The microorganism communities resided in mammalian gastrointestinal tract impacted the health and disease of the host. Our study complements metagenomic analysis with culture-based approach to establish a bacteria and genome collection and comprehensively investigate the microbiome composition and function of the gut of weanling piglets. We provide a valuable resource for further study of gut microbiota of weanling piglet and development of probiotics for prevention of disease.

Gut microbiomes in various fish species were widely investigated with the rapid development of next-generation sequencing technologies. However, little is known about gastrointestinal (GI) microbial communities in mudskippers, a representative group of marine amphibious fishes, and their comparisons with other vertebrate animals from different habitats. Here, we performed a comprehensive analysis on microbial composition in five representative vertebrate groups (including amphibious mudskippers, marine and freshwater aquatic fishes, amphibians, and terrestrial animals) via operational taxonomic unit (OTU) survey and obtained a microbial gene catalog of five common fish species by metagenome sequencing. We observed that Cyanobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria were the most substantial bacteria in mudskippers. Differential variances in composition patterns of GI microbiota among the vertebrate groups were determined, although Proteobacteria and Firmicutes were the shared phyla with high abundance. In addition, Cetobacterium and Photobacterium were the most abundant genera in core OTUs of these examined omnivores, carnivores, and herbivores. Our metagenomic analysis also showed significant differences between the representative blue-spotted mudskipper and grass carp (both are herbivorous fishes) in microbes at the phylum and class levels and functional gene terms. Moreover, several bacteriocin-related genes were identified in the five common fishes, suggesting their potential contributions to pathogen resistance. In summary, our present work not only sheds new light on the correlation of GI microbiota composition with living habitats and feeding habits of the hosts, but also provides valuable bacterial genetic resources for healthy growth of aquaculture fishes.

Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies. IMPORTANCE: This study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.

Background: Staphylococcus aureus is a prominent pathogen responsible for human pyogenic and nosocomial infections. Although numerous studies on S. aureus L-forms and virulence are available in the literatures, there are still various impediments in the research methods employed. Objectives: This study aimed to perform fluorescence reporter in studying S. aureus L-form and its virulence, and wild strain virulence. Methods: Newman-pCM29 strain which can express green fluorescent protein (GFP) was constructed and used to detect S. aureus L-form formation and virulence in vitro and in vivo. Results: “Fried egg” like L-form colonies of GFP reporter S. aureus and the dense core of the colonies embedded into soft agar can be observed obviously. GFP reporter can contribute to preparing L-form suspension for injection and track the protoplasts and reverted cells in lesions of mice. GFP reporter, also, can help to detect S. aureus wild strain distribution and inflammation scope in lesions, and the fluorescence intensity can be used as an effective surrogate to represent the bacterial quantity in lesions. Fluorescence can improve to distinguish the colonies of varying sizes derived from the injected bacteria or from contaminants. Conclusions: Fluorescence reporter in S. aureus is a powerful tool which can provide new insight into S. aureus L-form formation in vitro and its fate in vivo, and wild strain virulence in vivo in a non-traditional manner. Keywords: Fluorescence Reporter; GFP; L-Form; Virulence; Staphylococcus aureus

Background: The microbiota hosted in the pig gastrointestinal tract are important to health of this biomedical model. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Results: Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. 445 secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. Conclusions: A total of 266 isolated bacterial genomes and 482 MAGs were obtained and investigated their functional repertoires. This study provides a comprehensive view of the microbiome composition and the function landscape of the gut of weanling piglets and a valuable bacterial resource for further experimentations.