Safety Evaluation of a Novel Strain of Bacteroides fragilis

Abstract

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.

Human disease-related pathways increasing with opportunistic pathogens bloom in intestinal microbiome after vancomycin exposure and restoration with fecal transplantation by simulator of the human intestinal microbial ecosystem (SHIME)

“…Additionally, the multidrug resistant Pseudomonas aeruginosa with high virulence obtained from this research has also been well recorded in many previous research papers, indicating its immense threat to human health [38]. Some commensal microbiota in the human gut that decreased after vancomycin exposure such as Bacteroides fragilis and Parabacteroides are novel probiotics [39,40], and the decrease of these probiotics may cause dysbiosis of gut microbiota, which would lead human health problem [41,42].…”

In vivo Imaging of a Novel Strain of Bacteroides fragilis via Metabolic Labeling

“…It’s also capable of adhere to colon cells without cytotoxicity in vitro . ( Deng et al, 2016 ) ZY-312 possess similar characteristics to standard B. fragilis strains ATCC 25285 in morphology, growth kinetics, metabolic, and genetic profile and has been proved to be non-toxigenic in both normal and immune-deficient mice ( Wang et al, 2017 ). Furthermore, ZY-312 has been shown to be able to inhibit the growth and adhesion of Vibrio parahaemolyticus ( V. parahaemolyticus ) in vitro and protect both RAW 264.7 and LoVo cells from damage caused by V. parahaemolyticus ( Li et al, 2017 ).…”

“…Therefore, we can only investigate the migration and colonization of initial labeled ZY-312 but not the progeny strains. However, given that B. fragilis only makes up a very small part of the human intestinal commensal bacteria ( Wang et al, 2017 ), it is unlikely that descendants of ZY-312 would be proliferate massively in the intestine.…”

“…Bacteroides. fragilis strain ZY-312 was provided from Zhiyi Biological Technology Co., Ltd. [Guangzhou, Guangdong province, ( Deng et al, 2016 ; Wang et al, 2017 )]. The strain was cultured under anaerobic conditions (80% N2, 10% H2, 10% CO2) in basal peptone-yeast broth with azide-modified tetraacetylated-N-azidoacetylgalactosamine (GalNAz) at a final concentration of 100 μM at 37°C in an anaerobic incubator (Bugbox, Ruskinn) during the whole study.…”

Potential Use of Biotherapeutic Bacteria to Target Colorectal Cancer-Associated Taxa

“…fragilis is a Gram-negative obligate anaerobe, ubiquitous in nature, and a predominant species in the gut microbiota [59]. While there are strains of B. fragilis that contribute to gut health and are being assessed as potential probiotics [60], a possible association between other B. fragilis and CRC has also been uncovered. For example, Purcell et al [31] used qPCR analysis to show that elevated levels of Enterotoxigenic B. fragilis (ETBF) was associated with the early onset of colorectal carcinogenesis.…”