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Background Microgenderome or arguably more accurately microsexome refers to studies on sexual dimorphism of human microbiomes aimed at investigating bidirectional interactions between human microbiomes, sex hormones, and immune systems. It is important because of its implications to disease susceptibility and therapy, in which men and women demonstrate divergence in many diseases especially autoimmune diseases. In a previous report [1], we presented analyses of several key ecological aspects of microgenderome by leveraging the large datasets of the HMP (human microbiome project) but failed to offer species-level composition differences such as sexually unique species (US) and enriched species (ES). Existing approaches, for such tasks, including differential species relative abundance analysis and differential network analysis, possess certain limitations given that virtually all rely on species abundance alone or are univariate, while ignoring species distribution information across samples. Obviously, it is both species abundance and distribution that shape/drive the structure and dynamics of human microbiomes, and both should be equally responsible for the universal heterogeneity of microbiomes including the sexual dimorphism. Results Here, we fill the gap by taking advantages of a recently developed computational algorithm, species specificity, and specificity diversity (SSD) framework (refer to the companion article) to reanalyze the HMP and complementary seminovaginal microbiome datasets. The SSD framework can randomly search and catalogue the sexually specific unique/enriched species with statistical rigor, guided by species specificity (a synthetic metric of abundance and distribution) and specificity diversity (SD). The SSD framework reveals that men seem to have more unique species than women in their gut and reproductive system microbiomes, but women seem to have more unique species than men in the airway, oral, and skin microbiomes, which is likely due to sexual dimorphism in the hormone and immune systems. We further investigate co-dependency and heterogeneity of those sexually unique/enriched species across 15 body sites, with core/periphery network analyses. Conclusions This study not only produced sexually unique/enriched species in the human microbiomes and analyzed their codependency and heterogeneity but also further validated the robustness of the SSD framework presented in the companion article, by performing all negative control tests based on the HMP gut microbiome samples.

This review summarizes the information on biochemical and biological activity of the main Fusarium mycotoxins, focusing on toxicological aspects in terms of species-specific effects. Both in vitro and in vivo studies have centered on the peculiarity of the responses to mycotoxins, demonstrating that toxicokinetics, bioavailability and the mechanisms of action of these substances vary depending on the species involved, but additional studies are needed to better understand the specific responses. The aim of this review is to summarize the toxicological responses of the main species affected by Fusarium mycotoxins.

Background Differentiating the microbiome changes associated with diseases is challenging but critically important. Majority of existing efforts have been focused on a community level, but the discerning power of community or holistic metrics such as diversity analysis seems limited. This prompts many researchers to believe that the promise should be downward to species or even strain level—effectively and efficiently identifying unique or enriched species in diseased microbiomes with statistical rigor. Nevertheless, virtually, all species-level approaches such as differential abundance and differential network analysis methods exclusively rely on species abundances without considering species distribution information, while it can be said that distribution is equally, if not more, important than abundance in shaping the spatiotemporal heterogeneity of community compositions. Results Here, we fill the gap by developing a novel framework—species specificity and specificity diversity (SSD)—that synthesizes both abundance and distribution information to differentiate microbiomes, at both species and community scales, under different environmental gradients such as the healthy and diseased treatments. The proposed SSD framework consists of three essential elements. The first is species specificity (SS), a concept that reincarnates the traditional specialist-generalist continuum and is defined by Mariadassou et al. (Ecol Lett 18:974-82, 2015). The SS synthesizes a species’ local prevalence (distribution) and global abundance information and attaches specificity measure to each species in a specific habitat (e.g., healthy or diseased treatment). The second element is a new concept to introduce here, the (species) specificity diversity (SD), which is inspired by traditional species (abundance) diversity in community ecology and measures the diversity of specificity (a proxy for metacommunity heterogeneity, essentially) with Renyi’s entropy. The third element is a pair of statistical tests based on the principle of permutation tests. Conclusions The SSD framework can ( i ) identify and catalogue lists of unique species (US), significantly enriched species (ES) in each treatment based on SS and specificity permutation (SP) test and ( ii ) measure the holistic differences between assemblages (or treatments) based on SD and specificity diversity permutation (SDP) test. Both capacities can be enabling technologies for general comparative microbiome research including risk assessment, diagnosis, and treatment of microbiome-associated diseases.

Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.

1. Plant neighbours can strongly influence the interactions between herbivores and focal plants, for instance by providing food of different quality (consumptive effects) or by changing the behaviour and metabolism of the herbivore and the focal plant without being consumed (non-consumptive effects). Determining the species-specific contributions of consumptive and non-consumptive effects is important to understand the ecophysiological mechanisms which underlie neighbourhood effects. 2. We quantified the impact of nine different grassland plant species on the interaction between Taraxacum officinale and the root-feeding insect Melolontha melolontha. We investigated the contribution of consumptive and non-consumptive effects to the observed patterns, and evaluated the impact of neighbouring plants on the growth and physiology of T.officinale upon M.melolontha attack. 3. Melolontha melolontha growth was strongly affected by the presence of different neighbouring species. The three grass species increased larval growth when growing with T.officinale, with Poa pratensis having a synergistic effect in the mixture compared to both monocultures. The forb Centaurea stoebe reduced larval growth when growing with T.officinale or alone. The other five species had no measurable impact on larval performance. Based on these results, P.pratensis and C.stoebe were selected for further experiments. 4. Diet-mixing experiments showed that P.pratensis increased M.melolontha growth when offered together with T.officinale, while C.stoebe suppressed it. When feeding was restricted to artificial diet, larval growth was not changed by the presence of P.pratensis or C.stoebe. However, when feeding was restricted to T.officinale, larval growth was increased by both heterospecific neighbours. Biomass and primary metabolism of T.officinale under attack by M.melolontha was also altered by the presence of C.stoebe and P.pratensis. Together, these results show that consumptive and non-consumptive effects can explain the positive effect of P.pratensis. In contrast, the negative effect of C.stoebe is likely driven exclusively by intoxication. 5. Synthesis. The performed experiments suggest that different combinations of consumptive and non-consumptive effects are likely to contribute to the diversity of neighbourhood effects in nature. Furthermore, they show that neighbourhood effects are important factors in below-ground plant-insect interactions.

Invasive species threaten biodiversity globally, and invasive mammalian predators are particularly damaging, having contributed to considerable species decline and extinction. We provide a global metaanalysis of these impacts and reveal their full extent. Invasive predators are implicated in 87 bird, 45 mammal, and 10 reptile species extinctions—58% of these groups’ contemporary extinctions worldwide. These figures are likely underestimated because 23 critically endangered species that we assessed are classed as “possibly extinct.” Invasive mammalian predators endanger a further 596 species at risk of extinction, with cats, rodents, dogs, and pigs threatening the most species overall. Species most at risk from predators have high evolutionary distinctiveness and inhabit insular environments. Invasive mammalian predators are therefore important drivers of irreversible loss of phylogenetic diversity worldwide. That most impacted species are insular indicates that management of invasive predators on islands should be a global conservation priority. Understanding and mitigating the impact of invasive mammalian predators is essential for reducing the rate of global biodiversity loss.

The pattern of a few abundant species and many rarer species is a defining characteristic of communities worldwide. These abundant species are often referred to as dominant species. Yet, despite their importance, the term dominant species is poorly defined and often used to convey different information by different authors. Based on a review of historical and contemporary definitions we develop a synthetic definition of dominant species. This definition incorporates the relative local abundance of a species, its ubiquity across the landscape, and its impact on community and ecosystem properties. A meta-analysis of removal studies shows that the loss of species identified as dominant by authors can significantly impact ecosystem functioning and community structure. We recommend two metrics that can be used jointly to identify dominant species in a given community and provide a roadmap for future avenues of research on dominant species. In our review, we make the case that the identity and effects of dominant species on their environments are key to linking patterns of diversity to ecosystem function, including predicting impacts of species loss and other aspects of global change on ecosystems.

Societal Impact Statement Arbuscular mycorrhizal (AM) fungi support plant development by enhancing growth and resistance to pathogens through mycorrhiza‐induced resistance (MIR). However, the varying capacities of individual AM fungal species to induce MIR are not well‐understood, limiting their agricultural potential. This study reveals that specific AM fungal isolates differ in their ability to enhance tomato growth and reduce biomass losses due to Rhizoctonia solani infection, a major root pathogen. By identifying MIR‐effective fungal isolates and linking them to shifts in root‐associated chemical composition, we highlight potential to improve crop resilience and productivity, advancing agriculture by enabling more efficient use of AM fungi. Summary Mycorrhiza‐induced resistance (MIR) can increase plant resistance to pathogens, reducing disease symptoms and biomass losses. However, the beneficial effects of different arbuscular mycorrhizal (AM) fungal species vary greatly, and the mechanisms behind these differences are not well‐understood. This study investigates varying levels of MIR among AM fungal isolates and their impact on the plant root‐associated metabolome, examining the influence of AM fungi's functional diversity on plant growth, defence, and molecular patterns. Using phenotyping observations, we assessed temporal variation in growth responses of tomato plants inoculated with Rhizoctonia solani and four different AM fungal isolates from the Glomeraceae and Gigasporaceae families, comparing these responses to changes in the root‐associated metabolome. Our results show that most AM fungal isolates enhanced plant growth, with two out of four demonstrating MIR‐effective potential during symbiosis with tomatoes without trade‐offs. The effectiveness of MIR was reflected in variations in metabolomic profiles, with an increase in downregulated metabolomic compounds in effective species. This study enhances understanding of AM fungal species‐specific differences in growth‐related MIR responses in tomatoes and the roles of biochemistry, supporting findings that Glomeraceae species have better MIR abilities. Our results suggest greater MIR‐related biochemical capabilities within Glomeraceae compared to Gigasporaceae. Arbuscular mycorrhizal (AM) fungi support plant development by enhancing growth and resistance to pathogens through mycorrhiza‐induced resistance (MIR). However, the varying capacities of individual AM fungal species to induce MIR are not well‐understood, limiting their agricultural potential. This study reveals that specific AM fungal isolates differ in their ability to enhance tomato growth and reduce biomass losses due to Rhizoctonia solani infection, a major root pathogen. By identifying MIR‐effective fungal isolates and linking them to shifts in root‐associated chemical composition, we highlight potential to improve crop resilience and productivity, advancing agriculture by enabling more efficient use of AM fungi.

The search for traits associated with plant invasiveness has yielded contradictory results, in part because most previous studies have failed to recognize that different traits are important at different stages along the introduction–naturalization–invasion continuum. Here we show that across six different habitat types in temperate Central Europe, naturalized non-invasive species are functionally similar to native species occurring in the same habitat type, but invasive species are different as they occupy the edge of the plant functional trait space represented in each habitat. This pattern was driven mainly by the greater average height of invasive species. These results suggest that the primary determinant of successful establishment of alien species in resident plant communities is environmental filtering, which is expressed in similar trait distributions. However, to become invasive, established alien species need to be different enough to occupy novel niche space, i.e. the edge of trait space. Plant functional traits may help distinguish introduced species that will become invasive from those that do not. Here, Divíšek et al. show that functional profiles of naturalized plant species are similar to natives, while those of invasive plant species exist at the edge of the functional trait space.

Non-adrenergic prostate smooth muscle contractions may account for the limited effectiveness of α 1 -adrenoceptor antagonists, which are the first-line option for medical treatment of voiding symptoms suggestive of benign prostatic hyperplasia. In non-human prostates, purinergic agonists induce contractions reaching similar magnitudes as α 1 -adrenergic contractions. However, evidence for the human prostate is highly limited, and pointed to much weaker purinergic contractions. Here, we examined contractions of different purinergic agonists in human prostate tissues. Tissues were obtained from radical prostatectomy. Contractions were studied in an organ bath, and expression of purinergic receptors was studied by RT-PCR. Electric field stimulation (EFS)–induced contractions amounted to 104% of KCl-induced contractions (95% CI: 84–124%). From all tested agonists, only ATP induced concentration-dependent contractions, reaching an average maximum of 18% (12–24%) of KCl. Maximum tensions following application of other agonists averaged to 7.1% of KCl for α,β-methylene-ATP (1.8–12.4%), 3.9% for β,γ-methylene-ATP (2.0–5.4%), 3.1% for 2-methylthio-ATP (− 0.1–6.3%), and 5.1% for ATPγS (1.0–9.2%). Responses were not affected by the P2X antagonist NF023 or the P2Y antagonist PPADS. mRNA expression of P2X1-4 correlated with expression of a marker for catecholaminergic nerves, although neither ATP, NF023, nor PPADS changed EFS-induced contractions. Correlation between expression of receptors and the smooth muscle marker calponin was not observed. Our findings point to a low relevance of purinergic contractions in the human prostate, compared to other contractile stimuli in the human prostate and compared to purinergic contractions in non-human prostates. Purinergic contractions in the human prostate are not sensitive to NF023 or PPADS.