Taxonomic Assignment Research Articles

Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth.

The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g. genus vs. family), an empirical pattern previously evaluated in the context of the Diversity Begets Diversity (DBD) hypothesis (Madi et al., 2020). We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members, demonstrating that the DBD can be sufficiently explained using the SLM as a null model of ecology. Contrastingly, only by including correlations between the abundances of community members (e.g. as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.

Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults

The multitude of barriers between the mouth and colon may eliminate swallowed oral bacteria. Ascertaining the presence of the same bacteria in the mouth and colon is methodologically challenging partly because 16S rRNA gene sequencing – the most commonly used method to characterize the human microbiota – has low confidence in taxonomic assignments deeper than genus for most bacteria. As different species of the same genus can have low-level variation across the same 16S rRNA gene region, shotgun sequencing is needed to identify a true overlap. We analyzed a curated, multi-cohort, shotgun metagenomic database with species-level taxonomy and clade-specific marker genes to fill this knowledge gap. Using 500 paired fecal/oral (4 oral sites) samples from 4 healthy adult cohorts, we found a minute overlap between the two niches. Comparing marker genes between paired oral and fecal samples with species-level overlap, the pattern of overlap in only 7 individuals was consistent with same-strain colonization. These findings argue against ectopic colonization of oral bacteria in the distal gut in healthy adults.

Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in Cornus florida (Cornaceae).

Understanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted. The flowering dogwood tree (Cornus florida L.), an ecologically important species in North America, is threatened by powdery mildew and dogwood anthracnose diseases, and knowledge of the microbial diversity harbored within genetically and environmental distinct populations of this species remains largely unknown. We conducted a metagenomics study utilizing the sequences of RAD-tag/genotype-by-sequence libraries from leaf tissues of C. florida to examine such host-fungus interactions across the dogwood's US range. We performed various combinations of alignments to both host and pathogen genomes to obtain filtered sets sequences for metagenomics analysis. Taxonomic assignments were determined on each filtered set of sequences, followed by estimation of microbial diversity and correlation to environment and host-genetic variation. Our data showed that microbial community composition significantly differed between visually healthy and diseased sites. Several microbial taxa known to interact with dogwood were identified from these sequences. We found no correlation between microbial diversity and relative abundances of sequences aligning to draft genomes of either pathogen causing powdery mildew or dogwood anthracnose. We found a significant relationship between differences of fungal communities and geographic distances of plant populations, suggesting roles of environments in shaping fungal communities in leaf tissues. Significant correlations between the genetic differentiation of plant samples and fungal community dissimilarity (beta diversity) were also observed in certain sets of our analyses-suggesting the possibility of a relationship between microbial community composition and plant genetic distance. This relationship persisted in significance even after controlling for significant effects of geographic-bioclimatic variation of microbial diversity. Our results suggest that both genetics and the environment play a significant role in shaping foliar fungal communities. Our findings underscore the power of leveraging hidden microbial sequences within datasets originally collected for plant genetic studies to understand plant-pathogen interactions.

Systematics and spatio-temporal evolutionary patterns of the flavopilosa group of Drosophila (Diptera, Drosophilidae).

The Drosophila flavopilosa group comprises morphologically cryptic species that are ecologically restricted to feeding, breeding and ovipositing on flowers of Cestrum and Sessea (Solanaceae). Previous studies confirmed the monophyly of the group and the success of DNA barcoding in identifying a subset of its species, but several others remain yet to be evaluated. Furthemore, the taxonomy of the group remains incomplete, with only nine of the 17 species assigned to subgroups. Here, we accessed the phylogenetic relationships and spatio-temporal evolutionary patterns of the flavopilosa group based on a mitochondrial and two nuclear genes, providing the first molecular support to the subdivision of the group and suggesting a new taxonomic scheme for its species. Barcoding proved to be an effective tool, as all species were reciprocally monophyletic and different analyses of species delimitation yielded congruent results. The close relationship of D. flavopilosa with D. cestri and D. cordeiroi was strongly supported, suggesting that the latter should be placed in the flavopilosa subgroup together with the first. Furthermore, D. mariaehelenae was positioned as sister to D. incompta, supporting its inclusion in the nesiota subgroup. Despite new taxonomic assignments, the synapomorphic status of the diagnostic characters proposed for both subgroups was supported. Based on them, each of the remaining species were placed into one of both subgroups. Divergence time estimates suggest that their diversification coincided with the divergence of Sessea and Cestrum, providing an interesting case of coevolution.

GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis.

Amplicon-based 16S ribosomal RNA sequencing remains a widely used method to profile microbial communities, especially in low biomass samples, due to its cost-effectiveness and low-complexity approach. Reference databases are a mainstay for taxonomic assignments, which typically rely on popular databases such as SILVA, Greengenes, Genome Taxonomy Database (GTDB), or Ribosomal Database Project (RDP). However, the inconsistency of the nomenclature across databases and the presence of shortcomings in the annotation of these databases are limiting the resolution of the analysis. To overcome these limitations, we created the GSR database (Greengenes, SILVA, and RDP database), an integrated and manually curated database for bacterial and archaeal 16S amplicon taxonomy analysis. Unlike previous integration approaches, this database creation pipeline includes a taxonomy unification step to ensure consistency in taxonomical annotations. The database was validated with three mock communities, two real data sets, and a 10-fold cross-validation method and compared with existing 16S databases such as Greengenes, Greengenes 2, GTDB, ITGDB, SILVA, RDP, and MetaSquare. Results showed that the GSR database enhances taxonomical annotations of 16S sequences, outperforming current 16S databases at the species level, based on the evaluation of the mock communities. This was confirmed by the 10-fold cross-validation, except for Greengenes 2. The GSR database is available for full-length 16S sequences and the most commonly used hypervariable regions: V4, V1-V3, V3-V4, and V3-V5.IMPORTANCETaxonomic assignments of microorganisms have long been hindered by inconsistent nomenclature and annotation issues in existing databases like SILVA, Greengenes, Greengenes2, Genome Taxonomy Database, or Ribosomal Database Project. To overcome these issues, we created Greengenes-SILVA-RDP database (GSR-DB), accurate and comprehensive taxonomic annotations of 16S amplicon data. Unlike previous approaches, our innovative pipeline includes a unique taxonomy unification step, ensuring consistent and reliable annotations. Our evaluation analyses showed that GSR-DB outperforms existing databases in providing species-level resolution, especially based on mock-community analysis, making it a game-changer for microbiome studies. Moreover, GSR-DB is designed to be accessible to researchers with limited computational resources, making it a powerful tool for scientists across the board. Available for full-length 16S sequences and commonly used hypervariable regions, including V4, V1-V3, V3-V4, and V3-V5, GSR-DB is a go-to database for robust and accurate microbial taxonomy analysis.

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria.

Plant-microbiome research plays a pivotal role in understanding the relationships between plants and their associated microbial communities, with implications for agriculture and ecosystem dynamics. Metabarcoding analysis on variable regions of the 16S ribosomal RNA (rRNA) gene remains the dominant technology to study microbiome diversity in this field. However, the choice of the targeted variable region might affect the outcome of the microbiome studies. In our in silico analysis, we have evaluated whether the targeted variable region has an impact on taxonomic resolution in 16 plant-related microbial genera. Through a comparison of 16S rRNA gene variable regions with whole-genome data, our findings suggest that the V1-V3 region is generally a more suitable option than the widely used V3-V4 region for targeting microbiome analysis in plant-related genera. However, sole reliance on one region could introduce detection biases for specific genera. Thus, we are suggesting that while transitioning to full-length 16S rRNA gene and whole-genome sequencing for plant-microbiome analysis, the usage of genus-specific variable regions can achieve more precise taxonomic assignments. More broadly, our approach provides a blueprint to identify the most discriminating variable regions of the 16S rRNA gene for genera of interest.

Current Estimates of Philippine Marine Mollusks Taxonomic Diversity

Mollusks are among the most diverse and the most threatened invertebrate groups, with high records of recent extinctions. Yet, the assessment of mollusk diversity and records in megadiverse countries such as the Philippines greatly needs synthesis and updating. Here, we report on the current taxonomic diversity of the Philippine mollusk. Comprehensive records of mollusks in the Philippines from published literature, accessible museum records, and online databases were compiled and checked with the World Register of Marine Species. A total of 64,898 Philippine mollusk records were compiled, comprised of 14,482 distinct species. Of these distinct species records of Philippine mollusk, 51% have accepted names in WoRMS, whereas 35.8% had taxonomic name changes; 1.5% had unaccepted names in WoRMS but with no accepted names either (e.g. taxon inquirendum, nomen dubium, etc), and 11.7% did not have exactly matched records in WoRMS. After checking all Philippine mollusks records against WoRMS, there were 8,066 mollusk species in the Philippines belonging to 1,991 genera within 423 families and 51 orders, representing all molluscan classes. A total of 7,085 (88%) of the species records were marine (6,953 or 86% were strictly marine species) belonging to 1,780 genera, 368 families, and 50 orders, also representing all mollusk classes. This current account is the most comprehensive we know to date, but it certainly is an underestimate, as not all possible resources are accessible. A systematic national-scale survey of Philippine mollusk diversity is needed to improve the current account and to fill the gaps in [1] taxonomic status verification, and [2] the IUCN and conservation status of many Philippine mollusk species (which, to date, 96% of all species have no IUCN assessments).

DNA barcoding reference libraries of Italian Plecoptera: a gap analysis

Plecoptera is a small order of aquatic insects that is considered one of the most endangered groups of insects due to increasingly altered freshwater ecosystems. Plecoptera nymphs can be challenging to identify at the species level because diagnostic characters for most species are lacking, while adults can be difficult to collect routinely given their short life span. Species identification by DNA barcoding is increasingly used as an alternative to morphological identification, but gaps and inaccuracies in reference databases needed for taxonomic assignment can undermine the utility of barcoding in real case studies. Here we aim to: i) quantify the number of Italian species of Plecoptera with barcodes from specimens collected worldwide and from Italy; ii) perform a regional assessment of DNA barcoding coverage; iii) calculate the intraspecific distance among available sequences to evaluate the potential presence of errors and cryptic species. As reference databases, we used both a non-curated database (BOLD) and a curated database (MIDORI2) to test the effect of sequence selection on the availability of reference sequences. We found that 67.6% and 51.8% of the Italian Plecoptera species were represented in BOLD and MIDORI2. Most of the available sequences were obtained from specimens collected outside Italy, with only 21.8% and 13.5% of the Italian species having sequences from specimens collected in Italy. Endemisms were poorly represented, and intraspecific distances for some species were high, which suggest cryptic diversity or erroneous assignments. Our results support the growing need to increase international cooperation among barcode initiatives and to promote the integration between molecular biologists and zoologists to exploit the full potential of DNA barcoding to protect biodiversity.

Dickyyuellaargentinensis a tentative new genus and species of Cardiochilinae (Hymenoptera, Braconidae) from the Neotropical region.

Dickyyuella Kang & Sharkey, gen. nov. is a novel addition to the microgastroid complex of Braconidae. Taxonomic assignment within this complex posed challenges initially due to the presence of putatively plesiomorphic characters. However, closer examination revealed affiliations with the microgastroid complex, supported by morphological features such as the location of spiracles on the first metasomal tergum and the absence of spiracles on the seventh metasomal tergum. Based on the following two morphological characters, the presence of an inverted Y-shaped groove on the first metasomal tergum and pectinate tarsal claws, Dickyyuella Kang & Sharkey, gen. nov. is tentatively placed within Cardiochilinae Ashmead, 1900 despite uncertainties surrounding phylogenetic relationships. This article provides the diagnosis of Dickyyuella Kang & Sharkey, gen. nov., the description of Dickyyuellaargentinensis Kang & Sharkey, sp. nov., and a discussion of the taxonomic placement of the new genus within the microgastroid complex.

Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases.

This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.

A DNA‐based evaluation of North American river otter diet with respect to fishes: Implications for the conservation of aquatic predators and their prey

Abstract The North American river otter Lontra canadensis was once widespread in North America but became extinct in the State of Indiana owing to habitat losses and unregulated trapping. However, following reintroduction, the population has expanded markedly since 1995, representing a notable conservation success story. The recent population growth has led to conflict with recreational angling groups who perceive otters as competitors. To investigate the extent of this competition, a DNA‐based study was conducted to determine whether material from the stomachs of trapper‐harvested otters could be used to identify fish prey species they had eaten. Representative specimens from 33 wild fish species were used as positive controls for DNA assays of otter prey. Mitochondrial DNA barcoding sequences generated from each fish species were used to develop a piscine barcoding assay to identify otter prey species. Fourteen otter carcasses were dissected, and multiple independent DNA extractions and mitochondrial sequencing reactions were performed on the prey bolus from each stomach. The sequences were analysed bioinformatically for taxonomic assignment to prey species. DNA evidence of nearly two dozen fish species, including species of recreational (e.g. bass) or conservation interest (darters) was found in the stomach material. This approach could help to determine the presence of prey species in otter diets, including those fish of conservation concern. That, in turn, would help to determine the best management options for conserving both otters and fish.

Trematode species diversity in the faucet snail, Bithynia tentaculata at the western edge of its native distribution, in Ireland.

Trematodes and their snail hosts have developed intimate parasite-host associations, with snails supporting a diverse and often species-specific trematode fauna. In the faucet snail, Bithynia tentaculata (Caenogastropoda, Littorinimorpha), a unique trematode fauna has been recorded recently. However, knowledge of the exact species identity, phylogenetic relationships, and geographical distribution remains limited as many of the species belong to groups with unclear or controversial taxonomical assignment. To contribute to our knowledge of the trematodes, we investigated the trematode fauna of B. tentaculata by examining a total of 556 snails from lakes in County Galway, Ireland. Using an integrative taxonomic approach including DNA sequence data analyses (28S rRNA gene, ITS1-5.8S-ITS2, ITS2, cox1, nad1) and morphological tools (taxonomical drawings and measurements), we identified nine trematode species of seven families, with seven species occurring as cercariae (Cyathocotyle prussica, Lecithodendrium linstowi, Lecithodendrium sp., Asymphylodora progenetica, Sphaerostoma bramae, Metorchis xanthosomus, and Notocotylus sp.) and three species occurring as metacercariae (A. progenetica, Parasymphylodora parasquamosa, and Sphaeridiotrema sp.). Except for S. bramae, all are new species records for Ireland and provide the most western distribution of these trematodes in Europe. The trematode species recorded are known to use a wide range of definitive hosts and have a wide geographical distribution; among them are species members of genera that are zoonotic (Metorchis) and pathogenic to wildlife (Cyathocotyle, Sphaeridiotrema, and Notocotylus). There remains an ongoing need for precise identification of the trematode species to ensure that wider ecological contexts are correctly understood and biodiversity and disease threats can be accurately evaluated.

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

AbstractEffective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA (eDNA) by metabarcoding holds promise to achieve this relatively easily. However, taxonomy‐focused eDNA surveys need suitable molecular reference data, which are often lacking, particularly at the species level and for remote locations. To evaluate the comparability of environmental DNA surveys and traditional surveys in a real‐life case study in a marine area of high conservation value, we conducted a biodiversity survey of the fish in remote and pristine Te Wāhipounamu/Fiordland (Aotearoa/New Zealand), incorporating multiple data sources. We compared eDNA‐derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as eDNA. We also cross‐referenced both eDNA and BRUV data against literature and the Ocean Biodiversity Information System (OBIS), with literature and OBIS data representing a summary of multiple traditional surveying approaches. In total, we found 116 fish species in our study area. Environmental DNA detected 43 species; however, only three of those species overlap with species known from the literature, OBIS, or our BRUV analyses. A total of 61 fish species were known from the region from the literature, while OBIS listed 28 species, and our BRUV analyses picked up 26 species. BRUV data coincided more strongly than eDNA data with literature and OBIS data. Twenty of the 26 species detected by BRUV were known from literature and OBIS. We argue that limitated DNA reference databases are the main cause of this discrepancy, and our results indicate that eDNA of rare and endangered species can be detected if matching reference data were available. Environmental DNA analyses can only identify species present among reference data and with relaxed taxonomic assignment parameters may converge on relatives of detected species if the actually existing species themselves are missing among reference data. However, the high number of species detected by our eDNA analyses confirms that eDNA could be a powerful tool for biodiversity surveys if suitable investments in local reference databases were made.

ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies.

In microbial community sequencing, involving bacterial ribosomal 16S rDNA or fungal ITS, the targeted genes are the basis for taxonomical assignment. The traditional bioinformatical procedure has for decades made use of a clustering protocol by which sequences are pooled into packages of shared percent identity, typically at 97%, to yield Operational Technical Units (OTUs). Progress in the data processing methods has however led to the possibility of minimizing technical sequencers errors, which were the main reason for the OTU choice, and to analyze instead the exact Amplicon Sequence Variants (ASV) which is a choice yielding much less agglomerated reads. We have tested the two procedures on the same 16S metabarcoded bacterial amplicons dataset encompassing a series of samples from 17 adjacent habitats, taken across a 700 meter-long transect of different ecological conditions unfolding in a gradient spanning from cropland, through meadows, forest and all successional transitions up to the seashore, within the same coastal area. This design allowed to scan a high biodiversity basin and to measure alpha, beta and gamma diversity of the area, to verify the effect of the bioinformatics on the same data as concerns the values of ten different ecological indexes and other parameters. Two levels of progressive OTUs clustering, (99% and 97%) were compared with the ASV data. The results showed that the OTUs clustering proportionally led to a marked underestimation of the ecological indicators values for species diversity and to a distorted behaviour of the dominance and evenness indexes with respect to the direct use of the ASV data. Multivariate ordination analyses resulted also sensitive in terms of tree topology and coherence. Overall, data support the view that reference-based OTU clustering carries several misleading disadvantageous biases, including the risk of missing novel taxa which are yet unreferenced in databases. Since its alternatives as de novo clustering have on the other hand drawbacks due to heavier computational demand and results comparability, especially for environmental studies which contain several yet uncharacterized species, the direct ASV based analysis, at least for prokaryotes, appears to warrant significand advantages in comparison to OTU clustering at every level of percent identity cutoff.

Названия растений в Словаре Академии Российской (1789–1794): источники и принципы лексикографирования

The 18th century was the time of dramatic transformations in various life spheres of the Russian Empire. Significant changes occurred in scientific knowledge as well. After founding the Academy of Sciences and creating botanical and apothecary gardens in St. Petersburg, Moscow, Astrakhan, and Tobolsk, scientific botany was being established and botanical terminology was being formed. In 1789-1794, the Dictionary of the Russian Academy (DRA) was published. It was the first academic dictionary, and many famous natural scientists of that time participated in its compilation. The project authors actively used their predecessors’ works. Since DRA was conceived as a normative dictionary, not all phytonyms could be included. A thorough discussion of the materials preceded the work on the explanatory part. The headwords selection was based on analogous tables. They contain approximately 55,000 headwords; more than 1,800 are plant names, names of plant parts (such as apple), and adjectives derived from them. In analogous tables, we find references to the travels by 1.1. Lepekhin, P.S. Pallas, and I.G. Gmelin. Many of these references are confirmed on addressing the sources. Depending on the volume, 30% to 70% phytonyms from the analogous tables were included in DRA. DRA entries describing flora and fauna are notable for their encyclopedic style and include Linnaean Latin taxonomic names. Researchers see the reason in the fact that these entries were taken from a natural science reference work - the Lexicon of Natural History, compiled by 1.1. Lepekhin at that time. DRA also included phytonyms from the works by S.P. Krasheninnikov. Synonymous names with various geographical or stylistic marks could be explained independently of each other in different dictionary entries or through references from one entry to another. In DRA, as in other lexicographic works, there are looped references and so-called “blind links” leading to non-existing dictionary entries. To find the denotation of a phytonym without interpretation, researchers often need to address other texts containing the lexemes of interest. We are especially grateful to the project participants M.M. Pirogovskaya, O.S. Belichenko, and G.A. Molkov for valuable comments. The authors declare no conflicts of interests.

Longitudinal Changes of Ocular Surface Microbiome in Patients Undergoing Hemopoietic Stem Cell Transplant (HSCT).

To evaluate changes in the ocular surface microbiome (OSM) between pre- and post-haemopoietic stem cell transplant (HSCT) in the same patient, and to assess the potential impact of these changes in ocular graft-versus-host disease (o)GVHD development. Lower fornix conjunctival swabs of 24 patients were obtained before and after HSCT and subjected to DNA extraction for amplification and sequencing of the V3-V4 regions of the bacterial 16S rRNA gene. The obtained reads were reconstructed, filtered, and clustered into zero-radius operational taxonomic units (zOTUs) at 97% identity level before taxonomic assignment, and biodiversity indexes were calculated. Transplant characteristics were recorded, and dry eye was diagnosed and staged 1-4 according to the Dry Eye WorkShop (DEWS) score. No significant difference in OSM alpha diversity between pre- and post-transplant was found. A significant difference in beta diversity was observed between patients with a DEWS score of 1 versus 3 (p = 0.035). Increased corneal damage between pre- and post-HSCT was significantly associated with a decrease in alpha diversity. The changes in OSM were not associated with oGVHD, nor with any transplant parameter. This preliminary study is the first study to analyse changes in the OSM before and after HSCT longitudinally. No trend in OSM biodiversity, microbial profile, or overall composition changes before and after HSCT was significant or associated with oGVHD onset. The great variability in the observed OSM profiles seems to suggest the absence of a patient-specific OSM "signature".

Identification of archaeological barley grains using geometric morphometrics and experimental charring

Barley is one of the main cereals found in archaeological sites in the north-western Mediterranean basin, over the last 8 millennia. Grains are preserved in archaeological sediments by charring after or before dehusking. Morphological criteria for distinguishing 2-row from 6-row barley, but also hulled barley from naked barley, can be affected by charring and this can complicate identification of barley subgroups. In the last decade, geometric morphometrics applied to uncharred barley grains has shown the possibility of identifying barley subgroups, but its applicability to archaeological remains still needs to be ascertained. We used 3985 raw and charred grains of 113 current varieties to (1) assess charring effects on the shape of barley caryopses, depending on their subgroup and whether they were charred husked or dehusked and (2) select the best dataset for identifying barley subgroups. We also used 700 archaeological grains, from the Neolithic period to the end of the Middle Ages, to (3) compare the morphometric taxonomic assignment of the grains with their carpological identification based on discrete anatomical features in a series of 7 archaeological samples. Our results indicate size and shape differences between barley grains when charred husked or dehusked. Although the charring process results in greater morphometric homogeneity, it allows subgroups of barley to be identified. For the 2-row vs. 6-row identification, more than 71% of the charred modern grains can be correctly identified. For the hulled vs. naked identification, the correct cross-validation percentages range from 70 to 73%. Finally, the good correlation between carpological and morphometric identifications of archaeological grains suggests that it is possible to identify archaeobotanical samples in the future.

The metaproteome of the gut microbiota in pediatric patients affected by COVID-19.

The gut microbiota (GM) play a significant role in the infectivity and severity of COVID-19 infection. However, the available literature primarily focuses on adult patients and it is known that the microbiota undergoes changes throughout the lifespan, with significant alterations occurring during infancy and subsequently stabilizing during adulthood. Moreover, children have exhibited milder symptoms of COVID-19 disease, which has been associated with the abundance of certain protective bacteria. Here, we examine the metaproteome of pediatric patients to uncover the biological mechanisms that underlie this protective effect of the GM. We performed nanoliquid chromatography coupled with tandem mass spectrometry on a high resolution analytical platform, resulting in label free quantification of bacterial protein groups (PGs), along with functional annotations via COG and KEGG databases by MetaLab-MAG. Additionally, taxonomic assignment was possible through the use of the lowest common ancestor algorithm provided by Unipept software. A COVID-19 GM functional dissimilarity respect to healthy subjects was identified by univariate analysis. The alteration in COVID-19 GM function is primarily based on bacterial pathways that predominantly involve metabolic processes, such as those related to tryptophan, butanoate, fatty acid, and bile acid biosynthesis, as well as antibiotic resistance and virulence. These findings highlight the mechanisms by which the pediatric GM could contribute to protection against the more severe manifestations of the disease in children. Uncovering these mechanisms can, therefore, have important implications in the discovery of novel adjuvant therapies for severe COVID-19.

The influence of databases enrichment using local macroinvertebrate genetic references for metabarcoding based biodiversity studies in river monitoring

Water resources play a vital role in sustaining ecosystems, human life, food security, and biodiversity. However, these resources currently face serious threats caused primarily by human activities. Because of that, European Union have mandated that all its member states monitor the ecological status of their water bodies. One of the most commonly used bioindicator groups for routine river biomonitoring is benthic macroinvertebrates, which rely mainly on morphological identification at the family level and the use of diverse indices to estimate the ecological status of the river ecosystem. The morphological approach has certain limitations, and metabarcoding is now considered an alternative technique for biodiversity studies and biomonitoring of surface waters. However, the efficacy of this approach depends on the comparison of sequencing data with genetic databases, which are often incomplete and geographically biased. In this study, we collected 92 macroinvertebrate samples from rivers in the northern Iberian Peninsula to identify all possible species and generate new DNA sequences for the COI-5P region. The objectives were to perform region-specific enrichment of reference databases for the geographical area of northern Spain and to assess the impact, before and after this strategy, on the taxonomic assignments used for ecological status inference in metabarcoding samples. The results showed that 21% of morphospecies lacked reference sequences in the BOLD or GenBank databases, indicating that a significant number of macroinvertebrate species in the northwestern Iberian Peninsula lack reference sequences in major genetic databases. Enriching the BOLD databases with new sequences led to the detection of an average of 17.25 more BINs (species-assimilable gene cluster) and 1.54 more IBMWP taxa (river ecological status indicator macroinvertebrate taxa) per sample, causing changes in the ecological status determination for 16% of the samples, which clearly shows that improving the databases with local species sequences could enhance the detection and identification of new IBMWP taxa, potentially impacting ecological status inference from molecular data. Additionally, a historical analysis of Iberian macroinvertebrate addition in the BOLD database using public BOLD records revealed an asymptotic trend that can be partially mitigated by region-specific enrichment. These results indicate that a local biota sequencing effort can considerably improve metabarcoding results rather than waiting for a gradual improvement of genetic databases. In conclusion, we advocate for a creation an Iberian freshwater macroinvertebrate checklist and then the initiation of a coordinated effort for sequencing any unsequenced species from the region.

Association of Root Biofilm Bacteriome with Root Caries Lesion Severity and Activity

Introduction: This research aimed to assess the association of root biofilm bacteriome with root caries lesion severity and activity in institutionalised Colombian elderlies and was conducted to gather data on the root caries bacteriome in this population. Methods: A bacteriome evaluation of biofilm samples from sound and carious root surfaces was performed. Root caries was categorised (ICDAS Root criteria) based on severity (sound surfaces, initial: non-cavitated, moderate/extensive combined: cavitated) and activity status (active and inactive). DNA was extracted and the V4 region of the 16S rRNA gene was sequenced; afterwards the classification of features was conducted employing amplicon sequence variants and taxonomic assignment via the Human Oral Microbiome Database (HOMD). Bacterial richness, diversity (Simpson’s and Shannon’s indices), and relative abundance estimation were assessed and compared based on root caries severity and activity status (including Sound surfaces). Results: A total of 130 biofilm samples were examined: sound (n = 45) and with root caries lesions (n = 85; by severity: initial: n = 41; moderate/extensive: n = 44; by activity: active: n = 60; inactive: n = 25). Species richness was significantly lower in biofilms from moderate/extensive and active groups compared to sound sites. There was a higher relative abundance of species like Lechtotricia wadei, Capnocytophaga granulosa, Cardiobacterium valvarum, Porphyromonas pasteri – in sound sites; Dialister invisus, Streptococcus mutans, Pseudoramibacter alactolyticus and Bacteroidetes (G-5) bacterium 511 – in moderate/extensive lesions, and Fusobacterium nucleatum subsp. animalis, Prevotella denticola, Lactobacillus fermentum, Saccharibacteria (TM7) (G-5)bacterium HMT 356 – in active lesions. Conclusion: Root caries bacteriome exhibited differences in species proportions between the compared groups. Specifically, cavitated caries lesions and active caries lesions showed higher relative abundance of acidogenic bacteria.