Search Results (70)

The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets. Full article

Background: Periodontitis is a chronic inflammatory disease mostly associated with Porphyromonas gingivalis infection and characterized by progressive destruction of the supporting structures of the tooth, including the gingiva, periodontal ligament and alveolar bone. However, the impact of other members of the periodontal microbiome on stage of the severity of the periodontitis remains largely uncharacterized. Methods: This exploratory study employs whole-genome shotgun (WGS) metagenomics to characterize the periodontal microbiome in patients suffering from mild and severe periodontitis, aiming to identify microbial signatures linked to disease severity via analysis of taxonomic composition, predicted metabolic pathways and metagenome-assembled genomes (MAGs). After initial selection, 28 adult patients with a computer tomography (CT)-confirmed diagnosis of mild and severe stage of periodontitis from 2 clinics were included in the research project. Results: Taxonomic analysis confirms the presence of various commensal and pathogenic bacteria detectable at the species level, especially belonging to so-called “red, orange and green periodontal complexes”—P. gingivalis, T. forsythia, C. rectus, and Capnocytophaga spp. that may contribute to disease heterogeneity. The conducted investigation suggests that non-microbial factors such as cardiovascular diseases and antibiotic usage in the last 6 months prior to the hospital admission could explain variance of disease progression and impact on severity. Analysis of microbial functional composition revealed metabolic traits showing positive correlations with severe stage of periodontitis. Robust network analysis suggested interactions between pathogenic bacteria of the red complex and other members of the periodontal microbiome. Conclusions: These findings underscore the multifactorial nature of periodontitis pathogenesis, highlighting the need for integrated approaches combining microbial, host, and environmental data to unravel drivers of disease progression. The study provides a foundation for future large-scale investigations into personalized diagnostic or therapeutic strategies. Full article

The gut microbiome of pigs is important for energy supply and impacts the animals’ health. Additionally, the microbiota can act as a reservoir for antimicrobial resistance genes (ARG). Different husbandry systems in pig farming can influence the microbiome and the overall composition of the resistome, i.e., the complete collection of ARG. In this study, pooled fecal samples were collected repeatedly in one pig farm over a period of two years. One group of animals was kept in organic husbandry conditions with access to an outdoor run, while the other group was kept according to conventional standards. Shotgun metagenomic sequencing was performed on the samples. Additionally, E. coli isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing. Significant differences were observed in alpha and beta diversity in the microbiome between the two husbandry systems. Families enriched in the organic group included Prevotellaceae, Lachnospiraceae, and Cellulosilyticaceae, while Methanobacteriaceae showed a higher abundance in the conventional group. In the resistome, the differences were smaller, and the dominant genes were the same in both groups. However, there was a significant difference in beta diversity. In addition, the overall frequency of ARG, normalized by 16S rRNA gene content, was on average higher in the organic group. Overall, the husbandry system shaped the microbiome and—albeit to a lesser extent—the resistome in pigs from the same farm. Full article

Tall fescue toxicosis, caused by ingestion of endophyte-infected tall fescue (Lolium arundinaceum), impairs growth and reproduction in beef cattle and results in over USD 3 billion annual loss to the U.S. livestock industry. While the effects on host metabolism and rumen function have been described, the impact on the rectal microbiome remains poorly understood. In this study, we performed whole-genome shotgun metagenomic sequencing on fecal samples collected before and after a 30-day toxic fescue seed supplementation from eight pregnant Angus × Simmental cows and heifers. We generated 157 Gbp of sequencing data in 16 metagenomes, and assembled 13.1 Gbp de novo microbial contigs, identifying 22 million non-redundant microbial genes from the cattle rectum microbiome. Fescue toxicosis significantly reduced alpha diversity (p < 0.01) and altered beta diversity (PERMANOVA p < 0.01), indicating microbial dysbiosis. We discovered significant enrichment of 31 bacterial species post-treatment, including multiple core rumen taxa. Ruminococcaceae bacterium P7 showed an average of 16-fold increase in fecal abundance (p < 0.01), making it the top-featured species in linear discriminant analysis. Functional pathway analysis revealed a shift from energy metabolism to antimicrobial resistance and DNA replication following toxic seed consumption. Comparative analysis showed increased representation of core rumen taxa in rectal microbiota post-treatment, suggesting disrupted rumen function. These findings demonstrate that fescue toxicosis alters both the composition and functional landscape of the hindgut microbiota. Ruminococcaceae bacterium P7 emerges as a promising biomarker for monitoring fescue toxicosis through non-invasive fecal sampling, with potential applications in herd-level diagnostics and mitigation strategies. Full article

Consumers are increasingly concerned about the flavor quality of poultry meat, yet the relationship between inosine monophosphate (IMP), intramuscular fat (IMF), and the gut microbiota remains largely unclear. This study aimed to characterize the cecal microbiota associated with IMP/IMF deposition in Daheng broilers selectively bred for high-IMP/IMF levels (High group) and low levels (Control group). A two-stage microbiome analysis strategy was applied. Initially, 16S rRNA gene sequencing was conducted to assess microbial diversity and composition. Significant differences were observed between groups in alpha diversity indices (Chao1 and Faith_PD) and beta diversity (p < 0.05). LEfSe analysis identified 55 differentially abundant taxa (LDA > 3, p < 0.05), primarily within the Phylum bacteroidota. To achieve species-level and functional insights, whole-metagenome shotgun sequencing was performed. Taxonomic profiling of 62,443 microbial species revealed significant beta diversity differences (p < 0.05), with 120 dominant species differentially enriched (LDA > 3, p < 0.05), including 77 species in the High group such as Merdivivens faecigallinarum. Enriched functional genes were mainly involved in methane metabolism, starch and sucrose metabolism, and the nucleoside phosphate metabolic process. A total of 882 metagenome-assembled genomes (MAGs) were reconstructed and integrated with 19,628 publicly available chicken MAGs, resulting in 2609 non-redundant genomes, including 52 novel ones. These findings suggest that cecal microbial composition and function are associated with IMP/IMF levels in broilers, providing candidate bacterial species and functional pathways for further validation through gavage-based intervention and multi-omics analysis. Full article

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

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

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

When treating anaerobic brain abscesses, healthcare professionals often face the difficulty of identifying the causal pathogens, necessitating empiric therapies with uncertain efficacy. We present the case of a 57-year-old woman who was admitted to our hospital with a fever and headache. Brain magnetic resonance imaging revealed a hemorrhagic lesion with wall enhancement at the left hemisphere on contrast-enhanced T1-weighted imaging. Cerebrospinal fluid examination showed pleocytosis (23 cells/μL), an elevated protein level (125 mg/dL), and decreased glucose level (51 mg/dL; blood glucose was 128 mg/dL). Intracerebral hemorrhage accompanied by a brain abscess was clinically suspected. The patient received empirical treatment with intravenous meropenem and vancomycin for 2 weeks. However, conventional bacterial culture tests failed to identify the pathogen. We then performed shotgun sequencing and ribosomal multilocus sequence typing, which identified Paraclostridium tenue. Based on this finding, we de-escalated to benzylpenicillin potassium for 4 weeks, leading to a 2.5-year remission of the anaerobic brain abscess. Therefore, Paraclostridium can be a causative pathogen for brain abscesses. Furthermore, whole-metagenome sequencing is a promising method for detecting rare pathogens that are not identifiable by conventional bacterial culture tests. This approach enables more targeted treatment and contributes to achieving long-term remission in clinical settings. 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

Although glaucoma is a leading cause of irreversible blindness worldwide, its pathogenesis is incompletely understood, and intraocular pressure (IOP) is the only modifiable risk factor to target the disease. Several associations between the gut microbiome and glaucoma, including the IOP, have been suggested. There is growing evidence that interactions between microbes on the ocular surface, termed the ocular surface microbiome (OSM), and tear proteins, collectively called the tear proteome, may also play a role in ocular diseases such as glaucoma. This study aimed to find characteristic features of the OSM and tear proteins in patients with glaucoma. The whole-metagenome shotgun sequencing of 32 conjunctival swabs identified Actinobacteria, Firmicutes, and Proteobacteria as the dominant phyla in the cohort. The species Corynebacterium mastitidis was only found in healthy controls, and their conjunctival microbiomes may be enriched in genes of the phospholipase pathway compared to glaucoma patients. Despite these minor differences in the OSM, patients showed an enrichment of many tear proteins associated with the immune system compared to controls. In contrast to the OSM, this emphasizes the role of the proteome, with a potential involvement of immunological processes in glaucoma. These findings may contribute to the design of new therapeutic approaches targeting glaucoma and other associated diseases. Full article