Customizable 3D printed diffusion chambers for studies of bacterial pathogen phenotypes in complex environments

Gaps in our understanding of the natural ecology and survival mechanisms of pathogenic bacteria in complex microenvironments such as soil typically occur due to the difficulty in characterizing biochemical profiles and morphological characteristics as they exist in environmental samples. Conversely, accurate simulation of the abiotic and biotic chemistries of soil habitats within the laboratory is often a significant challenge. Herein, we present the fabrication of customizable and precisely engineered 3D printed diffusion chambers that can be used to incubate bacterial cultures directly in soil matrices within a controlled laboratory experiment, and study the dynamics between bacterial cells and soil components. As part of the design process, different types of 3D printing materials were evaluated for ease of sterilization, structural integrity throughout the experiment, as well as cost/ease of production. To demonstrate potential applications for environmental studies, the diffusion chamber was used to incubate cultures of Bacillus cereus T-strain and Escherichia coli strain O157 directly in soil matrices. We show that the chamber facilitates diffusion of abiotic/biotic components of the soil with target cells without contamination from in situ microbial communities, while allowing for single cell and ensemble level phenotypic analyses of bacteria cultured with and without soil matrices.

Safety Evaluation of a Novel Strain of Bacteroides fragilis

Commensal non-toxigenic Bacteroides fragilis confers powerful health benefits to the host, and has recently been identified as a promising probiotic candidate. We previously isolated B. fragilis strain ZY-312 and identified it as a novel strain based on 16S rRNA sequencing and morphological analyses. We also determined that ZY-312 displayed desirable probiotic properties, including tolerance to simulated digestive fluid, adherence, and in vitro safety. In this study, we aim to investigate whether ZY-312 meets the safety criteria required for probiotic bacteria through comprehensive and systematic evaluation. Consequently, the fatty acid profile, metabolite production, and biochemical activity of strain ZY-312 were found to closely resemble descriptions of B. fragilis in Bergey’s manual. Taxonomic identification of strain ZY-312 based on whole genome sequencing indicated that ZY-312 and ATCC 25285 showed 99.99% similarity. The 33 putative virulence-associated factors identified in ZY-312 mainly encoded structural proteins and proteins with physiological activity, while the lack of bft indicated that ZY-312 was non-toxigenic. In vivo safety was proven in both normal and immune-deficient mice. The 11 identified antibiotic resistance genes were located on the chromosome rather than on a plasmid, ruling out the risk of plasmid-mediated transfer of antibiotic resistance. In vitro, ZY-312 showed resistance to cefepime, kanamycin, and streptomycin. Finally, and notably, ZY-312 exhibited high genetic stability after 100 passages in vitro. This study supplements the foundation work on the safety evaluation of ZY-312, and contributes to the development of the first probiotic representative from the dominant Bacteroidetes phylum.

Taxonomy of Yersinia pestis

This chapter summarized the taxonomy and typing works of Yersinia pestis since it's firstly identified in Hong Kong in 1894. Phenotyping methods that based on phenotypic characteristics, including biotyping, serotyping, antibiogram analysis, bacteriocin typing, phage typing, and plasmid typing, were firstly applied in classification of Y. pestis in subspecies level. And then, with the advancement of molecular biological technology, the methods based on outer membrane protein profiles, fatty acid composition, and bacterial mass fingerprinting were also used to identify the populations within Y. pestis. However, Y. pestis is a highly homogenous species; therefore, the above typing methods could only provide low resolution, e.g., only one serotype and one phage type were observed for the whole species. Since the 1990s, molecular typing based on DNA variations, including single-nucleotide polymorphism, gene gain/loss, variable-number tandem repeats, clustered regularly interspaced short palindromic repeat, etc., was introduced and improved the resolution and robust of typing result. Especially in recent years, genotyping-based whole-genome-wide variations were successfully employed in Y. pestis, which built the "gold standard" of typing scheme of the species and could distinguish the samples under the strain level. The taxonomy and typing works leaved us enormous polymorphism data; therefore, a comprehensive fingerprint database of Y. pestis was needed to collect and standardize these data, for facilitating future works on evolution, plague surveillance and control, anti-bioterrorism, and microbial forensic researches.

Budvicia diplopodorum sp. nov. and emended description of the genus Budvicia

A Gram-negative, rod-shaped, weakly motile, non-spore-forming bacterium (D9T) was isolated from the gut of Cylindroiulus fulviceps (Diplopoda) on 1/3-strength nutrient agar plates. On the basis of 16S rRNA gene sequence similarity, strain D9T was shown to be phylogenetically closely related to the type strain of Budvicia aquatica , the sole species of the genus Budvicia , family Enterobacteriaceae . The similarity of the 16S rRNA gene sequences of strain D9T and B. aquatica DSM 5075T was 98.4 %. Other strains that showed high pairwise similarities with the isolate belonged to the genus Yersinia : Y. frederiksenii ATCC 33641T (96.8 % 16S rRNA gene sequence similarity), Y. massiliensis CCUG 53443T (96.8 %), Y. pestis NCTC 5923T (96.8 %), Y. pseudotuberculosis ATCC 29833T (96.8 %), Y. similis CCUG 52882T (96.7 %) and Y. ruckeri ATCC 29473T (96.5 % ). The similarities of sequences of the housekeeping genes rpoB, hsp60 and gyrB between strain D9T and B. aquatica DSM 5075T and other members of the Enterobacteriaceae were less than 94 %. Phylogenetic trees based on all four gene sequences unequivocally grouped the isolate with the type strain of B. aquatica and separately from the genus Yersinia . Cells contained the quinones Q-8, Q-7 and MK-8. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the DNA (48.3 mol%) and the whole-cell fatty acid composition of strain D9T (C14 : 0, C16 : 1ω7c, C16 : 0, cyclo-C17 : 0 and C18 : 1ω7c as major components) were typical for members of the Enterobacteriaceae . DNA–DNA hybridization of strain D9T with B. aquatica DSM 5075T resulted in a relatedness of 30.4 %, indicating that the isolate did not belong to B. aquatica . Physiological tests allowed the phenotypic differentiation of strain D9T from B. aquatica DSM 5075T as well as from members of the genus Yersinia . From these results, it is concluded that strain D9T represents a novel species, for which the name Budvicia diplopodorum sp. nov. is proposed (type strain D9T  = DSM 21983T  = CCM 7845T). The description of the genus Budvicia is emended.

Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces

Strains HM2-1 and HM2-2T were isolated from the faeces of a healthy infant and were characterized by determining their phenotypic and biochemical features and phylogenetic positions based on partial 16S rRNA gene sequence analysis. They were Gram-positive, obligately anaerobic, non-spore-forming, non-gas-producing, and catalase-negative non-motile rods. They did not grow at 15 or 45 °C in anaerobic bacterial culture medium, and their DNA G+C content was in the range 56–59 mol%. In enzyme activity tests, strains HM2-1 and HM2-2T were positive for α/β-galactosidases and α/β-glucosidases but negative for β-glucuronidase and cystine arylamidase. An analysis of the cell-wall composition of strains HM2-1 and HM2-2T revealed the presence of glutamic acid, alanine and lysine. The presence of fructose-6-phosphate phosphoketolase shows that isolates HM2-1 and HM2-2T are members of the genus Bifidobacterium. These two isolates belong to the same species of the genus Bifidobacterium. Strain HM2-2T was found to be related to Bifidobacterium catenulatum JCM 1194T (97.4 % 16S rRNA gene sequence identity: 1480/1520 bp), Bifidobacterium pseudocatenulatum JCM 1200T (97.2 %: 1472/1514 bp), Bifidobacterium dentium ATCC 27534T (96.7 %: 1459/1509 bp) and Bifidobacterium angulatum ATCC 27535T (96.5 %: 1462/1515 bp). The predominant cellular fatty acids of strains HM2-1 and HM2-2T were 16 : 0 and 18 : 1ω9c, with proportions greater than 18 % of the total. Phylogenetic analyses involving phenotypic characterization, DNA–DNA hybridization and partial 16S rRNA gene sequencing proves that the strains represent a novel species of the genus Bifidobacterium, for which the name Bifidobacterium kashiwanohense sp. nov. is proposed. The type strain is HM2-2T ( = JCM 15439T  = DSM 21854T).