Carboxymuconolactone decarboxylase is a prospective molecular target for multi-drug resistant Acinetobacter baumannii-computational modeling, molecular docking and dynamic simulation studies

Light-driven biodegradation of chloramphenicol by photosensitized Shewanella oneidensis MR-1

Efficient and sustainable degradation of chloramphenicol has piqued the interest of the scientific community. This study constructed a photosensitized biohybrid system using Shewanella oneidensis MR-1 and cadmium sulfide (CdS). This system could efficiently degrade chloramphenicol with robust stability. Inhibitor experiments and transcriptome analysis revealed that reduced nicotinamide adenine dinucleotide dehydrogenase, iron-sulfur cluster, menaquinone, cytochrome b561, cytochrome c, cytochrome P450, and formate dehydrogenase/hydrogenase are involved in direct electron transfer from S. oneidensis MR-1 to photogenerated holes of CdS. The S. oneidensis MR-1/CdS biohybrid alleviated chloramphenicol-induced physiological impairments, which can be attributed to the decreased levels of extracellular polymeric substances, malondialdehyde, and extracellular membrane permeability and the increased levels of superoxide dismutase and catalase activities. The GCN5-related N-acetyltransferase, alkene reductase, and carboxymuconolactone decarboxylase promoted the inactivation and further degradation of chloramphenicol. In summary, this study demonstrated the potential applications of the S. oneidensis MR-1/CdS biohybrid in the remediation of chloramphenicol contamination.

Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights

Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequences, we identify novel features distinguishing these divisions. Our study reveals a distinct geographic distribution with division I strains predominantly found in North America and division II strains in Asia. Additionally, division II strains are more frequently associated with bloodstream infections, suggesting a distinct pathogenic potential. We report differences between the two divisions in gene abundance related to metabolism, virulence, stress response, and colonization strategies. Notably, division II strains harbor more antimicrobial resistance (AMR) genes than division I strains. These findings offer new insights into the functional roles of division I and II strains, indicating specialized niches within the intestine and potential pathogenic roles in extraintestinal sites.

IMPORTANCE

Understanding the distinct functions of microbial species in the gut microbiome is crucial for deciphering their impact on human health. Classifying division II strains as Bacteroides fragilis can lead to erroneous associations, as researchers may mistakenly attribute characteristics observed in division II strains to the more extensively studied division I B. fragilis. Our findings underscore the necessity of recognizing these divisions as separate species with distinct functions. We unveil new findings of differential gene prevalence between division I and II strains in genes associated with intestinal colonization and survival strategies, potentially influencing their role as gut commensals and their pathogenicity in extraintestinal sites. Despite the significant niche overlap and colonization patterns between these groups, our study highlights the complex dynamics that govern strain distribution and behavior, emphasizing the need for a nuanced understanding of these microorganisms.

Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights

Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694 B. fragilis whole genome sequences and report differential gene abundance to further support the recent proposal that divisions I and II represent separate species. In division I strains, we identify an increased abundance of genes related to complex carbohydrate degradation, colonization, and host niche occupancy, confirming the role of division I strains as gut commensals. In contrast, division II strains display an increased prevalence of plant cell wall degradation genes and exhibit a distinct geographic distribution, primarily originating from Asian countries, suggesting dietary influences. Notably, division II strains have an increased abundance of genes linked to virulence, survival in toxic conditions, and antimicrobial resistance, consistent with a higher incidence of these strains in bloodstream infections. This study provides new evidence supporting a recent proposal for classifying divisions I and II B. fragilis strains as distinct species, and our comparative genomic analysis reveals their niche-specific roles.