The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands.

Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialization to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to 1) quantitatively delimit the different cheliceral morphotypes present in the archipelago, 2) test their association with trophic specialization, as reported for continental species, 3) reconstruct the evolution of these ecomorphs throughout the diversification of the group, 4) test the hypothesis of convergent evolution of the different morphotypes, and 5) examine whether specialization constitutes a case of evolutionary irreversibility in this group. We show the existence of 9 cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.

Effect of the addition of 4OHE2 and quercetin in culture media on ROS levels and gene expression in mouse blastocysts.

AIMS: The main objective of this work is to elucidate whether Quercetin (Qc) and 4-Hidroxistradiol (4OHE2 ) decrease the level of reactive oxygen species (ROS) in in vitro obtained embryos and to analyse which genes are activated under the treatments that could explain this improvement. METHODS: Oxidative stress was induced during embryo culture by H2 O2 treatment and ROS production was measured and compared with embryos treated with Qc or 4OHE2 . Gene expression was analysed by Q-PCR in control embryos obtained in utero (IU) or by IVF and compared with the levels found in embryos cultured with Qc or 4OHE2 to determine the effect of these compounds. KEY RESULTS: Qc strongly reduces ROS levels in embryos after a treatment of 4h. On the contrary, 4OHE2 had no effect in reducing ROS levels in embryos. The addition of these molecules to the culture media upregulate several hypoxia-related genes when Qc is added to the culture media, and implantation-related genes when 4OHE2 is used. CONCLUSIONS: Qc is a very strong antioxidant molecule that when used for short periods of time during culture can reduce ROS levels and improve embryo quality by activating antioxidant enzymes. 4OHE2 supplementation, despite having no effects in reducing ROS levels, acts directly in the molecular signalling implicated in the implantation process and could be also considered as a supplement for embryo culture during IVF. IMPLICATIONS: Proper supplementation of the culture media could greatly improve the quality of embryos cultured in vitro , resulting in better results in IVF clinics.

Global response of conservationists across mass media likely constrained bat persecution due to COVID-19.

Most people lack direct experience with wildlife and form their risk perception primarily on information provided by the media. The way the media frames news may substantially shape public risk perception, promoting or discouraging public tolerance towards wildlife. At the onset of the COVID-19 pandemic, bats were suggested as the most plausible reservoir of the virus, and this became a recurrent topic in media reports, potentially strengthening a negative view of this ecologically important group. We investigated how media framed bats and bat-associated diseases before and during the COVID-19 pandemic by assessing the content of 2651 online reports published across 26 countries, to understand how and how quickly worldwide media may have affected the perception of bats. We show that the overabundance of poorly contextualized reports on bat-associated diseases likely increased the persecution towards bats immediately after the COVID-19 outbreak. However, the subsequent interventions of different conservation communication initiatives allowed pro-conservation messages to resonate across the global media, likely stemming an increase in bat persecution. Our results highlight the modus operandi of the global media regarding topical biodiversity issues, which has broad implications for species conservation. Knowing how the media acts is pivotal for anticipating the propagation of (mis)information and negative feelings towards wildlife. Working together with journalists by engaging in dialogue and exchanging experiences should be central in future conservation management.

4-Hydroxyestradiol improves mouse embryo quality, epidermal growth factor-binding capability in vitro and implantation rates.

Embryo implantation in the uterus is a critical step to achieve success following ART. Despite favorable uterine conditions, a great number of good quality embryos fail to implant, often for reasons that are unknown. Hence, improving the implantation potential of embryos is a subject of great interest. 4-Hydroxyestradiol (4-OH-E2), a metabolic product of estradiol produced by endometrial cells, plays a key role in endometrial-embryonic interactions that are necessary for implantation. Nonetheless, the effects of 4-OH-E2 on embryos obtained in vitro have not been yet described. This study was designed to determine whether culture media enriched in 4-OH-E2 could improve the quality and implantation rate of embryos obtained in vitro, using both in vitro and in vivo models. We also analyzed its effects on the epidermal growth factor (EGF)-binding capability of the embryos. Our results showed that the presence of 4-OH-E2 in the culture media of embryos during the morula to blastocyst transition increases embryo quality and attachment to endometrial cells in vitro. 4-OH-E2 can also improve viable pregnancy rates of mouse embryos produced in vitro, reaching success rates that are similar to those from embryos obtained directly from the uterus. 4-OH-E2 improved the embryos' ability to bind EGF, which could be responsible for the increased embryo implantation potential observed. Therefore, our results strongly suggest that 4-OH-E2 is a strong candidate molecule to supplement human IVF culture media in order to improve embryo implantation. However, further research is required before these findings can be translated with efficacy and safety to fertility clinics.

Telemedicine in the face of the COVID-19 pandemic.

The novel coronavirus SARS-CoV-2 is a positive single-stranded RNA virus that can be immediately translated and integrated into the host cell with its own RNA messenger, facilitating replication inside the cell and infectivity. The rapid progression of the disease presents a real challenge for the whole world. As the usual capacity for citizen care is exceeded, health professionals and governments struggle. One of the most important strategies to reduce and mitigate the advance of the epidemic are social distance measures; this is where telemedicine can help, and provide support to the healthcare systems, especially in the areas of public health, prevention and clinical practices, just as it is doing in others sectors. Telemedicine connects the convenience, low cost, and ready accessibility of health-related information and communication using the Internet and associated technologies. Telemedicine during the coronavirus epidemic has been the doctors' first line of defense to slow the spread of the coronavirus, keeping social distancing and providing services by phone or videoconferencing for mild to focus personal care and limited supplies to the most urgent cases.

Extracellular vesicles derived from endometrial human mesenchymal stem cells enhance embryo yield and quality in an aged murine model†.

Advanced age is a risk factor undermining women's fertility. Hence, the optimization of assisted reproduction techniques is an interdisciplinary challenge that requires the improvement of in vitro culture systems. Here, we hypothesize that supplementation of embryo culture medium with extracellular vesicles from endometrial-derived mesenchymal stem cells (EV-endMSCs) may have a positive impact on the embryo competence of aged oocytes. In this work, 24 weeks old B6D2 female mice were used as egg donors and in vitro fertilization assays were performed using males from the same strain (8-12 weeks); the presumptive zygotes were incubated in the presence of 0, 10, 20, 40, or 80 µg/ml of EV-endMSCs. The results from the proteomic analysis of EV-endMSCs and the classification by Reactome pathways allowed us to identify proteins closely related with the fertilization process. Moreover, in our aged murine model, the supplementation of the embryo culture medium with EV-endMSCs improved the developmental competence of the embryos as well as the total blastomere count. Finally, gene expression analysis of murine blastocysts showed significant changes on core genes related to cellular response to oxidative stress, metabolism, placentation, and trophectoderm/inner cell mass formation. In summary, we demonstrate that EV-endMSCs increase the quality of the embryos, and according to proteomic and genomic analysis, presumably by modulating the expression of antioxidant enzymes and promoting pluripotent activity. Therefore, EV-endMSCs could be a valuable tool in human assisted reproduction improving the developmental competence of aged oocytes and increasing the odds of implantation and subsequent delivery.

Chance and predictability in evolution: The genomic basis of convergent dietary specializations in an adaptive radiation.

The coexistence of multiple eco-phenotypes in independently assembled communities makes island adaptive radiations the ideal framework to test convergence and parallelism in evolution. In the radiation of the spider genus Dysdera in the Canary Islands, species diversification occurs concomitant with repeated events of trophic specialization. These dietary shifts, to feed primarily on woodlice, are accompanied by modifications in morphology (mostly in the mouthparts), behaviour and nutritional physiology. To gain insight into the molecular basis of this adaptive radiation, we performed a comprehensive comparative transcriptome analysis of five Canary Island Dysdera endemics representing two evolutionary and geographically independent events of dietary specialization. After controlling for the potential confounding effects of hemiplasy, our differential gene expression and selective constraint analyses identified a number of genetic changes that could be associated with the repeated adaptations to specialized diet of woodlice, including some related to heavy metal detoxification and homeostasis, the metabolism of some important nutrients and venom toxins. Our results shed light on the genomic basis of an extraordinary case of dietary shift convergence associated with species diversification. We uncovered putative molecular substrates of convergent evolutionary changes at different hierarchical levels, including specific genes, genes with equivalent functions and even particular amino acid positions. This study improves our knowledge of rapid adaptive radiations and provides new insights into the predictability of evolution.

Extracellular vesicles derived from endometrial human mesenchymal stem cells improve IVF outcome in an aged murine model.

Advanced age reduces the success of in vitro fertilization (IVF) being this effect partly mediated by an overproduction of reactive oxygen species (ROS) that trigger apoptosis. It has been demonstrated that extracellular vesicles derived from endometrial mesenchymal stem cells (EV-endMSCs) exert an antioxidant effect and can be used as IVF coadjutants. In this work, endMSCs were isolated from human menstrual blood (n = 4) and characterized according to multipotentiality and surface marker expression prior EV-endMSCs isolation. Oocytes were obtained from 21 B6D2 mice (24 weeks) and coincubated with sperm from young males (8-12 weeks). Presumptive zygotes were incubated in the presence of 0, 10, 20, 40 or 80 µg/ml of EV-endMSCs in KSOM medium. Blastocyst yield was evaluated, and 25 blastocysts per group were used for qPCR. Blastocyst rate was 29.4% in control; 45.2% for 10 µg/ml, 62.9% for 20 µg/ml, 55.5% for 40 µg/ml and 53.8% in the 80 µg/ml (n = 124-130 oocytes) being all the increases significantly different when compared against control (p < 0.05). The 20-80 µg/ml treatments decreased the expression of glutathione peroxidase (Gpx1), and the 10-40 µg/ml treatments reduced the expression of superoxide dismutase (Sod1; p < 0.05) compared to control; Bax mRNA expression did not vary. Our results suggest that the increased developmental competence of the embryos could be partly mediated by the EV-endMSCs' ROS scavenger activity.

Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome.

Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.

The imprint of geologic history on within-island diversification of woodlouse-hunter spiders (Araneae, Dysderidae) in the Canary Islands.

Geological processes and ecological adaptation are major drivers of diversification on oceanic islands. Although diversification in these islands is often interpreted as resulting from dispersal or island hopping rather than vicariance, this may not be the case in islands with complex geological histories. The island of Tenerife, in the Canary Islands, emerged in the late Miocene as 3 precursor islands that were subsequently connected and reisolated by volcanic cycles. The spider Dysdera verneaui is endemic to the island of Tenerife, where it is widely distributed throughout most island habitats, providing an excellent model to investigate the role of physical barriers and ecological adaptation in shaping within-island diversity. Here, we present evidence that the phylogeographic patterns of this species trace back to the independent emergence of the protoislands. Molecular markers (mitochondrial genes cox1, 16S, and nad1 and the nuclear genes ITS-2 and 28S) analyzed from 100 specimens (including a thorough sampling of D. verneaui populations and additional outgroups) identify 2 distinct evolutionary lineages that correspond to 2 precursor islands, each with diagnostic genital characters indicative of separate species status. Episodic introgression events between these 2 main evolutionary lineages explain the observed incongruence between mitochondrial and nuclear markers, probably as a result of the homogenization of their ITS-2 sequence types. The most widespread lineage exhibits a complex population structure, which is compatible with either secondary contact, following connection of deeply divergent lineages, or alternatively, a back colonization from 1 precursor island to another.

Dispersal ability and niche breadth influence interspecific variation in spider abundance and occupancy.

The relationship between species local abundance and their regional distribution (occupancy) is one of the most extensively recognized and investigated patterns in ecology. While exceptions exist, the generally held model is that locally abundant species also tend to be more widespread geographically. However, there is only a limited understanding of both the mechanisms driving this relationship, and their scale dependency. Here we use occupancy and abundance data for 123 species of spider from across the Canary Islands to understand how both dispersal ability and niche breadth might mediate variation among species for local abundance and occupancy. We test the predictions that (i) dispersal ability explains variation among species for both abundance and occupancy, and (ii) species with a higher degree of habitat specialization, reflecting more limited niche breadth, will have both higher occupancy and abundance. We find no evidence within habitat patches for an effect of dispersal ability on either local abundance or site occupancy, while across all patches species with higher dispersal ability tend to occupy more sites. Species largely restricted to laurel forests have higher abundance than species with broader niche breadth, but similar occupancy. The study revealed that dispersal ability and niche breadth were significant predictors of the abundance-occupancy relationship, highlighting the importance of both factors for understanding patterns of abundance and occupancy among spider species.

Almond (Prunus dulcis) Bagasse as a Source of Bioactive Compounds with Antioxidant Properties: An In Vitro Assessment.

The presence of components of nutritional interest makes fresh almond bagasse an interesting by-product for obtaining functional ingredients. Stabilization through a dehydration process is an interesting option for its integral use, ensuring its conservation and management. Subsequently, it can be turned into powder, facilitating its use as an ingredient. The aim of this paper was to determine the effects of hot air drying at 60 and 70 °C and lyophilization on the release of phenolic components and antiradical capacity in in vitro gastrointestinal digestion and colonic fermentation, as well as on growing microbiota composition by applying high throughput sequencing. The novelty of this study lies in this holistic approach; considering both technological and physiological aspects related to gastrointestinal digestion and colonic fermentation will provide the best conditions for functional foods. The results obtained showed that lyophilization provides a powder with a total phenol content and antiradical capacity higher than hot air drying. Furthermore, in dehydrated samples, both in vitro digestion and colonic fermentation revealed a phenol content and anti-radical capacity superior to those existing in undigested products. In addition, after colonic fermentation, beneficial bacteria species have been identified. Obtaining powders from almond bagasse is presented as an interesting opportunity for the valorization of this by-product.

BAY-6096: A Potent, Selective, and Highly Water-Soluble Adrenergic α2B Antagonist.

After acute myocardial infarction, early reperfusion is the most effective strategy for reducing cardiac damage and improving clinical outcome. However, restoring blood flow to the ischemic myocardium can paradoxically induce injury by itself (reperfusion injury), with microvascular dysfunction being one contributing factor. α2B adrenergic receptors have been hypothesized to be involved in this process. To assess α2B-related pharmacology, we identified a novel α2B antagonist by HTS. The HTS hit showed limited α2A selectivity as well as low solubility and was optimized toward BAY-6096, a potent, selective, and highly water-soluble α2B antagonist. Key aspects of the optimization were the introduction of a permanently charged pyridinium moiety to achieve very good aqueous solubility and the inversion of an amide to prevent genotoxicity. BAY-6096 dose-dependently reduced blood pressure increases in rats induced by an α2B agonist, demonstrating the role of α2B receptors in vascular constriction in rats.

Effects of different foods and cooking methods on the gut microbiota: an in vitro approach.

To support personalized diets targeting the gut microbiota, we employed an in vitro digestion-fermentation model and 16S rRNA gene sequencing to analyze the microbiota growing on representative foods of the Mediterranean and Western diets, as well as the influence of cooking methods. Plant- and animal-derived foods had significantly different impacts on the abundances of bacterial taxa. Animal and vegetable fats, fish and dairy products led to increases in many taxa, mainly within the Lachnospiraceae. In particular, fats favored increases in the beneficial bacteria Faecalibacterium, Blautia, and Roseburia. However, butter, as well as gouda cheese and fish, also resulted in the increase of Lachnoclostridium, associated to several diseases. Frying and boiling produced the most distinct effects on the microbiota, with members of the Lachnospiraceae and Ruminococcaceae responding the most to the cooking method employed. Nevertheless, cooking effects were highly individualized and food-dependent, challenging the investigation of their role in personalized diets.

How much biodiversity is concealed in the word 'biodiversity'?

Amidst a global biodiversity crisis1, the word 'biodiversity' has become indispensable for conservation and management2. Yet, biodiversity is often used as a buzzword in scientific literature. Resonant titles of papers claiming to have studied 'global biodiversity' may be used to promote research focused on a few taxonomic groups, habitats, or facets of biodiversity - taxonomic, (phylo)genetic, or functional. This usage may lead to extrapolating results outside the target systems of these studies with direct consequences for our understanding of life on Earth and its practical conservation. Here, we used a random sample of papers with the word 'biodiversity' in their title to take a long view of the use of this term. Despite improvements in analytical tools, monitoring technologies, and data availability3,4, we found that the taxonomic scope of research articles has not increased in recent years. We also show that studies with a wider taxonomic scope attract more citations and online attention. Our results have broad ramifications for understanding how extrapolating from studies with narrow taxonomic scope affects our view of global biodiversity and conservation.

Evaluation of the Effects of a Short Supplementation With Tannins on the Gut Microbiota of Healthy Subjects.

Western diet, high in fats and sugars and low in greens, contributes to dysbiosis of the gut microbiota, which can lead to a variety of chronic diseases related with inflammation. Supplementation with bioactive compounds can help to maintain a healthy eubiotic state. Thus, we performed a 4-weeks nutritional intervention on healthy volunteers to investigate whether a blend of natural tannin extracts could induce healthy changes in the microbial intestinal ecosystem. Changes in the composition and functionality of the microbiota could be observed from the first two weeks onward. 16S rRNA amplicon next-generation sequencing (NGS) revealed a significant increase in microbial diversity at the end of the intervention, as well as trends toward increases in the relative abundances of several beneficial taxa, such as Ruminococcus bicirculans, Faecalibacterium prausnitzii, Lachnospiraceae UCG 010, Lachnospiraceae NK4A136, Bacteroides thetaiotaomicron and B. uniformis. Remarkably, some of the identified taxa were also identified as responsible for an increase in the production of short-chain fatty acids (SCFAs), microbial metabolites that contribute to the modulation of the immune system and have various other anti-inflammatory functions in the gut. Taken together, these results suggest that the tannin supplementation could exert a prebiotic effect by selectively stimulating the growth and the activity of bacteria that are advantageous for the host.

A Circular Economy Approach to Restoring Soil Substrate Ameliorated by Sewage Sludge with Amendments.

This study examined the use of an artificial soil substrate in a mine waste reclamation area and its effect on plant metabolic functions. Research was conducted by determining the relationship between the plants' biochemical features and the properties of plant growth medium derived from post-flotation coal waste, sewage sludge, crushed stone and fly ash on the surface of the mine waste disposal area. Trees and shrubs were established on the material and allowed to grow for eight years. The study determined that the applied plants and the naturally occurring Taraxacum officinale were suitable for physio-biochemical assessment, identification of derelict areas and reclamation purposes. An evaluation of a soil substrate applied to post-mining areas indicated that it was beneficial for plant growth since it activated the metabolic functions of herbaceous plants, shrubs, and trees. The study showed that soil substrate can be targeted to improve plant stress tolerance to potentially toxic elements (PTEs). These data suggest the potential for growth and slower susceptible response to Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn. It is possible that the constructed soil-substitute substrate (biosolid material) would be an effective reclamation treatment in areas where natural soil materials are polluted by PTEs. This observation may reflect a more efficient use of soil substrate released from the cycling of organic biogene pools, in accordance with the circular economy approach. In further studies related to land reclamation using sewage sludge amendments, it would be necessary to extend the research to other stress factors, such as salinity or water deficiency.

Pulmonary hypertension in adults with congenital heart disease. Clinical phenotypes and outcomes in the advanced pulmonary vasodilator era.

BACKGROUND: Mortality of pulmonary hypertension associated with congenital heart disease (PAH-CHD) in adults remains high. OBJECTIVES: To identify predictors of death and to assess the impact of treatment on outcome. METHODS: Retrospective, multicenter cohort study of 103 adults with PAH-CHD followed-up for 8.6 ± 4.6 years. Patients were grouped according to underlying shunt type into pre-tricuspid, post-tricuspid and complex. Survival rates were analyzed and predictors of death were investigated with Cox regression models. RESULTS: In the post-tricuspid and complex groups (38 and 37 patients, respectively), the most common clinical PAH-CHD subgroup was Eisenmenger syndrome (76.3% and 59.5%, respectively) whereas, in the pre-tricuspid group (28 patients), 46.5% of patients had small or corrected defects. Overall, 88 patients received vasodilators; 39% required combination-therapy. Overall survival at 10 years was 65%. Mortality was highest in the pre-tricuspid group, FC-III-IV and amongst patients receiving monotherapy (p < 0.050). On multivariate analysis, predictors of poor outcome were pericardial effusion (HR: 4,520 [1,470-13,890]; p = 0,008), oxygen saturation(HR: 0.940 [0,900 - 0,990]; p = 0,018) and genetic syndromes(HR: 3,280 [1,098-9,780]; p = 0,033). CONCLUSIONS: Patients in advanced stages at initiation of treatment were at high risk of death and strong consideration should be given for more aggressive therapy.

Nutritional Supplementation to Increase Influenza Vaccine Response in Children Living With HIV: A Pilot Clinical Trial.

Aims: Vaccine response is poor among children living with HIV. The gut microbiota has been identified as a potential target to improve vaccine immunogenicity, but data are scarce in the context of HIV infection. Methods: Pilot, double-blind, randomized placebo-controlled trial in which 24 HIV-infected children were randomized to receive a mixture of symbiotics, omega-3/6 fatty acids, and amino acids or placebo for 4 weeks, each in combination with ART, and were then immunized against influenza. Vaccine response and safety of the nutritional supplementation were the primary outcomes. Results: Eighteen HIV-infected children completed the follow-up period (mean age 11.5 ± 4.14 years, 61% female). The nutritional supplement was safe but did not enhance the response to the influenza vaccine. A 4-fold rise in antibody titers was obtained in only 37.5% of participants in the intervention arm vs. 40% in the placebo. No immunological or inflammatory predictors of vaccine response were identified. Conclusions: In this exploratory study, a 4-week course of symbiotics did not increase influenza vaccine immunogenicity in HIV-infected children. Larger studies are warranted to address the potential of modulating the microbiome in children living with HIV.

Interactions among the mycobiome, bacteriome, inflammation, and diet in people living with HIV.

While the intestinal microbiome seems a major driver of persistent immune defects in people with HIV (PWH), little is known about its fungal component, the mycobiome. We assessed the inter-kingdom mycobiome-bacteriome interactions, the impact of diet, and the association with the innate and adaptive immunity in PWH on antiretroviral therapy. We included 24 PWH individuals and 12 healthy controls. We sequenced the Internal Transcribed Spacer 2 amplicons, determined amplicon sequence variants, measured biomarkers of the innate and adaptive immunity in blood and relations with diet. Compared to healthy controls, PWH subjects exhibited a distinct and richer mycobiome and an enrichment for Debaryomyces hansenii, Candida albicans, and Candida parapsilosis. In PWH, Candida and Pichia species were strongly correlated with several bacterial genera, including Faecalibacterium genus. Regarding the links between the mycobiome and systemic immunology, we found a positive correlation between Candida species and the levels of proinflammatory cytokines (sTNF-R2 and IL-17), interleukin 22 (a cytokine implicated in the regulation of mucosal immunity), and CD8+ T cell counts. This suggests an important role of the yeasts in systemic innate and adaptive immune responses. Finally, we identified inter-kingdom interactions implicated in fiber degradation, short-chain fatty acid production, and lipid metabolism, and an effect of vegetable and fiber intake on the mycobiome. Therefore, despite the great differences in abundance and diversity between the bacterial and fungal communities of the gut, we defined the changes associated with HIV, determined several different inter-kingdom associations, and found links between the mycobiome, nutrient metabolism, and systemic immunity.