Taxonomic Changes Research Articles

The oral cavity and intestinal microbiome in children with functional constipation

Constipation is a widespread problem in paediatric practice, affecting almost 30% of children. One of the key causal factors of constipation may be disturbances in the homeostasis of the gastrointestinal microbiome. The aim of the study was to determine whether the oral and fecal microbiomes differ between children with and without constipation. A total of 91 children over three years of age were included in the study. Of these, 57 were qualified to a group with constipation, and 34 to a group without. The saliva and stool microbiomes were evaluated using 16S rRNA gene amplicon sequencing. Functional constipation was associated with characteristic bacterial taxa in the fecal microbiota. Statistically significant differences were found at the family level: Burkholderiaceae (q = 0.047), Christensenellaceae (q = 0.047), Chlostridiaceae (q = 0.047) were significantly less abundant in the constipation group, while the Tannerellaceae (q = 0.007) were more abundant. At the genus level, the significant differences were observed for rare genera, including Christensenellaceae r-7 (q = 2.88 × 10−2), Fusicatenibacter (q = 2.88 × 10−2), Parabacteroides (q = 1.63 × 10−2), Romboutsia (q = 3.19 × 10−2) and Subdoligranulum (q = 1.17 × 10−2). All of them were less abundant in children with constipation. With the exception of significant taxonomic changes affecting only feces, no differences were found in the alpha and beta diversity of feces and saliva. Children with functional constipation demonstrated significant differences in the abundance of specific bacteria in the stool microbiome compared to healthy children. It is possible that the rare genera identified in our study which were less abundant in the constipated patients (Christensellaceae r-7, Fusicatenibacter, Parabacteroides, Romboutsia and Subdoligranulum) may play a role in protection against constipation. No significant differences were observed between the two groups with regard to the saliva microbiome.

Reappraisal of the genus Visia (Batrachospermales, Rhodophyta) and proposal for a new genus and species

ABSTRACT The genus Visia is reappraised based on new morphological and molecular data (rbcL and COI-5P sequences), from recently collected and previously studied materials, resulting in the need for several taxonomic changes. Based on our phylogeny and sequence divergence, the genus Visioidea gen. nov. is proposed for two samples from Brazil, forming a distinct clade that is morphologically undistinguishable from the generitype of Visia (V. cayennensis). Two lineages of Visia with high genetic divergences from other species are proposed as new species: 1) V. verviridis sp. nov. from Australia; 2) V. amazonensis sp. nov. from Brazil. Although genetically distinct, both species are morphologically very similar to V. cayennensis. A new record of V. cylindrocellularis was found in Australia, expanding the geographic distribution and the morphometric ranges for this species. The number of species currently recognized in Visia is now six, four with DNA sequence data and two identified based solely on morphology (V. longiarticulata and V. turgida). Cryptic genera within the order Batrachospermales were not recognised until recently with the proposals of Volatus, morphologically indistinct from Kumanoa, and Macrosporophycos undistinguishable from Montagnia and here a third cryptic genus Visioidea is described.

Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study

Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.

Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host–microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

Supplement to the Rubiaceae in the Flora dos Estados de Goiás e Tocantins, Brazil: Nomenclatural revision, typifications, new records, new identifications, and new combinations

The contribution of the family Rubiaceae for the Flora dos Estados de Goiás e Tocantins – Coleção Rizzo (FGT), published in November 2010, includes the treatment of 61 genera and 245 species. Nomenclatural types were cited in various ways, depending on the information and photographs available to the author before 2008. For numerous names, lectotype designations were not accompanied by “here designated” or a similar expression, which is required by the Internation Code of Nomenclature starting from 1 January 2001, therefore those designations are not valid. Also, the barcodes of type specimens were not cited in that treatment, because at that time, it was not common practice to cite that information, especially in floristic treatments, and also because barcodes were not yet assigned to specimens in many herbaria. The type citations are here corrected, type citations correctly cited with additional information added, and designate lectotypes or neotypes of names that still need to be designated, are deginated. A total of 81 lectotypifications and 11 neotypifications are here presented. A list of names newly typified is available in Appendix 1. Updates of the taxonomic and systematic changes that occurred during the last 15 years, are provided. Major changes regarding generic delimitations, mostly in the tribes Palicoureeae, Psychotriae, and Spermacoceeae, have recently been proposed, and numerous new combinations have recently been published by several authors, which are here included. Following those recent generic rearragements, three new combinations in Palicourea are here published, namely P. leiocarpa, P. stachyoides, and P. subtriflora.

Nomenclatural problems raised by the recent description of a new anaconda species (Squamata, Serpentes, Boidae), with a nomenclatural review of the genus Eunectes

A recent paper proposing taxonomic changes in the South American snake genus Eunectes Wagler, 1830 (anacondas) is analysed. This paper raises an unusually high number of taxonomic and nomenclatural problems. The work does not rely on an explicit species concept, the analysis of the molecular data based on three mitochondrial genes is shown to be unreliable, and the validity of the ‘clades’ proposed in this work is questioned. The nomen proposed for a purported new species is a nomen nudum (nomenclaturally unavailable), and the designation of a ‘lectotype’ for the nominal species Eunectes murinus (Linnaeus, 1758) is invalid. We provide a review of the nomenclatural status of 18 nominal species (including four unavailable ones) once or still now referred to the genus Eunectes, we identify their ‘types’ (nomen-bearing specimens), we designate five lectotypes, which are all specimens figured and briefly described in ancient publications, and we explain the rationale behind this action, which will allow the subsequent designation as neotypes of recently collected specimens associated with precise type localities and molecular data. We show that the generic nomen Eunectes Wagler, 1830 does not apply to the taxonomic genus accommodating anacondas but, this nomen having been used for these giant and spectacular snakes for about 200 years and being well-known even outside the field of taxonomy, we argue that its traditional use should be maintained through an action of the International Commission of Zoological Nomenclature using its plenary power. Finally, we provide various recommendations regarding nomenclatural actions and publications presenting them.
  

How taxonomic change influences forecasts of the Linnean shortfall (and what we can do about it)?

AbstractThe gap between the number of described species and the number of species that actually exist is known as the Linnean shortfall and is of fundamental importance for biogeography and conservation. Unsurprisingly, there have been many attempts to quantify its extent for different taxa and regions. In this Perspective, we argue that such forecasts remain highly problematic because the extent of the shortfall does depend not only on the rates of exploration (sampling undescribed taxa) on which estimates have been commonly based but also on the rates of taxonomic change (lumping and splitting). These changes highly depend on the species concepts adopted and the information and methods used to delimit species. Commonly used methods of estimating the number of unknown species (e.g. discovery curves, taxon ratios) can underestimate or overestimate the Linnean shortfall if they do not effectively account for trends and rates of taxonomic change. A further complication is that the history of taxonomic change is not well documented for most taxa and is not typically available in biodiversity databases. Moreover, wide geographic and taxonomic variation in the adoption of species concepts and delimitation methods mean that comparison of estimates of the Linnean shortfall between taxa and even for the same taxon between regions may be unreliable. Given the high likelihood of future taxonomic changes for most major taxa, we propose two main strategies to consider the influence of taxonomic change on estimates of unknown species: (i) a highly conservative approach to estimating the Linnean shortfall, restricting analysis to groups and regions where taxonomies are relatively stable and (ii) explicitly incorporating metrics of taxonomic change into biodiversity models and estimates. In short, relevant estimates of the number of known and unknown species will only be achieved by accounting for the dynamic nature of the taxonomic process itself.

ЗООКОМПОНЕНТ ОБЪЁМНЫХ ФРАГМЕНТОВ БИОГЕОЦЕНОЗОВ В ЭКСПОЗИЦИИ МУЗЕЯ ЗЕМЛЕВЕДЕНИЯ МГУ

The exposition of the department "Natural Zones" in the Earth Science Museum of Moscow State University (25th floor, halls Nos 18-20) presents 15 full-scale exhibits of dry 3D fragments of biogeocenoses, namely: spotted tundra; forest tundra; swamps: flat-hummocky tundra, oligotrophic upland and mesotrophic lowland sedge; sprucegreen grass; grass-grass and tipchak-grass steppes; subtropical mountain forest; alpine meadows; semi-deserts; deserts - clay, wormwood-solyanka and ilak belosaksaulnik on ridge sands; and savannas. These exhibits demonstrate the interaction of the main natural components characteristic of the respective climatic conditions (soils, flora, and fauna). The article gives a description of the animal species represented in the exposition based on a visual examination of zoological exhibits and a study of their nomenclature and taxonomic changes.

Changes in Bacterial Gut Composition in Parkinson's Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach.

Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease with the major symptoms comprising loss of movement coordination (motor dysfunction) and non-motor dysfunction, including gastrointestinal symptoms. Alterations in the gut microbiota composition have been reported in PD patients vs. controls. However, it is still unclear how these compositional changes contribute to disease etiology and progression. Furthermore, most of the available studies have focused on European, Asian, and North American cohorts, but the microbiomes of PD patients in Latin America have not been characterized. To address this problem, we obtained fecal samples from Colombian participants (n = 25 controls, n = 25 PD idiopathic cases) to characterize the taxonomical community changes during disease via 16S rRNA gene sequencing. An analysis of differential composition, diversity, and personalized computational modeling was carried out, given the fecal bacterial composition and diet of each participant. We found three metabolites that differed in dietary habits between PD patients and controls: carbohydrates, trans fatty acids, and potassium. We identified six genera that changed significantly in their relative abundance between PD patients and controls, belonging to the families Lachnospiraceae, Lactobacillaceae, Verrucomicrobioaceae, Peptostreptococcaceae, and Streptococcaceae. Furthermore, personalized metabolic modeling of the gut microbiome revealed changes in the predicted production of seven metabolites (Indole, tryptophan, fructose, phenylacetic acid, myristic acid, 3-Methyl-2-oxovaleric acid, and N-Acetylneuraminic acid). These metabolites are associated with the metabolism of aromatic amino acids and their consumption in the diet. Therefore, this research suggests that each individual's diet and intestinal composition could affect host metabolism. Furthermore, these findings open the door to the study of microbiome-host interactions and allow us to contribute to personalized medicine.

Butyric Acid Supplementation Reduces Changes in the Taxonomic and Functional Composition of Gut Microbiota Caused by H. pylori Eradication Therapy.

Twenty two H. pylori-positive patients, aged 19 to 64 years, were enrolled in the study and randomized into two treatment groups, as follows: (1) ECAB-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, per os, for 14 days, and (2), ECAB-Z-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, along with butyric acid+inulin (Zacofalk), two tablets daily, each containing 250 mg of butyric acid, and 250 mg of inulin, per os, for 14 days. Fecal samples were collected from each subject prior to eradication therapy (time point I), after the end of eradication therapy (time point II), and a month after the end of eradication therapy (time point III). The total DNA from the fecal samples was isolated for whole genome sequencing using the Illumina NextSeq 500 platform. Qualitative and quantitative changes in gut microbiota were assessed, including alpha and beta diversity, functional potential and antibiotic resistance gene profiling. Gut microbiota alpha diversity significantly decreased compared with the baseline immediately after eradication therapy in both treatment groups (ECAB-14 and ECAB-Z-14). This diversity reached its baseline in the ECAB-Z-14 treatment group a month after the end of eradication therapy. However, in the ECAB-14 treatment arm, a reduction in the Shannon index was observed up to a month after the end of H. pylori eradication therapy. Fewer alterations in the gut microbiota functional potential were observed in the ECAB-Z-14 treatment group. The abundance of genes responsible for the metabolic pathway associated with butyrate production decreased only in the ECAB-14 treatment group. The prevalence of antibiotic-resistant genes in the gut microbiota increased significantly in both treatment groups by the end of treatment. However, more severe alterations were noted in the ECAB-14 treatment group. H. pylori eradication therapy leads to taxonomic changes, a reduction in the alpha diversity index, and alterations in the functional potential of the gut microbiota and gut resistome. Taking butyric acid+inulin supplements during H. pylori eradication therapy could help maintain the gut microbiota in its initial state and facilitate its recovery after H. pylori eradication.

Особенности микробиоты кишечника у женщин с идиопатическим привычным выкидышем

Currently, researchers show considerable interest in the link between gut microbiota and idiopathic recurrent miscarriage (IRM). This study aimed to analyze taxonomic changes of gut microbiota and assess its relationship with plasma levels of cortisol, melatonin, TNFa and IL17 in women with IRM. We invited 55 women with IRM and 60 women with normal pregnancy, studied their gut microbiota, and registered serum concentrations of cortisol, melatonin, TNFa and IL17. Women with IRM had changed gut microbiota: significantly decreased — diversity (Chao1 p = 0.014), significantly decreased abundance of Bifidobacterium (p < 0.001), Lachnospira (p = 0.032), Roseburia (p = 0.003), Coprococcus (p = 0.012), and significantly increased abundance of Ruminococcus (p < 0.001) and Klebsiella (p = 0.002). We have shown a statistically significant relationship between cortisol level and abundance of Lachnospira (r = –0.51; p = 0.002), melatonin level and abundance of Coprococcus (r = –0.49; p = 0.012), and identified connections between TNF and IL17 concentrations and Chao1 index (r = –0.51; p = 0.002, r = –0.54; p = 0.001, respectively), TNF concentration and abundance of Ruminococcus (r = 0.51; p = 0.002), IL17 concentration and abundance of Bifidobacterium (r = –0.52; p = 0.001). Modulation of gut microbiota may have preventive and therapeutic effects in women with IRM.

Late Cenozoic Faunal and Ecological Change in Africa

Africa's fossil record of late Cenozoic mammals documents considerable ecological and evolutionary changes through time. Here, we synthesize those changes in the context of the mechanisms proposed to account for them, including bottom-up (e.g., climate change) and top-down (e.g., hominin impacts) processes. In doing so, we ( a) examine how the incompleteness of the fossil record and the varied spatiotemporal scales of the evidence complicate efforts to establish cause-effect relationships; ( b) evaluate hypothesized drivers of long-term ecological and evolutionary change, highlighting key unknowns; and ( c) synthesize major taxonomic and functional trends through time (e.g., downsizing of faunal communities) considering the proposed drivers. Throughout our review, we point to unresolved questions and highlight research avenues that have potential to inform on the processes that have shaped the history of what are today the most diverse remaining large mammal communities on Earth. ▪ The study of late Cenozoic African mammal communities is intertwined with questions about the context, causes, and consequences of hominin evolution. ▪ The fossil record documents major functional (e.g., loss of megaherbivores) and taxonomic (e.g., rise of the Bovidae) changes over the past ∼7 Myr. ▪ Complexities inherent to the fossil record have made it difficult to identify the processes that drove ecological and evolutionary changes. ▪ Unanswered questions about the drivers of faunal change and the functioning of past ecosystems represent promising future research directions. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 52 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Subchronic inhalation exposure to ultrafine particulate matter alters the intestinal microbiome in various mouse models

Exposure to ultrafine particles (UFPs) has been associated with multiple adverse health effects. Inhaled UFPs could reach the gastrointestinal tract and influence the composition of the gut microbiome. We have previously shown that oral ingestion of UFPs alters the gut microbiome and promotes intestinal inflammation in hyperlipidemic Ldlr−/− mice. Particulate matter (PM)2.5 inhalation studies have also demonstrated microbiome shifts in normolipidemic C57BL/6 mice. However, it is not known whether changes in microbiome precede or follow inflammatory effects in the intestinal mucosa. We hypothesized that inhaled UFPs modulate the gut microbiome prior to the development of intestinal inflammation. We studied the effects of UFP inhalation on the gut microbiome and intestinal mucosa in two hyperlipidemic mouse models (ApoE−/− mice and Ldlr−/− mice) and normolipidemic C57BL/6 mice. Mice were exposed to PM in the ultrafine-size range by inhalation for 6 h a day, 3 times a week for 10 weeks at a concentration of 300–350 μg/m3.16S rRNA gene sequencing was performed to characterize sequential changes in the fecal microbiome during exposures, and changes in the intestinal microbiome at the end. PM exposure led to progressive differentiation of the microbiota over time, associated with increased fecal microbial richness and evenness, altered microbial composition, and differentially abundant microbes by week 10 depending on the mouse model. Cross-sectional analysis of the small intestinal microbiome at week 10 showed significant changes in α-diversity, β-diversity, and abundances of individual microbial taxa in the two hyperlipidemic models. These alterations of the intestinal microbiome were not accompanied, and therefore could not be caused, by increased intestinal inflammation as determined by histological analysis of small and large intestine, cytokine gene expression, and levels of fecal lipocalin. In conclusion, 10-week inhalation exposures to UFPs induced taxonomic changes in the microbiome of various animal models in the absence of intestinal inflammation.

Identification of taxonomic changes in the fecal bacteriome associated with colorectal polyps and cancer: potential biomarkers for early diagnosis.

Colorectal cancer (CRC) commonly arises in individuals with premalignant colon lesions known as polyps, with both conditions being influenced by gut microbiota. Host-related factors and inherent characteristics of polyps and tumors may contribute to microbiome variability, potentially acting as confounding factors in the discovery of taxonomic biomarkers for both conditions. In this study we employed shotgun metagenomics to analyze the taxonomic diversity of bacteria present in fecal samples of 90 clinical subjects (comprising 30 CRC patients, 30 with polyps and 30 controls). Our findings revealed a decrease in taxonomic richness among individuals with polyps and CRC, with significant dissimilarities observed among the study groups. We identified significant alterations in the abundance of specific taxa associated with polyps (Streptococcaceae, Lachnoclostridium, and Ralstonia) and CRC (Lactobacillales, Clostridiaceae, Desulfovibrio, SFB, Ruminococcus, and Faecalibacterium). Clostridiaceae exhibited significantly lower abundance in the early stages of CRC. Additionally, our study revealed a positive co-occurrence among underrepresented genera in CRC, while demonstrating a negative co-occurrence between Faecalibacterium and Desulfovibrio, suggesting potential antagonistic relationships. Moreover, we observed variations in taxonomic richness and/or abundance within the polyp and CRC bacteriome linked to polyp size, tumor stage, dyslipidemia, diabetes with metformin use, sex, age, and family history of CRC. These findings provide potential new biomarkers to enhance early CRC diagnosis while also demonstrating how intrinsic host factors contribute to establishing a heterogeneous microbiome in patients with CRC and polyps.

A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade.

Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.

Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis.

Factors such as the Andean uplift, Isthmus of Panama, and climate changes have influenced bird diversity in the Neotropical region. Studying bird species that are widespread in Neotropical highlands and lowlands can help us understand the impact of these factors on taxa diversification. Our main objectives were to determine the biogeographic factors that contributed to the diversification of Euphoniinae and re-evaluate their phylogenetic relationships. The nextRAD and mitochondrial data were utilized to construct phylogenies. The ancestral distribution range was then estimated using a time-calibrated phylogeny, current species ranges, and neotropical regionalization. The phylogenies revealed two main Euphoniinae clades, Chlorophonia and Euphonia, similar to previous findings. Furthermore, each genus has distinctive subclades corresponding to morphology and geography. The biogeographic results suggest that the Andean uplift and the establishment of the western Amazon drove the vicariance of Chlorophonia and Euphonia during the Miocene. The Chlorophonia lineage originated in the Andes mountains and spread to Central America and the Mesoamerican highlands after the formation of the Isthmus of Panama. Meanwhile, the ancestral area of Euphonia was the Amazonas, from which it spread to trans-Andean areas during the Pliocene and Pleistocene due to the separation of the west lowlands from Amazonas due to the Northern Andean uplift. Chlorophonia and Euphonia species migrated to the Atlantic Forest during the Pleistocene through corridors from the East Andean Humid Forest and Amazonas. These two genera had Caribbean invasions with distinct geographic origins and ages. Finally, we suggested taxonomic changes in the genus Euphonia based on the study's phylogenetic, morphological, and biogeographic findings.

Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation.

Host-associated microbiomes can play key roles in the metamorphosis of animals. Most scyphozoan jellyfish undergo strobilation in their life cycles, similar to metamorphosis in classic bilaterians. The exploration of jellyfish microbiomes may elucidate the ancestral mechanisms and evolutionary trajectories of metazoan-microbe associations and interactions during metamorphosis. However, current knowledge of the functional features of jellyfish microbiomes remains limited. Here, we performed a genome-centric analysis of associated microbiota across four successive life stages (polyp, early strobila, advanced strobila, and ephyra) during strobilation in the common jellyfish Aurelia coerulea. We observed shifts in taxonomic and functional diversity of microbiomes across distinct stages and proposed that the low microbial diversity in ephyra stage may be correlated with the high expression of the host-derived antimicrobial peptide aurelin. Furthermore, we recovered 43 high-quality metagenome-assembled genomes and determined the nutritional potential of the dominant Vibrio members. Interestingly, we observed increased abundances of genes related to the biosynthesis of amino acids, vitamins, and cofactors, as well as carbon fixation during the loss of host feeding ability, indicating the functional potential of Aurelia-associated microbiota to support the synthesis of essential nutrients. We also identified several potential mechanisms by which jellyfish-associated microbes establish stage-specific community structures and maintain stable colonization in dynamic host environments, including eukaryotic-like protein production, bacterial secretion systems, restriction-modification systems, and clustered regularly interspaced short palindromic repeats-Cas systems. Our study characterizes unique taxonomic and functional changes in jellyfish microbiomes during strobilation and provides foundations for uncovering the ancestral mechanism of host-microbe interactions during metamorphosis.

Functional host-specific adaptation of the intestinal microbiome in hominids

Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.

Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade

The class Myxomycetes consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, andplasmodia). Withinit, theorder Physarales, with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some keyspecies, itprevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded data setinterms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, EF-1α , α-Tub, and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family Didymiaceae is paraphyletic to the rest of Physarales. Within Didymiaceae s. lat., the recent reinstatement of the genus Polyschismium for most species traditionally ascribed to Lepidoderma, except for the type (Ronikieretal.2022), is further supported here, as well as the definite inclusion of the genus Mucilago in Didymium and Lepidoderma s. str.(L. tigrinum) in Diderma (Prikhodkoetal.2023). Additionally, thegenus Diachea is redefined to include some species previously treated in Physaraceae (Craterium spp. with true columella). Within the monophyletic family Physaraceae, most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within Physaraceae prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level:1) a new genus, Nannengaella, is proposed for a major clade containing Physarum globuliferum and other species with heavily calcified sporophores and, often, a true calcareous columella;2) Lignydium is resurrected for the clade containing Fuligo muscorum. Additionally, Trichamphora is suggested as the correct name for the clade containing Physarum pezizoideum. The taxonomy and nomenclature of some provisional genera, currently synonymous with Fuligo and Physarum, are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. Aprovisional key to the genera of the order is also provided.

Revision of the genus Ultragryllacris (Orthoptera: Stenopelmatidae: Gryllacridinae), with description of new species.

The genus Ultragryllacris was revised. All its species and subspecies, including U. jiaranaisakuli sp. nov., U. chandra sp. nov. from Western Thailand and U. intermediata sp. nov. from Northern Thailand are here described and redescribed. They are known from Thailand and China. The new species differs from all the other representatives of this genus mainly in different body coloration, shape of projection of male 9th abdominal tergite and sclerotized area of female subgenital plate. The following taxonomical changes are also proposed: U. pulchra alboclypeata Gorochov et Dawwrueng, 2015, U. p. nan Ingrisch, 2018 and U. p. rubricapitis Bin et Bian, 2021 are raised to species status (U. alboclypeata stat. nov., U. nan stat. nov. and U. rubricapitis stat. nov.) due to some characteristic structures in both male and female; U. triangula Ingrisch, 2018 is downgraded to subspecies of U. alboclypeata (U. a. triangula stat. nov.). Previously unknown male of U. a. alboclypeata and female of U. nan are described. A key to all known species is given.