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Dietary changes expose consumers to risks from Anisakis larvae in seafood, leading to parasitic diseases and allergies. Anisakis is recognized by EFSA as a significant hazard, with potential oncogenic implications. Diagnostic advancements, like the Basophil Activation Test (BAT), enhance sensitivity and accuracy in identifying Anisakis sensitization, complementing traditional IgE tests. We conducted a cross-sectional study on patients with allergic symptoms from April 2021 to April 2023 at two outpatient clinics in western Sicily. Our goal was to assess the prevalence of Anisakis-related allergies and to identify risk profiles using specific Anisakis IgE and the BAT, especially in regions with high raw fish consumption. The study evaluated specific Anisakis IgE as a screening tool for Anisakis sensitization, using questionnaires, blood samples, and immuno-allergology analyses. Anisakis-specific IgE values were compared with the BAT results, with statistical analyses including Fisher’s exact test and logistic regression. The results showed an 18.5% seroprevalence of Anisakis IgE, while the BAT as a second-level test showed 4.63%, indicating the BAT’s superior specificity and accuracy. The study highlighted the importance of the BAT in diagnosing Anisakis sensitization, especially in cases of cross-reactivity with Ascaris and tropomyosin. The findings confirm the BAT’s exceptional specificity in identifying Anisakis sensitization and support using Anisakis-specific IgE for population-based risk profiling. The BAT can effectively serve as a confirmatory test.

The rising popularity of undercooked or raw seafood containing larvae of the Anisakis parasite has led to issues of public health concern due to allergic manifestations. We conducted an observational study on the use of an innovative Anisakis allergy diagnostic algorithm in a convenience sample of 53 allergic outpatients recruited in Western Sicily, between April 2021 and March 2022. We included individuals with an anamnesis suggestive of IgE sensitization to Anisakis reporting clinical manifestation in the last month due to allergic reactions after eating fresh fish, or in subjects at high exposure risk with sea products while abstaining from fish ingestion, excluding those with documented fish sensitization. Outpatients were tested via Skin Prick Test, IgE-specific dosage and Basophil Activation Test (BAT). Twenty-six outpatients were diagnosed with Anisakis, while 27 with Chronic Urticaria (CU). We found a seven-fold excess risk for Anisakis (p4) positivity in the Anisakis allergic outpatients, as compared to the CU ones. BAT showed the best diagnostic accuracy (92.45%) and specificity (100%), while specific IgE to Ascaris (p1) documented the best sensitivity (92.31%) but a very low specificity (37.04%). In conclusion, our findings may represent a potentially useful contribution to the future development of updated clinical guidelines.

Abstract Background Hepatocellular carcinoma (HCC) is the most frequent primary invasive cancer of the liver. During the last decade, the epidemiology of HCC has been continuously changing in developed countries, due to more effective primary prevention and to successful treatment of virus-related liver diseases. The study aims to examine survival by level of access to care in patients with HCC, for all patients combined and by age. Methods We included 2018 adult patients (15–99 years) diagnosed with a primary liver tumour, registered in the Palermo Province Cancer Registry during 2006–2015, and followed-up to 30 October 2019. We obtained a proxy measure of access to care by linking each record to the Hospital Discharge Records and the Ambulatory Discharge Records. We estimated net survival up to 5 years after diagnosis by access to care (“easy access to care” versus “poor access to care”), using the Pohar-Perme estimator. Estimates were age-standardised using International Cancer Survival Standard (ICSS) weights. We also examined survival by access to care and age (15–64, 65–74 and ≥ 75 years). Results Among the 2018 patients, 62.4% were morphologically verified and 37.6% clinically diagnosed. Morphologically verified tumours were more frequent in patients aged 65–74 years (41.6%), while tumours diagnosed clinically were more frequent in patients aged 75 years or over (50.2%). During 2006–2015, age-standardised net survival was higher among HCC patients with “easy access to care” than in those with “poor access to care” (68% vs. 48% at 1 year, 29% vs. 11% at 5 years; p

On December 31, 2019, an outbreak of lower respiratory infections was documented in Wuhan caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the beginning, SARS-CoV-2 has caused many infections among healthcare workers (HCWs) worldwide. Aims of this study were: a. to compare the distribution among the HCWs and the general population of SARS-CoV-2 infections in Western Sicily and Italy; b. to describe the characteristics of HCWs infected with SARS-CoV-2 in the western Sicilian healthcare context during the first wave of the epidemic diffusion in Italy. Incidence and mean age of HCWs infected with SARS-CoV-2 were comparable in Western Sicily and in the whole Italian country. The 97.6% of infections occurred in HCWs operating in non-coronavirus disease 2019 (COVID-19) working environments, while an equal distribution of cases between hospital and primary care services context was documented. Nurses and healthcare assistants, followed by physicians, were the categories more frequently infected by SARS-CoV-2. The present study suggests that healthcare workers are easily infected compared to the general population but that often infection could equally occur in hospital and non-hospital settings. Safety of HCWs in counteracting the COVID-19 pandemic must be strengthened in hospital [adequate provision of personal protective equipment (PPE), optimization of human resources, implementation of closed and independent groups of HCWs, creation of traffic control building and dedicated areas in every healthcare context] and non-hospital settings (influenza vaccination, adequate psychophysical support, including refreshments during working shifts, adequate rest, and family support).

Objectives In response to public health concern about effects of arson at solid waste management plants in July 2012, we analysed vital statistics data to evaluate any potential effect on pregnancies at different gestational ages of pollutants emitted from the landfill on fire.Setting A community living near the largest landfill plant in Sicily.Participants The study group comprised 551 births, live births and stillbirths from pregnancies of mothers residing in the extra-urban exposed area, conceived during a 40 week period during which the highest fire’s peak might have influenced pregnancy.Primary and secondary outcome measures Birth outcomes (gestational age

Influenza is an infectious disease with a high impact on the population in terms of morbidity and mortality, but despite International and European guidelines, vaccination coverage rates among healthcare workers (HCWs) remain very low. The aim of the present study was to evaluate influenza vaccination adherence in the three Sicilian University Hospitals of Catania, Messina, and Palermo and to understand the attitudes and perceptions of vaccinated healthcare workers and the main reasons for vaccination refusal. A cross-sectional survey through a self-administered questionnaire was conducted during the 2019/2020 influenza season. Overall, 2356 vaccinated healthcare workers answered the questionnaire. The main reason reported for influenza vaccination adherence during the 2019/2020 season was to protect patients. Higher self-perceived risk of contracting influenza and a positive attitude to recommending vaccination to patients were significantly associated with influenza vaccination adherence during the last five seasons via multivariable analysis. Fear of an adverse reaction was the main reason for influenza vaccine refusal. In accordance with these findings, Public Health institutions should develop and tailor formative and informative campaigns to reduce principal barriers to the immunization process and promote influenza vaccination adherence among HCWs.

Although open tools for manual text annotation and the creation of lexical resources have been available for some years, there is currently no integrated tool that allows, within the same environment, annotating a text corpus, building a computational lexicon, and linking linguistic annotations to lexical elements. For this reason, we have developed Maia, an open and collaborative web tool based on semantic web and linked open data technologies for text annotation, e-lexicography, and lexical linking, primarily designed and developed for use by digital humanists. This article presents the first version of Maia, describing its functionality, and outlining its software architecture and development prospects.

Early diagnosis of oncologic pathologies has a crucial role to determine patient’s prognosis and therapeutic path. Nonetheless, clinical errors and omissions that can occur during diagnostic, as well as detection of preneoplastic or neoplastic condition, may result in devasting consequences both for patients in terms of health and for professionals in terms of medico-legal responsibility. This study is aimed at examining in depth, through the presentation of a specific clinical case, the medico-legal aspects inherent to the diagnosis of oral cancer, analyzing the preventive, interceptive, and diagnostic strategies, the legal implications of clinical evaluation errors and diagnostic omission, and the type of medical damage produced and professional liability. The medico-legal landscape surrounding oral squamous cell carcinoma is multifaceted and characterized by diagnostic challenges, treatment complexities, and legal considerations. Health-care providers must remain vigilant in navigating these complexities to ensure optimal patient care while mitigating legal risks. By prioritizing high-quality medical records, fostering transparent communication with patients, and implementing preventive strategies, health-care institutions can strive to minimize the incidence of litigation and uphold standards of ethical practice in oral carcinoma cases. Additionally, continued research and education in forensic and legal medicine are essential in informing evidence-based practices and promoting patient safety in this evolving field.

Abstract Background Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. Results We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. Conclusion This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract

Abstract The mammalian gastrointestinal tract harbours a highly complex ecosystem composed of a variety of micro- (bacteria, fungi, viruses, protozoans) and macro-organisms (helminths). Although most microbiota research focuses on the variation of single gut components, the crosstalk between components is still poorly characterized, especially in hosts living under natural conditions. We investigated the gut micro-biodiversity (bacteria, fungi and helminths) of 158 individuals of two wild non-human primates, the Udzungwa red colobus (Procolobus gordonorum) and the yellow baboon (Papio cynocephalus). These species have contrasting diets and lifestyles, but live sympatrically in both human-impacted and pristine forests in the Udzungwa Mountains of Tanzania. Using non-invasive faecal pellets, helminths were identified using standard microscopy while bacteria and fungi were characterized by sequencing the V1–V3 variable region of the 16S rRNA gene for bacteria and the ITS1–ITS2 fragment for fungi. Our results show that both diversity and composition of bacteria and fungi are associated with variation in helminth presence. Although interactions differed by habitat type, in both primates we found that Strongyloides was negatively associated and Trichuris was positively associated with bacterial and fungal richness. To our knowledge, this is one of the few studies demonstrating an interaction between helminth and gut microbiota communities in wild non-human primates.

Abstract Background Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.). Results A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The “Candidatus Jiangella antarctica” has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa. Conclusions Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life. Video abstract

By greatly expanding the number of assembled genomes for Wolbachia (a group of intracellular bacteria) and constructing robust phylogenies, this study finds strong rate heterogeneity among Wolbachiapopulations and no support for synchronous divergence between Wolbachia and host mitochondria.

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

Metagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.

Abstract Background Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management. Results Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil. Conclusions Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.

ABSTRACT Human exploitation and destruction of tropical resources are currently threatening innumerable wild animal species, altering natural ecosystems and thus, food resources, with profound effects on gut microbiota. Given their conservation status and the importance to tropical ecosystems, wild nonhuman primates make excellent models to investigate the effect of human disturbance on the diversity of host-associated microbiota. Previous investigations have revealed a loss of fecal bacterial diversity in primates living in degraded compared to intact forests. However, these data are available for a limited number of species, and very limited information is available on the fungal taxa hosted by the gut. Here, we estimated the diversity and composition of gut bacterial and fungal communities in two primates living sympatrically in both human-modified and pristine forests in the Udzungwa Mountains of Tanzania. Noninvasively collected fecal samples of 12 groups of the Udzungwa red colobus (Procolobus gordonorum) (n = 89), a native and endangered primate (arboreal and predominantly leaf-eating), and five groups of the yellow baboon (Papio cynocephalus) (n = 69), a common species of least concern (ground-feeding and omnivorous), were analyzed by the V1-V3 region of the 16S rRNA gene (bacterial) and ITS1-ITS2 (fungal) sequencing. Gut bacterial diversities were associated with habitat in both species, most likely depending on their ecological niches and associated digestive physiology, dietary strategies, and locomotor behavior. In addition, fungal communities also show distinctive traits across hosts and habitat type, highlighting the importance of investigating this relatively unexplored gut component. IMPORTANCE Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.

The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.

Developing robust catalysts for alkyne semi-hydrogenation remains a challenge. Here, the authors introduce a scalable protocol to prepare crystal phase and orientation controlled Pd3S nanoparticles supported on carbon nitride, exhibiting unparalleled semi-hydrogenation performance due to a high density of active and selective ensembles.

Microbiota is often a complex mixture of multiple coexisting species and strains with high level of phenotypic and genomic variability. Here, Albanese and Donati develop StrainEst for estimating the number and identity of coexisting strains and their relative abundances in mixed metagenomic samples.

Nell’ambito del Progetto Traduzione del Talmud Babilonese, l’Istituto di Linguistica Computazionale del CNR ha sviluppato Traduco, uno strumento web collaborativo con alcune caratteristiche che lo rendono particolarmente adatto alla traduzione di testi che pongono problemi interpretativi. Ad oggi, gli strumenti per la traduzione assistita (in inglese, Computer-Assisted Translation, o CAT) sono utilizzati tipicamente per la traduzione di manuali tecnici, testi legislativi o siti Web e hanno principalmente lo scopo di accelerare il processo di traduzione. Traduco riprende la maggior parte dei componenti standard di uno strumento di traduzione assistita tradizionale, ma li estende con caratteristiche specifiche necessarie per supportare l’interpretazione e la traduzione di testi complessi che pongono particolari problemi di comprensione. In questo articolo presenteremo un caso di studio specifico, relativo a un testo con queste caratteristiche: il Talmud Babilonese. Traduco include funzionalità per l’aggiunta di note, riferimenti bibliografici, annotazioni semantiche e creazione di glossari. Traduttori, revisori, redattori, supervisori e utenti finali che accedono al Sistema sono supportati nell’intero processo di traduzione, che va dall’interpretazione del testo originario alla fase editoriale per la stampa delle traduzioni, attraverso l’uso di tecnologie di traduzione assistita, l’annotazione semantica del testo, l’arricchimento delle traduzioni con informazioni esplicative, l’esportazione delle traduzioni in XML e in TEI e l’integrazione di tecniche per il trattamento automatico della lingua. La progettazione e lo sviluppo di Traduco ha richiesto l’adozione di un approccio multidisciplinare che combina aspetti di ingegneria del software, linguistica computazionale, ingegneria della conoscenza ed editoria digitale.

Diet is one of the main factors that affects the composition of gut microbiota. When people move from a rural environment to urban areas, and experience improved socio-economic conditions, they are often exposed to a “globalized” Western type diet. Here, we present preliminary observations on the metagenomic scale of microbial changes in small groups of African children belonging to the same ethnicity and living in different environments, compared to children living on the urban area of Florence (Italy). We analyzed dietary habits and, by pyrosequencing of the 16S rRNA gene, gut microbiota profiles from fecal samples of children living in a rural village of Burkina Faso (n = 11), of two groups of children living in different urban settings (Nanoro town, n = 8; Ouagadougou, the capital city, n = 5) and of a group of Italian children (n = 13). We observed that when foods of animal origin, those rich in fat and simple sugars are introduced into a traditional African diet, composed of cereals, legumes and vegetables, the gut microbiota profiles changes. Microbiota of rural children retain a geographically unique bacterial reservoir (Prevotella, Treponema, and Succinivibrio), assigned to ferment fiber and polysaccharides from vegetables. Independently of geography and ethnicity, in children living in urban areas these bacterial genera were progressively outcompeted by bacteria more suited to the metabolism of animal protein, fat and sugar rich foods, similarly to Italian children, as resulted by PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a predictive functional profiling of microbial communities using 16S rRNA marker gene. Consequently, we observed a progressive reduction of SCFAs measured by gas chromatography–mass spectrometry, in urban populations, especially in Italian children, respect to rural ones. Our results even if in a limited number of individuals point out that dietary habit modifications in the course of urbanization play a role in shaping gut microbiota, and that ancient microorganisms, such as fiber-degrading bacteria, are at risk of being eliminated by the fast paced globalization of foods and by the advent of westernized lifestyle.

Alteration of gut microbiota is involved in several chronic inflammatory and autoimmune diseases, including rheumatoid arthritis, and gut microbial pro-arthritogenic profiles have been hypothesized. Intestinal inflammation may be involved in spondyloarthropathies and in a subset of patients affected by Juvenile Idiopathic Arthritis (JIA), the most common chronic rheumatic disease of childhood. We compared the fecal microbiota composition of JIA patients with healthy subjects (HS), evaluating differences in microbial profiles between sub-categories of JIA, such as enthesitis-related arthritis (JIA-ERA), in which inflammation of entheses occurs, and polyarticular JIA, non-enthesitis related arthritis (JIA-nERA). Through taxon-level analysis, we discovered alteration of fecal microbiota components that could be involved in subclinical gut inflammation, and promotion of joint inflammation. We observed abundance in Ruminococcaceae in both JIA categories, reduction in Clostridiaceae and Peptostreptococcaceae in JIA-ERA, and increase in Veillonellaceae in JIA-nERA, respectively compared with HS. Among the more relevant genera, we found an increase in Clostridium cluster XIVb, involved in colitis and arthritis, in JIA-ERA patients compared with HS, and a trend of decrease in Faecalibacterium, known for anti-inflammatory properties, in JIA-nERA compared with JIA-ERA and HS. Differential abundant taxa identified JIA patients for the HLA-B27 allele, including Bilophila, Clostridium cluster XIVb, Oscillibacter and Parvimonas. Prediction analysis of metabolic functions showed that JIA-ERA metagenome was differentially enriched in bacterial functions related to cell motility and chemotaxis, suggesting selection of potential virulence traits. We also discovered differential microbial profiles and intra-group variability among active disease and remission, suggesting instability of microbial ecosystem in autoimmune diseases with respect to healthy status. Similarly to other chronic autoimmune and inflammatory diseases, different microbial profiles, as observed among different JIA subgroups compared to HS, and potential functional acquisition related to migration could promote inflammation and contribute to the disease pathogenesis.

The fungal component of the human gut microbiota has been neglected for long time due to the low relative abundance of fungi with respect to bacteria, and only recently few reports have explored its composition and dynamics in health or disease. The application of metagenomics methods to the full understanding of fungal communities is currently limited by the under representation of fungal DNA with respect to the bacterial one, as well as by the limited ability to discriminate passengers from colonizers. Here we investigated the gut mycobiota of a cohort of healthy subjects in order to reduce the gap of knowledge concerning fungal intestinal communities in the healthy status further screening for phenotypical traits that could reflect fungi adaptation to the host. We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals. We then characterized the isolated fungi for their tolerance to gastrointestinal tract-like challenges and their susceptibility to antifungals. A total of 34 different fungal species were isolated showing several phenotypic characteristics associated with intestinal environment such as tolerance to body temperature (37°C), to acidic and oxidative stress and to bile salts exposure. We found a high frequency of azoles resistance in fungal isolates, with potential and significant clinical impact. Analyses of fungal communities revealed that the human gut mycobiota differs in function of individuals’ life stage in a gender-related fashion. The combination of metagenomics and fungal cultivation allowed an in-depth understanding of the fungal intestinal community structure associated to the healthy status and the commensalism-related traits of isolated fungi. We further discussed comparatively the results of sequencing and cultivation to critically evaluate the application of metagenomics-based approaches to fungal gut populations.

Metagenomics is revolutionizing our understanding of microbial communities, showing that their structure and composition have profound effects on the ecosystem and in a variety of health and disease conditions. Despite the flourishing of new analysis methods, current approaches based on statistical comparisons between high-level taxonomic classes often fail to identify the microbial taxa that are differentially distributed between sets of samples, since in many cases the taxonomic schema do not allow an adequate description of the structure of the microbiota. This constitutes a severe limitation to the use of metagenomic data in therapeutic and diagnostic applications. To provide a more robust statistical framework, we introduce a class of feature-weighting algorithms that discriminate the taxa responsible for the classification of metagenomic samples. The method unambiguously groups the relevant taxa into clades without relying on pre-defined taxonomic categories, thus including in the analysis also those sequences for which a taxonomic classification is difficult. The phylogenetic clades are weighted and ranked according to their abundance measuring their contribution to the differentiation of the classes of samples, and a criterion is provided to define a reduced set of most relevant clades. Applying the method to public datasets, we show that the data-driven definition of relevant phylogenetic clades accomplished by our ranking strategy identifies features in the samples that are lost if phylogenetic relationships are not considered, improving our ability to mine metagenomic datasets. Comparison with supervised classification methods currently used in metagenomic data analysis highlights the advantages of using phylogenetic information.