First case report on Empedobacter falsenii bacteremia

Uncovering the microbiome landscape in sashimi delicacies

It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.

Microbial Community Establishment, Succession, and Temporal Dynamics in an Industrial Semi-Synthetic Metalworking Fluid Operation: A 50-Week Real-Time Tracking

Microorganisms colonizing modern water-based metalworking fluids (MWFs) have been implicated in various occupational respiratory health hazards to machinists. An understanding of the exposure risks from specific microbial groups/genera/species (pathogenic or allergenic) and their endotoxins and the need for strategies for effective, timely fluid management warrant real-time extended tracking of the establishment of microbial diversity and the prevailing fluid-related factors. In the current study, the microbial community composition, succession, and dynamics of a freshly recharged industrial semi-synthetic MWF operation was tracked in real-time over a period of 50 weeks, using a combination of microbiological and molecular approaches. Substantial initial bacterial count (both viable and non-viable) even in the freshly recharged MWF pointed to the inefficiency of the dumping, cleaning, and recharge (DCR) process. Subsequent temporal analysis using optimized targeted genus/group-specific qPCR confirmed the presence of Pseudomonads, Enterics, Legionellae, Mycobacteria (M. immunogenum), Actinomycetes, and Fungi. In contrast, selective culturing using commercial culture media yielded non-specific isolates and collectively revealed Gram-negative (13 genera representing 19 isolates) and Gram-positive (2 genera representing 6 isolates) bacteria and fungi but not mycobacteria. Citrobacter sp. and Bacillus cereus represented the most frequent Gram-negative and Gram-positive isolates, respectively, across different media and Nectria haematococca isolation as the first evidence of this fungal pathogen colonizing semi-synthetic MWF. Unbiased PCR-DGGE analysis revealed a more diverse whole community composition revealing 22 bacterial phylotypes and their succession. Surges in the endotoxin level coincided with the spikes in Gram-negative bacterial population and biocide additions. Taken together, the results showed that semi-synthetic MWF is conducive for the growth of a highly diverse microbial community including potential bacterial and fungal pathogens, the current DCR practices are inefficient in combating microbial reestablishment, and the practice of periodic biocide additions facilitates the build-up of endotoxins and non-viable bacterial population.

Impact of Season on Intestinal Bacterial Communities and Pathogenic Diversity in Two Captive Duck Species

Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4-V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds.