbial communities in health and disease. Such investigation relies on sequencing 18S ribosomal RNA genes (rDNA), which serve as taxonomic markers; however, this is compromised by contaminating host rDNA sequences. To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rDNA sequences of the host. Validation shows that >96.5% of rDNA amplicons from ten model organisms were cleaved, while rDNA from protists and fungi were unaffected. In oyster spat, CCSAS resolved ∼8.5-fold more taxa, and several additional major phylogenetic groups when compared to the best available alternative approach. We designed taxon-specific sgRNA for ∼16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected because of methodological challenges.