Editorial: Unveiling microbiome interactions and functions in soil hotspots
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Big data and artificial intelligence in animal nutrition: a new era of precision feeding
The convergence of Big Data and Artificial Intelligence (AI) is redefining animal nutrition by enabling precision feeding systems that are individualized, data-driven, and sustainability-oriented. This review synthesizes recent advances in multi-omics technologies, sensor-based monitoring, and …
Read PDFAcute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review
Acute respiratory infections (ARIs) remain a leading cause of global morbidity and mortality, disproportionately affecting vulnerable populations such as children, the elderly, and immunocompromised individuals. Despite the availability of traditional diagnostic tools, including viral culture …
Read PDFAuthor Correction: Unbinned contigs expand known diversity in the global microbiome
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Read PDFInterstitial pneumonias of undetermined etiology in foals in California, 1990-2020
Interstitial and bronchointerstitial pneumonias of undetermined etiology in young foals are relatively common in autopsy services with an equine focus. Unknown viruses, toxins, hyperthermia, surfactant or alveolar macrophage function deficiency, certain antibiotics, and aberrant responses …
Read PDFMetagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye
We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla …
Read PDFComparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida
Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, …
Read PDFUnraveling Tempeh through omics: a scoping review of fermentation pathways and functional health benefits
Tempeh, a traditional Indonesian fermented soybean product, is widely recognized for its functional properties and for containing bioactive compounds produced by microbial fermentation. This study integrates recent advances in multi-omics technologies to elucidate the microbial …
Read PDFCo-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with …
Read PDFEndolithic fungal diversity is present in the unique phosphatized rocks of an environmentally extreme equatorial archipelago revealed by DNA amplicon metagenomics
We evaluated endolithic fungal diversity associated with rocks sampled at the polyextreme Brazilian São Pedro and São Paulo archipelago using a DNA amplicon metagenomics approach. We detected 808,547 fungal DNA reads grouped into 92 amplicon …
Read PDFThe role of the gut microbiome in antibiotic-driven antimicrobial resistance
Antimicrobial resistance (AMR) is one of the most pressing threats to global health system. The human gut harbors a complex microbial ecosystem coordinated through mechanisms of metabolic interdependence. The gut microbiota plays a vital role …
Read PDFGut check: Exploring tools, techniques, and future directions in microbiome research
Poultry microbial communities are now recognized as key contributors to host nutrition, immune function, disease resilience, and overall health and performance, driving growing interest in this research field. This symposium brought together leading experts to …
Read PDFImpact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle
BACKGROUND: Dietary trace mineral (TM) concentrations for lactating cows often exceed national recommendations under commercial feeding practices. Excess TM supplementation may exert selection pressure on the gut microbiota, promoting metal resistance and potentially co-selecting for …
Read PDFMetagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans)
BACKGROUND: The microbiome is significant for conservation biology and should be considered in threatened species management programs. Commensal microbes contribute important functions for host health, while pathogenic microbes can negatively impact the host, leading to …
Read PDFArtificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance
Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in …
Read PDFDual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds
Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain …
Read PDFIntegrating metagenomics and metatranscriptomics into <i>Orthoflavivirus</i> diagnosis: a transformative approach for clinical virology
Diagnostic inaccuracies are a major yet often overlooked threat to global health, leading to delayed treatment, preventable harm and systemic gaps in disease control. Among the most affected domains are <i>Orthoflavivirus</i> infections, which pose ongoing …
Read PDFAntibiotic Resistance Genes in the Subgingival Microbiome in Periodontitis: A Scoping Review of Prevalence, Mobility, and Future Directions
The objective of the study is to evaluate the prevalence, diversity, and mobility of antibiotic-resistant species and resistance genes within the subgingival microbiome of patients with periodontitis. A systematic scoping review was conducted in accordance …
Read PDFExploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling
Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in …
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