Abstract
The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia–Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.
Highlights
Cholecystitis leads to gallbladder inflammation or even perforation, tissue death, gangrene, fibrosis, and shrinking of the gallbladder, which is a hospitalized disease with increasing medical and financial burden (Wadhwa et al, 2017; Wang et al, 2021)
To explore the bile bacterial community, the fresh bile specimens collected from cholecystitis patients were cultivated using seven different media under both aerobic and anaerobic conditions
Tajeddin et al (2016) found that enterobacteria were the dominant biliary bacteria based on cultivate-dependent methods
Summary
Cholecystitis leads to gallbladder inflammation or even perforation, tissue death, gangrene, fibrosis, and shrinking of the gallbladder, which is a hospitalized disease with increasing medical and financial burden (Wadhwa et al, 2017; Wang et al, 2021). Positive bile culture rates from laparoscopic cholecystectomy patients ranged from 25.1 to 60.3%, suggesting the presence of bacteria in the cholecystitis patients’ bile (Nitzan et al, 2017; Yun and Seo, 2018). Due to the limitation of culture conditions, most bile bacterial isolates from clinical samples are aerobic bacteria especially Gram stain-negative Enterobacteriaceae, such as Escherichia coli, Klebsiella spp., Enterobacter spp., and less frequently anaerobic bacteria, including Bacteroides and Clostridium spp., as well as microaerophilic Helicobacter pylori (Nitzan et al, 2017; Cen et al, 2018). For culture-independent methods, denaturing gradient gel electrophoresis (DGGE) was applied for the investigation of microbiota composition (Liu et al, 2015); low throughput and complex operation were its limitations. Owing to nearly 80% of the human intestinal bacteria were unculturable (Tajeddin et al, 2016), with the advancement in bacterial culturomics technology (Tidjani Alou et al, 2020), it is reasonable to infer that abundant bile bacteria are waiting to be isolated
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