Search Results (76)

Background: Insomnia is one of the most prevalent health concerns and has a major impact on human health and quality of life. Increasing evidence indicates the gut microbiota’s role in sleep regulation through the gut–brain axis. This systematic review aims to summarise current evidence on the role of gut microbiota alterations in insomnia. Methods: We searched PubMed, Embase, and Cochrane Library through November 2024 for case–control studies comparing gut microbiota in insomnia subjects and controls. The primary outcome was changes in microbiota diversity and bacteria taxonomy. Results: We included 15 case–control studies from 14 articles, consisting of 1321 subjects (603 insomnia; 718 controls). Eight studies showed reduced alpha diversity and eleven showed altered beta diversity in insomnia subjects. Depletions of specific taxa such as Lactobacillales (class Bacilli), Faecalibacterium, and Lachnospira and the enrichment of Actinobacteria, Bacteroidales (class Bacteroidia), and several genera, including Streptococcus, Blautia, Lactobacillus, Clostridium, Holdemanella, and Eubacterium hallii, were observed in insomnia subjects. There was a negative association between insomnia severity and abundance of Faecalibacterium and Lachnospira, and positive associations with Blautia. Conclusions: This systematic review identifies specific alterations in gut microbiota among insomnia subjects characterised by taxonomic changes that may serve as promising therapeutic targets for sleep disorders. Full article

In Mexico, hospital wastewater (HWW) is a source of chemical and microbiological contamination, and it is released into the municipal sewage system without prior treatment. This water may contain pathogenic bacteria and antimicrobial resistance genes, which represent a risk to Public Health and the environment. So far, there are no studies that analyse this problem comprehensively, relating bacterial population structures, chemical contaminants, and seasonality. The aim of this work was to seasonally characterise the bacterial communities of HWW, including clinically relevant bacteria and resistance genes in Hospital Juárez de México (HJM), and to evaluate the impact of physicochemical factors on their composition. A one-year observational, cross-sectional study was conducted at five HWW discharge points of HJM. Fourteen physicochemical parameters were determined by using standard methodologies, and statistical differences between discharges and seasons were evaluated. Bacterial communities were analysed by targeted amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In addition, the presence of eight antimicrobial resistance genes of local epidemiological importance was assessed. Data were analysed using alpha and beta diversity indices, principal component analysis, and multivariate statistical tests. HWW showed high taxonomic diversity, with Proteobacteria, Firmicutes, and Bacteroidetes standing out. Clinically relevant bacteria were identified in 73.3% of the analyses, with Enterobacter and Escherichia-Shigella predominating. Total and dissolved solids, temperature, nitrate, and pH significantly influenced the bacterial composition of HWW. Seven out of the eight genes evaluated were identified, with bla_KPC, bla_OXA-40, and mcr-1 being the most frequent, showing significant seasonal differences. This study underlines the microbiological and chemical complexity of HWW, highlighting the impact of clinically relevant bacteria and antimicrobial resistance genes on Public Health. The findings emphasise the need to implement hospital waste management programmes and ideally specific treatment plants to minimise the associated risks and protect the environment and human health. Full article

The suite of fungi that associate with mosses, bryophilous fungi, can be explored further to provide insights into the symbiotic functionality of mosses as well as the ecosystems in which they reside. So far, in-depth studies on the taxonomic diversity, ecology, and physiological functions of bryophilous fungi associated with the Australasian moss species Leucobryum candidum are lacking. To generate information on the physiology, biology, and ecology of these organisms and their interactions with the moss host, the combined use of selective isolation and molecular characterisation of the fungal associates was carried out. Once the pure cultures of the fungal associates were obtained, a bioactivity assay was used to investigate the effect of fungal metabolites on moss growth in vitro. Overall, L. candidum species collected from six different locations within Southeast Queensland exposed to different environmental parameters were found to have a highly diverse community of fungal species from 10 orders and 17 families. A total of 25 of the 33 isolates that were identified using molecular sequencing techniques were unique species, confirming high beta diversity of the fungal associates of L. candidum collected from coastal, forest, and urban environments in Southeast Queensland. The highest numbers of culturable isolates came from coastal and forest sites. Urban sites accounted for the lowest numbers of culturable isolates. The taxonomic matches for these associates were known to have diverse endophytic, saprophytic, and parasitic roles within vascular plants. Selected moss samples were inoculated with fermentation extracts of fungal isolates (USC-F426 and USC-F427) and their effects on the moss samples were observed for any change in heights, weights, diameters, and morphological characteristics. A significant (p ≤ 0.05) difference in the heights of the in vitro-assessed L. candidum between treatments was observed. No significant differences, however, were seen between the weights and diameters and no discernible host symptoms were detected, other than a few morphological change observations. Full article

Background/Objectives: The overuse and misuse of antibiotics has contributed significatively to the growing problem of the emergence and spread of antibiotic resistance genes among bacteria, posing a serious global challenge to the treatment of bacterial infectious diseases. For these reasons, there is a current and growing interest in the development of effective alternative or complementary strategies to antibiotic therapy for the prevention of fish diseases, which are mainly based on the use of probiotics—in particular, those belonging to the Lactic Acid Bacteria (LAB) group. In this context, the aim of the present study was to characterise, evaluate the genetic diversity and assess the safety of candidate probiotic LAB strains for aquaculture isolated from faeces and intestines of European hakes (Merluccius merluccius, L.) caught in the Northeast Atlantic Ocean (Ireland). Methods: The direct antimicrobial activity of the LAB isolates was tested by the Stab-On-Agar method against key ichthyopathogens. Subsequently, their taxonomic classification and genetic diversity were determined by 16SrDNA sequencing and Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR), respectively. To ensure the in vitro safety of the LAB isolates, their biofilm-forming ability was assessed by a microtiter plate assay; their sensitivity to major antibiotics used in aquaculture, human and veterinary medicine by a broth microdilution method and their haemolytic and gelatinase activity by microbiological assays. Results: All LAB isolates were biofilm producers and susceptible to chloramphenicol, oxytetracycline, flumequine and amoxicillin. A total of 30 isolates (85.7%) were resistant to at least one of the tested antibiotics. None of the 35 LAB isolates showed haemolytic or proteolytic activity. Conclusions: Among the isolated strains, five LAB strains exhibiting the highest antimicrobial activity against aquaculture-relevant ichthyopathogens, taxonomically identified as Streptococcus salivarius, Enterococcus avium and Latilactobacillus sakei, were selected for further characterisation as potential probiotic candidates to promote sustainable aquaculture. To our knowledge, this is the first study to report that hake intestines and faeces represent viable ecological niches for the isolation of LAB strains with antimicrobial activity. Full article

In the late Cenozoic, the south-west of Eastern Europe was a region affected by extensive hydrological transformations that resulted in the retreat of the Eastern Paratethys and the emergence and further evolution of freshwater communities. In recent decades, a relatively rich fossil actinopterygian fauna has been described from this area. The present study was based on previous systematic studies and aimed to assess and trace the temporal dynamics of the diversity of fish assemblages that existed in the area from the Late Miocene until the end of the Pleistocene. Species diversity, taxonomic diversity, taxonomic complexity, and functional diversity were analysed. It was found that the diversity of the fish assemblages notably decreased during the Late Miocene, when representatives of the families Clariidae, Moronidae, Sciaenidae, and Gobiidae disappeared, and remained relatively low during the Pliocene. During the Pleistocene, however, functional diversity gradually increased, despite fluctuating species and taxonomic diversity and taxonomic richness and complexity, which suggests an increasing stability of the coenotic structure within the fish communities. The revealed temporal trends reflect the impact of the palaeoenvironmental and palaeoecological processes that characterised the region during the late Cenozoic, particularly orogenic and climatic changes, and the evolution of a typical limnophilous, lacustrine-riverine fish fauna. Full article

The allopolyploid complexes in Crocus series Verni represent taxonomic challenges due to their variable or mostly overlapping morphology with one parental species. Moreover, their diploid ancestors remain unidentified, even with genome-wide SNP data. One such case, collected from the southeasternmost point of the series’ geographical distribution, is herein characterised and described as a new species, C. bachofenii. This study integrates phylogenomics and cytogenetics to infer the parental origin of C. bachofenii and establish its diagnostic morphological characteristics. Genome skimming of C. bachofenii and 10 other C. ser. Verni species enabled the development of novel satellite repeats as cytogenetic markers and the assembly of their complete chloroplast genomes that were employed for phylogenetic analysis alongside GBS data. The allopolyploid origin of C. bachofenii (2n = 16) was confirmed with C. vernus as the maternal parent. The probably extinct paternal parent was affiliated with a clade comprising C. heuffelianus, C. tommasinianus, C. kosaninii, and C. bertiscensis. Morphologically, C. bachofenii is distinguished by larger flowers, perigone segment coloration, and a stigma–anther ratio from its close relatives. In conclusion, its phylogenetic affiliation, distinctive cytological status, and unique morphological features justified the description of this taxon as a new species. Full article

(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. Acanthamoeba spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease. (2) Methods and Results: In a suspected case of Acanthamoeba keratitis, in addition to Acanthamoeba spp., an endosymbiont of acanthamoebae belonging to the taxonomic order of Holosporales was detected by chance in a bacterial 16S rDNA-based pan-PCR and subsequently classified as Candidatus Paracaedibacter symbiosus through an analysis of an enlarged 16S rDNA region. We used Oxford Nanopore Technology to evaluate the usefulness of whole-genome sequencing (WGS) as a one-step diagnostics method. Here, Acanthamoeba castellanii and the endosymbiont Candidatus Paracaedibacter symbiosus could be directly detected at the species level. No other microbes were identified in the specimen. (3) Conclusions: We recommend the introduction of WGS as a diagnostic approach for keratitis to replace the need for multiple species-specific qPCRs in future routine diagnostics and to enable an all-encompassing characterisation of the polymicrobial community in one step. Full article

The Nearctic aphid genus Drepanaphis Del Guercio, 1909, the largest within the subfamily Drepanosiphinae (Hemiptera: Aphididae), is characterised by distinctive dorsal abdominal tubercles. This study presents a comprehensive taxonomic revision of the genus, expanding the recognised species to 18, including the newly described Drepanaphis robinsoni Malik sp. nov. Detailed descriptions and figures for 44 morphs, encompassing alate viviparous females, oviparous females and males, are provided, with new identification keys for all known species and morphs. The sexual morphs of 15 species, particularly oviparous females, are documented for the first time. Morphometric and principal component analyses (PCA) are employed to distinguish the studied taxa. This study identifies and corrects numerous misidentifications in museum collections, previously labelled as D. acerifoliae, D. choanotricha, D. kanzensis, D. knowltoni, D. parva, D. sabrinae or D. tissoti. Furthermore, it revalidates the distinct status of D. nigricans and D. tissoti, which had been synonymised in earlier works. Current range maps for all species and images of key morphological features obtained through light and scanning electron microscopy are also presented, providing a more complete understanding of this understudied genus. Full article

The Channichthyidae, a monophyletic fish group belonging to the suborder Notothenioidei, are uniquely adapted to the polar environment. However, while their physiology has been extensively studied, studies on their ecology are relatively rare. Here, we investigated the trophic ecology of seven icefish species (Chaenodraco wilsoni, Chionobathyscus dewitti, Chionodraco hamatus, Dacodraco hunteri, Neopagetopis ionah, Pagetodes antarcticus and Pagetopsis macropterus) by using the traditional morphometric approach to assess the relationship between form and feeding function. The suction index (SI), the mechanical advantage in jaw closing (MA) and nine morphological traits related to feeding structures have been analysed. Icefish species are characterised by non-protractible, elongate jaws and a wide gape; such morphological features influence the low values of both MA and SI, supporting their ram-feeding habit. The ecomorphological differences among species resulted mainly determined by the anatomical structures related to SI. Such differences do not seem to be determined primarily by the type of prey, as is the case in other taxonomic groups of Notothenioidei, but rather by phylogenetic proximity. A 3D animation was developed to visualise the different feeding modes of two icefish species (C. hamatus and P. macropterus) which are characterised by different approaches to prey. Full article

Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases’ pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. Methods: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. Results: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. Conclusion: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology. Full article

Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high-TB-burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI in PLHIV. We characterised the stool microbiota of PLHIV with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n = 25 per group). The 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet-Multinomial Mixtures, DESeq2, and PICRUSt2. No α- or β-diversity differences occurred by LTBI status; however, LTBI-positive people were Faecalibacterium-, Blautia-, Gemmiger-, and Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, and Streptococcus-depleted. Inferred metagenome data showed that LTBI-negative-enriched pathways included several metabolite degradation pathways. Stool from LTBI-positive people demonstrated differential taxa abundance based on a quantitative response to antigen stimulation. In LTBI-positive people, older people had different β-diversities than younger people, whereas in LTBI-negative people, no differences occurred across age groups. Amongst female PLHIV, those with LTBI were, vs. those without LTBI, Faecalibacterium-, Blautia-, Gemmiger-, and Bacteriodes-enriched, which are producers of short-chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome’s potential role in LTBI. Full article

(1) Background: Although Physaloptera retusa is one of the most widespread species infecting reptiles in the Americas, numerous taxonomic problems and little genetic data are associated with it. To clarify the taxonomy of this species, we used an integrative approach. (2) Methods: Physaloptera retusa-infecting Erythrolamprus typhlus (snake) from the Pantanal wetlands, Brazil, was morphologically and genetically characterised (18S and 28S rDNA; COI mtDNA) and compared with conspecific sequences available in GenBank, from parasites of Tupinambis teguixin (lizard), using species delimitation methods. Type specimens of P. liophis were re-evaluated given its morphological similarities with P. retusa. (3) Results: The morphology of the present specimens was equal to that of P. retusa, in which the only difference from P. liophis was the relative position of the vulva. Species delimitation methods were more accurate for the COI dataset; all of them (except ABGD) indicated interspecificity among P. retusa sequences. However, a lack of morphological data or voucher material, associated with the deposited sequences, prevented more assertive conclusions. (4) Conclusions: The present results highlight the importance of a clear association between genetic data and morphology of the isolation source, or at least its adequate vouchering. Moreover, P. retusa may represent a species complex in cryptic speciation, since it is widespread and has low hosts specificity. Full article

Plankton studies serve as a basis for marine ecosystem research, but knowledge of marine plankton is still incomplete due to its extreme taxonomic and functional complexity. The application of metabarcoding is very valuable for the characterisation of the plankton community. The plankton community of the Southern Adriatic is subject to strong environmental fluctuations and changes, which underlines the need for frequent, reliable and comprehensive characterisation of the plankton. The aim of this study was to determine the taxonomic composition and seasonal distribution of eukaryotic plankton in the Southern Adriatic. Plankton samples were collected monthly for one year at the coastal station of the Southern Adriatic and metabarcoding was used for taxonomic identification. The results showed a high taxonomic diversity and dynamic seasonal distribution patterns for both the protist and metazoan plankton communities. Metabarcoding revealed both the core, year-round plankton community and previously unrecorded plankton organisms in the Southern Adriatic. The results provide for the first time a comprehensive overview of the plankton community in this area by metabarcoding. The identified seasonal patterns of plankton genera and species in the Southern Adriatic will contribute to the understanding of plankton interactions and future changes in community diversity characterisation. Full article

Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease. Full article

Phytoplankton guilds are commonly characterised by dominance effects, while the main contribution to biological diversity is given by rare species. Here, we analysed the influence of rare species on taxonomic and functional diversity, which is described by taxa richness and composition, cell size, and size–abundance relationships in phytoplankton guilds. We explore these relationships at global and regional scales by analysing phytoplankton guilds from five biogeographical regions: the Northern Atlantic Ocean (Scotland), the South-Western Atlantic Ocean (Brazil), the South-Western Pacific Ocean (Australia), the Indo-Pacific Ocean (Maldives), and the Mediterranean Sea (Greece and Turkey). We have comparatively analysed the phytoplankton taxonomic diversity of the whole dataset and with the datasets obtained by progressively subtracting taxa occurring in the last 1%, 5%, 10%, and 25% of both numerical abundance and overall biomass. Globally, 306 taxa were identified across five ecoregions with only 27 taxa accounting for 75% of overall numerical abundance and biomass; almost 50% of taxa were lost on every step. The removal of 1% of most rare taxa significantly affected the phytoplankton size–abundance relationships and body-size structure, strongly impacting on small taxa. The progressive removal of additional rare taxa did not further affect phytoplankton size–abundance relationships and size structure. Full article