Search Results (77)

Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m²), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m²), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m²) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m² had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m². Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m² obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index. Full article

Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings. Full article

Vitiligo is an autoimmune skin disease with a significant psychological burden and complex pathogenesis. While genetic factors contribute approximately 30% to its development, recent evidence suggests a crucial role of the gut microbiome in autoimmune diseases. This study investigated differences in gut microbiome composition and metabolic pathways between active spreading vitiligo patients and healthy controls using shotgun whole-genome sequencing in a Korean cohort. Taxonomic profiling reveals distinct characteristics in microbial community structure, with vitiligo patients showing an imbalanced proportion dominated by Actinomycetota and Bacteroidota. The vitiligo group exhibited significantly reduced abundance of specific species including Faecalibacterium prausnitzii, Faecalibacteriumduncaniae, and Meamonas funiformis, and increased Bifidobacterium bifidum compared to healthy controls. Metabolic pathway analysis identified significant enrichment in O-glycan biosynthesis pathways in vitiligo patients, while healthy controls showed enrichment in riboflavin metabolism and bacterial chemotaxis pathways. These findings provide new insights into the gut–skin axis in vitiligo pathogenesis and suggest potential therapeutic targets through microbiota modulation. Full article

Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia’s rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant–root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial–fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability. Full article

A whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, Ornithobacterium rhinotracheale (ORT) and a putative prophage candidate were found in one of the swab samples. A multi-locus sequence typing (MLST) scheme of the ORT genome involved the adk, aroE, fumC, gdhA, pgi, and pmi genes. Antibiotic resistant analysis demonstrated tetracycline-resistan t ribosomal protection protein, tetQ, the aminoglycoside-(3)-acetyltransferase IV gene, aminoglycoside antibiotic inactivation and macrolide resistance, and the ermX gene in the ORT genome. A putative prophage candidate was predicted using Prophage Hunter and PHAST, while BLAST analyses were utilized to identify genes encoding bacteriophage proteins. Interestingly, genes encoding endolysins were detected in bacteriophage genomes. The gene products encoded in the prophage sequence were most closely related to bacteriophages in the N4-like family among the Authographiviridae in the Caudovirales. This study demonstrates the potential of sWGS for the rapid detection and characterization of etiologic agents found in clinical samples. Full article

Bioinformatic methodologies play a crucial role in the assessment of gut microbiota, offering advanced tools for analyzing complex microbial communities. These methodologies involve high-throughput sequencing technologies, such as 16S rRNA gene sequencing and metagenomics, which generate vast amounts of data on microbial diversity and functional potential, as well as whole-genome sequencing, which, while being more costly, has a more expansive potential. Bioinformatics tools and algorithms process these data to identify microbial taxa and quantify and elucidate their roles within the microbiome. Advanced statistical and computational models further enable the identification of microbiota patterns associated with various diseases and health conditions. Overall, bioinformatic approaches are essential for deciphering the complexities of gut microbiota so that, in the future, we may be able to discover treatments and technologies aimed at restoring or optimizing the microbiome. The goal of this review is to describe the differences in methodology and utilization of 16S versus whole-genome sequencing to address the increased understanding of the role that the gut microbiome plays in human physiology and pathology. Full article

Antarctica has attracted increasing interest in understanding its microbial communities, metabolic potential, and as a source of microbial hydrolytic enzymes with industrial applications, for which advances in next-generation sequencing technologies have greatly facilitated the study of unculturable microorganisms. In this work, soils from seven sub-Antarctic islands and Union Glacier were studied using a whole-genome shotgun metagenomic approach. The main findings were that the microbial community at all sites was predominantly composed of the bacterial phyla Actinobacteria and Cyanobacteria, and the families Streptomycetaceae and Pseudonocardiaceae. Regarding the xenobiotic biodegradation and metabolism pathway, genes associated with benzoate, chloroalkane, chloroalkene, and styrene degradation were predominant. In addition, putative genes encoding industrial enzymes with predicted structural properties associated with improved activity at low temperatures were found, with catalases and malto-oligosyltrehalose trehalohydrolase being the most abundant. Overall, our results show similarities between soils from different Antarctic sites with respect to more abundant bacteria and metabolic pathways, especially at higher classification levels, regardless of their geographic location. Furthermore, our results strengthen the potential of Antarctic soils as a source of industrially relevant enzymes. Full article

Six hundred million cases of disease and roughly 420,000 deaths occur globally each year due to foodborne pathogens. Current methods to screen and identify pathogens in swine, poultry, and cattle products include immuno-based techniques (e.g., immunoassay integrated biosensors), molecular methods (e.g., DNA hybridization and PCR assays), and traditional culturing. These methods are often used in tandem to screen, quantify, and characterize samples, prolonging real-time comprehensive analysis. Next-generation sequencing (NGS) is a relatively new technology that combines DNA-sequencing chemistry and bioinformatics to generate and analyze large amounts of short- or long-read DNA sequences and whole genomes. The goal of this project was to evaluate the quantitative capabilities of the real-time NGS Oxford Nanopore Technologies’ MinION sequencer through a shotgun-based sequencing approach. This investigation explored the correlation between known amounts of the analyte (lambda DNA as a pathogenic bacterial surrogate) with data output, in both the presence and absence of a background matrix (Bos taurus DNA). A positive linear correlation was observed between the concentration of analyte and the amount of data produced, number of bases sequenced, and number of reads generated in both the presence and absence of a background matrix. In the presence of bovine DNA, the sequenced data were successfully mapped to the NCBI lambda reference genome. Furthermore, the workflow from pre-extracted DNA to target identification took less than 3 h, demonstrating the potential of long-read sequencing in food safety as a rapid method for screening, identification, and quantification. Full article

Objectives: This study examined the effect of a 4-week unsweetened cranberry beverage (CRAN) (317 mg polyphenols) versus placebo beverage (PLAC) ingestion (240 mL/day) on moderating exercise-induced changes in innate immunity. Methods: Participants included 25 male and female non-elite cyclists. A randomized, placebo-controlled, double-blind crossover design was used with two 4-week supplementation periods and a 2-week washout period. Supplementation periods were followed by an intensive 2.25 h cycling bout. Six blood samples were collected before and after supplementation (in an overnight fasted state) and at 0 h, 1.5 h, 3 h, and 24 h post-exercise. Stool and urine samples were collected pre- and post-supplementation. Outcome measures included serum creatine kinase, myoglobin, and cortisol, complete blood counts, plasma untargeted proteomics, plasma-targeted oxylipins, untargeted urine metabolomics, and stool microbiome composition via whole genome shotgun (WGS) sequencing. Results: Urine CRAN-linked metabolites increased significantly after supplementation, but no trial differences in alpha or beta microbiota diversity were found in the stool samples. The 2.25 h cycling bout caused significant increases in plasma arachidonic acid (ARA) and 53 oxylipins (FDR q-value < 0.05). The patterns of increase for ARA, four oxylipins generated from ARA-cytochrome P-450 (CYP) (5,6-, 8,9-, 11,12-, and 14,15-diHETrEs), two oxylipins from linoleic acid (LA) and CYP (9,10-DiHOME, 12,13-DiHOME), and two oxylipins generated from LA and lipoxygenase (LOX) (9-HODE, 13-HODE) were slightly but significantly higher for the CRAN versus PLAC trial (all interaction effects, p < 0.05). The untargeted proteomics analysis showed that two protein clusters differed significantly between the CRAN and PLAC trials, with CRAN-related elevations in proteins related to innate immune activation and reduced levels of proteins related to the regulation of the complement cascade, platelet activation, and binding and uptake of ligands by scavenger receptors. No trial differences were found for cortisol and muscle damage biomarkers. Conclusions: CRAN versus PLAC juice resulted in a significant increase in CRAN-related metabolites but no differences in the gut microbiome. CRAN supplementation was associated with a transient and modest but significant post-exercise elevation in selected oxylipins and proteins associated with the innate immune system. Full article

The objective of this investigation is to ascertain the distinctive profile of the rhizospheric soil resistome within the Mecca region, while also evaluating the potential risks associated with the horizontal transfer of resistome determinants to the open environment and human clinical isolates. We have made metagenomic whole-genome shotgun sequencing for rhizospheric microbiomes of two endemic plants, namely Moringa oleifera and Abutilon fruticosum. The rhizospheric resistomes of the two plants and the abundance of antibiotic resistance genes (ARGs) were identified by cross-referencing encoded proteins with the comprehensive antibiotic resistance database (CARD). The identified ARGs were then analyzed for their antimicrobial resistance (AMR) mechanisms. Predominantly within this soil are the two bacterial species Pseudomonas aeruginosa and Mycobacterium tuberculosis. These opportunistic human pathogens are implicated in respiratory infections and are correlated with heightened mortality rates. The most prevalent array of ARGs existing in this soil comprises mexA, mexC, mexE, and cpxR, associated with mechanisms of antibiotic active efflux, along with ACC(2), ACC(3), AAC(6), and APH(6), in addition to arr1, arr3, arr4, iri, rphA, and rphB, implicated in antibiotic inactivation. Furthermore, vanS, vanR, and vanJ are identified for antibiotic target alteration, while rpoB2 and RbpA are noted for antibiotic target replacement and protection, respectively. These mechanisms confer resistance against a diverse spectrum of drug classes encompassing fluoroquinolones, aminoglycosides, glycopeptides, and rifampicins. This study underscores the potential hazards posed to human health by the presence of these pathogenic bacteria within the rhizospheric soil of the Mecca region, particularly in scenarios where novel ARGs prevalent in human populations are harbored and subsequently transmitted through the food chain to human clinical isolates. Consequently, stringent adherence to good agricultural and food transportation practices is imperative, particularly with regard to edible plant parts and those utilized in folkloric medicine. Full article

The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients. Full article

Cabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of reference genomes of plant-associated microbes together with recent advances in metagenomic approaches provide new opportunities to identify microbes linked to distinct symptomatology in Brassica leaves. In this study, shotgun metagenomics was used to investigate the microbial community in leaves of B. oleracea plants from agricultural farmlands. Compared with conventional techniques based on culture-based methods, whole-genome shotgun sequencing allows the reliable identification of the microbial population inhabiting a plant tissue at the species level. Asymptomatic and symptomatic leaves showing different disease symptoms were examined. In the asymptomatic leaves, Xanthomonas species were the most abundant taxa. The relative abundance of bacterial and fungal communities varied depending on disease symptoms on the leaf. The microbiome of the leaves showing mild to severe levels of disease was enriched in bacterial populations (Sphingomonas, Methylobacterium, Paracoccus) and to a lesser degree in some fungal taxa, such as Alternaria and Colletotrichum (e.g., in leaves with high levels of necrotic lesions). Sclerotinia species were highly abundant in severely damaged leaves (S. sclerotium, S. trifolium, S. bolearis), followed by Botrytis species. The common and specific bacterial and fungal species associated to disease symptoms were identified. Finally, the analysis of the gene functions in the metagenomic data revealed enrichment in carbohydrate-active enzymes potentially involved in pathogenicity, whose distribution also varied among disease severity groups. Understanding the B. oleracea leaf microbiome in agricultural ecosystems will pave the way for the efficient management of diseases in this crop. Full article

From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed the precise alpha satellite higher-order repeat (HOR) structure using the novel high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified alpha satellite HORs in the centromere of orangutan chromosome 13, discovering a novel 59mer HOR—the longest HOR unit identified in any primate to date. Additionally, it revealed the first intertwined sequence of three HORs, 18mer/27mer/45mer HORs, with a common aligned “backbone” across all HOR copies. The major 7mer HOR exhibits a Willard’s-type canonical copy, although some segments of the array display significant irregularities. In contrast, the 14mer HOR forms a regular Willard’s-type HOR array. Surprisingly, the GRM2023 high-precision analysis of chromosome 13 of human genome assembly T2T-CHM13v2.0 reveals the presence of only a 7mer HOR, despite both the orangutan and human genome assemblies being derived from whole genome shotgun sequences. Full article

Unraveling the multisymptomatic Gulf War Illness (GWI) pathology and finding an effective cure have eluded researchers for decades. The chronic symptom persistence and limitations for studying the etiologies in mouse models that differ significantly from those in humans pose challenges for drug discovery and finding effective therapeutic regimens. The GWI exposome differs significantly in the study cohorts, and the above makes it difficult to recreate a model closely resembling the GWI symptom pathology. We have used a double engraftment strategy for reconstituting a human immune system coupled with human microbiome transfer to create a humanized-mouse model for GWI. Using whole-genome shotgun sequencing and blood immune cytokine enzyme linked immunosorbent assay (ELISA), we show that our double humanized mice treated with Gulf War (GW) chemicals show significantly altered gut microbiomes, similar to those reported in a Veteran cohort of GWI. The results also showed similar cytokine profiles, such as increased levels of IL-1β, IL-6, and TNF R-1, in the double humanized model, as found previously in a human cohort. Further, a novel GWI Veteran fecal microbiota transfer was used to create a second alternative model that closely resembled the microbiome and immune-system-associated pathology of a GWI Veteran. A GWI Veteran microbiota transplant in humanized mice showed a human microbiome reconstitution and a systemic inflammatory pathology, as reflected by increases in interleukins 1β, 6, 8 (IL-1β, IL-6, IL-8), tumor necrosis factor receptor 1 (TNF R-1), and endotoxemia. In conclusion, though preliminary, we report a novel in vivo model with a human microbiome reconstitution and an engrafted human immune phenotype that may help to better understand gut–immune interactions in GWI. 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