Search Results (92)

Camel milk is widely consumed in the world’s arid and semi-arid regions because of its favorable nutritional profile and associated human health benefits. The indigenous microbiota of raw camel milk is diverse and composed of different bacterial and fungal groups. This community drives spontaneous milk fermentation, resulting in a variety of traditional products, including Gariss, Shubat, Chal, Dhanaan, Lfrik, and Suusac (or Suusa), depending on geographic region and cultural practice. This fermented milk has improved sensory, nutritional, and health profiles, as well as an extended shelf life, compared to raw milk. Fermentation alters the microbial community structure, with lactic acid bacteria (LAB) consistently becoming dominant, while yeasts and molds are also detected in some products. These patterns have been identified using both culture-dependent and culture-independent approaches, including 16S rRNA gene sequencing and whole-genome shotgun metagenomics. However, the milk’s microbial composition is highly variable and is influenced by the original composition, geographical location, fermentation and hygiene practices. The detection of opportunistic pathogens such as E. coli, Salmonella and Listeria in some traditional products raises important food safety concerns. This review presents current knowledge on fermented camel milk microbiology using a cross-regional approach, identifying key gaps in microbial safety and process standardization to support wider acceptance and potential commercialization. Full article

Abortion in cattle entails substantial economic loss, and rapid identification of abortigenic pathogens is critical for timely on-farm response and reduction in human exposure risk. In 2024, two Holstein cows from a small farm in Inner Mongolia aborted in close succession without an obvious cause. Vulvar swabs from both cows, one afterbirth sample, and whole blood from one aborted fetus were collected. Shotgun metagenomic sequencing was performed, followed by host-read removal, taxonomic profiling with Kraken2, de novo assembly of Brucella-aligned reads, and whole-genome comparison. Serological tests, Gram-stained smears, and Brucella genus- and species-specific qPCR assays were used as orthogonal verification. Putative resistance and virulence determinants were screened against CARD and VFDB. Brucella reads were detected in all samples, with the highest relative abundance in the 138-afterbirth (96%). qPCR assays detected Brucella DNA and B. abortus-specific signals in all four samples. A draft Brucella genome was assembled from the 138-afterbirth sample and was phylogenetically placed within B. abortus, showing relatedness to previously circulating Chinese lineages. Cows 138 and 198 were RBT-positive with SAT titres of 1:100 (++). No acquired Brucella resistance genes were identified in CARD. Within 72 h of sample receipt, B. abortus was reported to the farm and local authorities and emergency biosecurity measures were implemented. This field investigation shows that metagenomic sequencing, when combined with conventional serology, microscopy, and targeted qPCR, can support rapid etiological investigation when culture is delayed, hazardous, or biosafety level 3 facilities are unavailable. Full article

A clinical strain of the opportunistic pathogen Serratia rubidaea, a known contaminant of healthcare environments and an emerging cause of invasive infections, is described. The studied isolate, recovered from a nurse’s hand skin swab during routine screening, exhibits a broad profile of antibiotic resistance combined with reduced susceptibility to several disinfectants. Phenotypic susceptibility testing using a tablet-based microdilution and disk diffusion method was employed to determine the minimum inhibitory concentrations (MICs) of antimicrobial agents from different classes, while broth microdilution assays with disinfectants revealed high-level tolerance to widely used agents, including 70% C₂H₅OH, 3% H₂O₂, 0.05% polyhexamethylene guanidine (PHMG) and others. Whole-genome sequencing identified multiple resistance-associated determinants, such as chromosome-encoded class C $\beta$-lactamase (ampC), several efflux systems (sdeXY, macAB, and emrAB) combined with multicopy tolC, and specific transferases (fos and arnT). Shotgun bottom-up HPLC-MS/MS proteomics confirmed baseline expression of these and other stress-tolerance-related proteins under non-inducing conditions. Taken together, these data underscore the importance of surveillance for Serratia spp. in healthcare facilities to detect strains that combine intrinsic or acquired multidrug resistance with robust survival traits such as disinfectant tolerance and biofilm formation. The present study provides a reference-level phenotypic, genomic, and proteomic characterization of a S. rubidaea clinical isolate, contributing to the understanding of the adaptive potential of this resilient opportunistic pathogen in clinical environments. Full article

Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects. Full article

Background: Perivascular adipose tissue (PVAT) contains adipocytes and a stromal-vascular fraction with immune cells that modulate the adjacent vasculature. The presence of immune cells in PVAT of vascular beds is poorly understood—are they resident or recruited? We propose a novel resident microbiome present in PVAT, given the immune-rich stromal environment. Hypothesis: We hypothesized the existence of distinct bacterial and viral communities in healthy PVAT compared to non-PVAT adipose tissues. Methods: PVAT samples from thoracic and abdominal aorta, mesenteric resistance arteries, non-PVAT tissues (subscapular brown adipose tissue, retroperitoneal white adipose tissue), and fecal samples were collected one year apart from male Dahl SS rats, split into two cohorts (2023 and 2024, n = 3 each). Whole-genome shotgun sequencing (CosmosID) and 16S rRNA gene analysis assessed microbial relative abundance. Results: PVAT harbored bacterial and viral sequences, and species composition varied significantly between cohorts. Bacterial and viral fecal samples showed lower variability. Conclusions: PVAT microbiome differed dramatically from the fecal microbiome, with temporal influences on bacterial and viral diversity, marking the first such report. Despite inherent limitations, these findings establish the potential of PVAT microbiota in vascular biology and immune modulation, paving the development of microbiome-targeted drugs to address vascular dysfunctions. Full article

Basal cell carcinoma (BCC) is the most common malignancy worldwide, yet the role of the skin microbiome in BCC remains poorly defined. In this cross-sectional observational case series, we compared the cutaneous microbiome of BCC lesions with matched perilesional and control skin using whole-genome shotgun sequencing in an intra-patient, multi-site sampling design. BCC samples demonstrated reduced microbial richness and significant shifts in community composition compared with matched control skin. Specifically, BCC lesions exhibited significantly lower Chao1 diversity (β = −484.6, 95% CI: −772.1 to −197.2, p = 0.003). Differences in overall microbial composition were confirmed by PERMANOVA analysis based on Bray–Curtis and Jaccard distance metrics (R² = 12.6% and 9.7%, respectively; both p = 0.01). At the species level, Cutibacterium acnes was significantly reduced in BCC samples compared with controls (β = −0.31, 95% CI: −0.45 to −0.16, p = 0.0004), corresponding to an approximately 27% lower geometric mean relative abundance. Functional profiling suggested shifts in microbial metabolic potential, with pathways related to redox balance and lipid-associated processes differentially represented in BCC samples relative to controls. Together, these findings demonstrate that BCC lesions are associated with localized alterations in microbial diversity, community composition, and inferred functional potential. These results support the presence of a tumor-associated microbiome signature in BCC; however, further studies in larger and more diverse cohorts are needed to determine whether these changes contribute to tumor development or reflect adaptation to the tumor microenvironment. Full article

While essential oils are gaining momentum as a strategy to modulate rumen function and potentially reduce enteric methane in cattle, little is known about how their bioactive components, terpenes, affect rumen microbes. Our objective was to evaluate how in vivo doses of thymol affect the structure and function of the rumen microbial community via whole genome shotgun sequencing (WGS). Four beef steers were used in a 4 × 4 Latin square with four 28 d periods. Steers consumed ad libitum forage and received one of four thymol doses (0 [CON], 120 [120-T], 240 [240-T], and 480 [480-T] mg/kg forage intake). Rumen contents were separated into liquid and solid fractions, DNA was extracted, analyzed via WGS, and assessed with orthogonal contrasts. After FDR correction, no taxa were affected by thymol; however, raw p-values demonstrated responses to thymol supplementation for solid-associated uncultured Lachnospiraceae bacterium (p = 0.04), uncultured Methanobrevibacter (p = 0.05), and uncultured Coriobacteriaceae bacterium (p = 0.02). Liquid-associated uncultured Prevotellaceae bacterium (p = 0.03), Prevotella sp. (p = 0.04), and Bacteroides sp. (p = 0.02) also responded to thymol, with the highest abundances observed at various thymol doses. Genes involved in energy production and amino acid metabolism transport were observed at the highest abundances at 240-T, while genes associated with cell cycle control, cell division, and chromosome partitioning were present in the highest abundances at 120-T. The findings suggest that thymol exerts dose-dependent effects on rumen microbial abundances and functional pathways, with 240 mg/kg forage intake appearing to be the most effective dose to downregulate methanogenic enzymes while also enhancing the enzymes associated with metabolism without negatively impacting microbial diversity. Full article

The grapevine (Vitis vinifera L.) is one of the most important horticultural crops, with thousands of varieties cultivated worldwide. In this study, we analyzed chloroplast SNV markers using a whole-genome shotgun sequencing approach to investigate the genetic diversity and phylogeny of 409 cultivated V. vinifera accessions originating from nine countries across Southeast and Central Europe, as well as a heterogeneous set of additional accessions maintained by INRAE. Shotgun sequencing allowed high coverage, enabling the detection of 93 SNVs across 24 chloroplast genes, including 11 non-synonymous variants. The ycf1 gene showed the highest variability, consistent with its role in species differentiation. Haplotype analysis revealed 102 distinct haplotypes, with clear geographic structuring: ATT predominated in the eastern Mediterranean, ATA in western Europe, and GTA mainly in a heterogeneous group of varieties from a French collection. To validate the shotgun approach, seven SNV markers were analyzed using target capture sequencing, confirming the accuracy of detected variants with only minimal discrepancies, which is mostly attributable to homopolymeric regions and low-frequency alleles. Phylogenetic analyses using both trees and networks delineated three major haplotype clusters, reflecting human-mediated dispersal of grapevine cultivars through historical viticultural practices. This study represents the largest chloroplast genome analysis of cultivated V. vinifera to date, providing a large cpDNA resource for assessing chloroplast diversity and maternal haplotype structure in cultivated grapevine. The results highlight the power of combining high-throughput sequencing and chloroplast genomics for population-level studies in perennial crops. Full article

Low-density polyethylene (LDPE) and poly (butylene adipate-co-terephthalate) (PBAT) agricultural films are major components of microplastics (MPs) and their contamination in agriculture due to their difficulty to recycle. However, potential degradation mechanisms of MPs from LDPE and PBAT in agricultural soils are still unclear. Here, we isolated a strain of Bacillus cereus L6 from long-term agricultural MP-contaminated soil and analyzed its potential biochemical pathways involved in LDPE and PBAT turnover through functional prediction from shotgun genome sequencing. After 28 days of incubation with MPs, Bacillus cereus L6 caused a net mass loss of 0.99% LDPE-MPs/28 days and 3.58% PBAT-MPs/28 days. The surfaces of LDPE and PBAT degraded in bioassays added with Bacillus cereus L6 showed wrinkles, cracks, and pits, accompanied by an increase in roughness. The crystallinity and thermal stability of both LDPE- and PBAT-MPs were decreased and the hydrophobicity of PBAT-MPs was reduced. Whole-genome sequencing analysis showed that Bacillus cereus L6 potentially encoded genes for enzymes related to the biodeterioration of additives in LDPE and PBAT. Moreover, genomic CAZymes predictive analysis showed that genes related to oxygenases and lyases were annotated in the strain L6 Auxiliary Activities family. These findings offer a theoretical foundation for deeper exploration into the degradation and metabolic processes of MPs from discarded agricultural plastics in the environment. Full article

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/Objectives: We conducted an untargeted metabolomic study in serum, urine, and fecal water in colorectal cancer (CRC) patients compared to healthy controls. The aim was to define the interactions between metabolites and microbiota. Methods: Effluents were collected before colonoscopy. Metabolites were analyzed using LC-HRMS. Bioinformatics analyses included Limma test, along with spectral house and public databases for annotations. Whole-genome shotgun sequencing was performed on fecal samples. Species–metabolite interactions were calculated using Spearman correlation. Interleukins and inflammatory proteins were measured. Results: Fifty-three patients (11 stage I, 10 stage II, 10 stage III, and 22 stage IV) and twenty controls were included. Derivatives of deoxycholic acid, cholic acid, and fatty acids were lower in serum, while urinary bile acids were higher in stage IV CRC patients (versus controls). Metabolites related to tryptophan and glutamate were found significantly altered in stage IV: upregulation of kynurenine and downregulation of indole pathways. This was linked to increased inflammatory protein and microbial metabolites and to the imbalance between virulent pro-inflammatory bacteria (Escherichia and Desulfovibrio) and symbiotic (Ruminococcus and Bifidobacterium) bacteria. Conclusions: E. coli-related tryptophan catabolism shift is shown through stage IV CRC as compared to controls. As a consequence, tryptophan/kynurenine metabolite may become a promising marker for detecting the failure to immune response during therapy. Full article

Azaleas (Ericaceae) are among the most diverse ornamental plants, celebrated for their cultural and economic significance. R. simsii has been extensively utilized in horticulture as a parent species for both “pot azalea” cultivars and various cultivars grown in the warmer regions of China. From 2021 to 2023, approximately 15% of R. simsii in nurseries situated in the Xuanwu District, Nanjing, exhibited symptoms of wilting and chlorosis. Investigations revealed that these symptoms were caused by a pathogen responsible for crown and root rot. Strains were isolated from the roots of affected plants. The morphology of the colonies was predominantly radial to stellate, characterized by intercalary and terminal hyphal swelling. The sporangia appeared spherical, pyriform, or ovoid with a single papillae. For accurate identification, the 28S rDNA gene (Large subunit, LSU), cytochrome oxidase subunit I (COXI), and cytochrome oxidase subunit II (COXII) genes were amplified through PCR and then sequenced. The species was identified as P. vexans after completing the phylogenetic analysis. Healthy R. simsii plants were infected with zoospores and developed symptoms similar to those of natural infection. Furthermore, the morphological characteristics of the isolates from the experimentally infected plants were similar to those of the original inoculated strains. This study identified P. vexans as the pathogen causing root rot in R. simsii. During the sampling process, several strains were isolated from the rhizosphere soil of healthy rhododendron plants. Based on this, research was immediately initiated to explore whether there are specific bacterial species in the soil that have the potential to inhibit the occurrence of root rot. Additionally, an endophytic bacterial strain BL1 was isolated from rhizosphere soil and subjected to Whole-Genome Shotgun (WGS) sequencing, thus constructing a bacterial genome framework for this isolate. The strain BL1 was identified as Bacillus licheniformis. To our knowledge, this is the first report of the occurrence of P. vexans causing crown and root rot of R. simsii in China. In this study, we also focused on exploring the potential of biological control agents against P. vexans. The isolation and identification of the endophytic bacterial strain BL1 (Bacillus licheniformis) from the rhizosphere soil of healthy soil show strong in vitro antagonism, identifying it as a promising candidate for future biological control studies of root rot in R. simsii. The genomic component analysis and coding gene annotation of BL1 provide insights into its genetic makeup and potential mechanisms of action against pathogens. However, these findings are based on in vitro assays. Therefore, further research, including in planta experiments, is essential to confirm the efficacy of BL1 in controlling P. vexans infections in R. simsii and to evaluate its potential for practical application. 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