BMC Microbiology最新文献

Since the discovery of antibiotics, they have served as a potent weapon against bacterial infections; however, natural evolution has allowed bacteria to adapt and develop coping mechanisms, ultimately leading to the concerning escalation of multidrug resistance. Bacterial persisters are a subpopulation that can survive briefly under high concentrations of antibiotic treatment and resume growth after lethal stress. Importantly, bacterial persisters are thought to be a significant cause of ineffective antibiotic therapy and recurrent infections in clinical practice and are thought to contribute to the development of antibiotic resistance. Therefore, it is essential to elucidate the molecular mechanisms of persister formation and to develop precise medical strategies to combat persistent infections. However, there are many difficulties in studying persisters due to their small proportion in the microbiota and their non-heritable nature. In this review, we discuss the similarities and differences of antibiotic resistance, tolerance, persistence, and viable but non-culturable cells, summarize the molecular mechanisms that affect the formation of persisters, and outline the emerging technologies in the study of persisters.

This study is to investigate the relationship between the intestinal microbiota and urine levels of the ellagic acid-derived polyphenols, the urolithins, in a cohort of subjects following a three-week walnut dietary intervention. We longitudinally collected fecal and urine samples from 39 subjects before and after walnut consumption (2 oz per day for 21 days). 16S RNA gene sequencing was performed on fecal DNA to study the association between microbiota composition and the levels of nine urolithin metabolites, which were measured using UHPLC/Q-TOF-MS/MS. Fecal microbial composition was found to be significantly different between pre- and post-walnut intervention (beta diversity, FDR-p = 0.018; alpha diversity, p = 0.018). Roseburia, Rothia, Parasutterella, Lachnospiraceae UCG-004, Butyricicoccus, Bilophila, Eubacterium eligens, Lachnospiraceae UCG-001, Gordonibacter, Paraprevotella, Lachnospira, Ruminococcus torques, and Sutterella were identified as the 13 most significantly enriched genera after daily intake of walnuts. We observed 26 genera that were significantly associated with 7 urolithin metabolites, with 22 genera positively correlating after walnut supplementation (FDR-p ≤ 0.05). PICRUSt analysis showed that several inferred KEGG orthologs were associated with 4 urolithin metabolites after walnut intake. In this study, we found that walnut supplementation altered urolithin metabolites, which associates with specific changes in bacterial taxa and inferred functional contents.

Background: Plesiomonas shigelloides is a gram-negative opportunistic pathogen associated with gastrointestinal and extraintestinal diseases in humans. There have been reports of specific functional genes in the study of P. shigelloides, but there are also many unknown genes that may play a role in P. shigelloides pathogenesis as global regulatory proteins or virulence factors.

Results: In this study, we found a transcriptional regulator of the PadR family in P. shigelloides and named it PstR (GenBank accession number: EON87311.1), which is present in various pathogenic bacteria but whose function has rarely been reported. RNA sequencing (RNA-Seq) was used to analyze the effects of PstR on P. shigelloides, and the results indicated that PstR regulates approximately 9.83% of the transcriptome, which includes impacts on motility, virulence, and physiological metabolism. RNA-seq results showed that PstR positively regulated the expression of the flagella gene cluster, which was also confirmed by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and Luminescence screening assay. Meanwhile, the ΔpstR mutant strains lacked flagella and were non-motile, as confirmed by motility assays and transmission electron microscopy (TEM). Additionally, PstR also positively regulates T3SS expression, which aids in P. shigelloides' capacity to infect Caco-2 cells. Meanwhile, we also revealed that PstR negatively regulates fatty acid degradation and metabolism, as well as the regulatory relationship between PsrA, a regulator of fatty acid degradation and metabolism, and its downstream genes in P. shigelloides.

Conclusions: Overall, we revealed the effects of PstR on motility, virulence, and physiological metabolism in P. shigelloides, which will serve as a foundation for future research into the intricate regulatory network of PstR in bacteria.

Irrigation with saline groundwater has become necessary to overcome freshwater scarcity in the agricultural industry in arid areas. However, the effects of long-term saline groundwater irrigation on soil salinity and bacterial diversity have rarely been examined. In this study, a Lycium ruthenicum field was divided into two parts and subjected to flooding irrigation with saline groundwater (pH 7.81, total salinity 0.95 g L^-1) and surface water (pH 7.76, total salinity 0.36 g L^-1) for 8 years. After 8 years of irrigation, the soil salinity and salt ion content (i.e., Na⁺, Mg²⁺, K⁺, Ca²⁺, Cl^- and CO₃^2-) in the groundwater irrigation group were significantly greater than those in the surface water irrigation group (p < 0.001), with notable accumulation in the topsoil (0-5 cm) (p < 0.01). The bacterial community structure differed between the surface water and groundwater irrigation groups. Salt-tolerant bacterial groups (e.g., Balneolaceae and Halomonadaceae) and species (e.g., the marine bacterium JK1007, the bacterium YC-LK-LKJ35, and Methylohalomonas lacus) dominated in the groundwater irrigation environment. Additionally, bacterial communities were associated primarily with soil salt ions (RV = 0.66, p < 0.001). The characteristic bacterial taxa in long-term groundwater irrigation soils were salt-tolerant species (e.g., the marine bacterium JK1007, the bacterium YC-LK-LKJ35, and Methylohalomonas lacus). These findings suggest that salinity is the key factor driving differences in bacterial community structure between long-term groundwater and surface water irrigation. The long-term use of surface water and groundwater for irrigation has different impacts on soil environments, with groundwater irrigation having a more pronounced negative effect. Highlights. The long-term effects of this practice on soil salt accumulation and bacterial diversity were examined. This study provides potential applications for sustainable land management in similar ecological contexts. Groundwater irrigation is characterized by saline-tolerant keystone species. Salinity filtering was used to determine the pattern of bacterial community construction.

Purpose: This study analyzed antibiotic resistance mechanisms and molecular epidemiology of multidrug-resistant Pseudomonas aeruginosa (MDR-PA), aiming at providing clues for prevention and control of MDR-PA infections.

Methods: The carbapenemase resistance genes (VIM, IMP, NDM, KPC, GES, OXA-40) of MDR-PA strains were detected by polymerase chain reaction (PCR) and sequencing. The efflux pump system (MexA, MexC, MexE, MexX), AmpC and OprD2 were detected by real-time fluorescent quantitative PCR (qPCR) in MDR-PA group and sensitive-Pseudomonas aeruginosa (S-PA) group. The homology analysis of MDR-PA strains was performed by multilocus sequence typing (MLST).

Results: A total of 81 MDR-PA strains were collected from the First Affiliated Hospital of Guangxi Medical University from October 2022 to October 2023. Among the carbapenemase detected, the detection rate of NDM-1 was the highest, with a rate of 34.57% (28/81). MexA had a higher expression in MDR-PA group than that in S-PA group (P<0.0001). 81 MDR-PA strains belonged to 40 different ST types, mainly including ST1971, ST244, ST357 and ST308, and the predominant ST type was ST1971 (34.57%, 28/81).

Conclusion: The mechanisms of antibiotic resistance of MDR-PA strains mainly were the production of MBLS and higher expression of MexA in our study, and ST1971 was the predominant ST type of MDR-PA strains in our hospital, our findings may assist in prevention and control of MDR-PA infections.

Background: Citrus reticulata Blanco 'Orah' is one of the most widely grown citrus varieties in southern China. It has been proven that microbial and organic manure fertilization improve the yields and appearances of 'Orah' fruits. However, details regarding the mechanisms underlying the effects of combined fertilization on the agronomic traits and rhizosphere bacterial community of plants still need to be elucidated.

Results: This study compared the rhizosphere bacterial community and carotenoids of 'Orah' with (WYT group) and without (WYCK group) combined fertilization in a local orchard in Wuming town from Nanning, Guangxi, China. The WYT group was sprayed with 50 ml Strongreen and 250 g of Yumeiren five times while WYCK group did not sprayed. Combined fertilization increased fruit weight and the Citrus color index (CCI) significantly (p < 0.05). By 16s rRNA sequencing, 7,126 operational taxonomic units (OTU) were obtained. A higher Shannon index was observed in the WYT group compared to that in the WYCK group. Comparison between the two groups showed that Pseudomonas was enriched in the WYT group with LDA (log10) score of 4.32, and Cyanobacteria was enriched in the WYCK group with LDA (log10) score of -4.11. At the family level, Phyllobacteriaceae (abundance mean: 0.0046 in WYCK vs. 0.0073 in WYT) was significantly abundant in the WYT group, whereas Thermosporothrix (abundance mean: 0.00053 in WYCK vs. 0.0019 in WYT) and Sphingobium (abundance mean: 0.00053 in WYCK vs. 0.0013 in WYT) were significantly abundant in the WYCK group. A total of 51 carotenoid components were tested by UPLC-MS/MS. In the pulp tissues, 37 carotenoid components were decreased in the WYT group compared to those in the WYCK group. In fruit skin, 24 significantly different components (7 downregulated and 17 upregulated) were identified in WYT compared to those in WYCK. Correlation analysis revealed that the network between OTUs and carotenoids contained seven carotenoid components and four OTUs. Four OTUs, strain TRA3-20 (a eubacterium), Roseiflexus, OPB35, and Fictibacillus correlated to carotenoid accumulation regulation in fruit skin.

Conclusions: This study demonstrates the impact of the fertilization on soil microorganisms and carotenoid components. It constructs the regulatory network contained four OTUs for seven carotenoid components, providing evidence on precise fertilization in Orah.

Inquilinus limosus belongs to the class of the Alphaproteobacteria and was first described in 2002. So far, the species has mainly been isolated from respiratory specimens of patients with cystic fibrosis. A main characteristic of Inquilinus limosus is the prolonged time until bacterial colony growth is detectable. As the defined incubation times in many laboratories are too short to detect the growth of Inquilinus limosus, it is likely that the species is less frequently detected in the clinical setting than it actually occurs. This also explains why there are currently only very few data on the incidence available. Furthermore, as an uncommon pathogen, Inquilinus limosus may be familiar to only a few specialised clinicians. Due to these reasons, only little research (e.g. case reports and research papers) have been published on this species to date. However, given that a clear human pathogenic significance can be deduced from the existing literature, we have decided to present the current state of knowledge in this review and to address further aspects for the future elucidation of the pathogenesis of Inquilinus limosus.

Background: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) complex infection, is a leading cause of death worldwide from a single infectious agent. The emergence of drug resistance Mtb clinical strains makes the situation more serious. The role of Mtb outer membrane protein A (OmpA) in antimicrobial resistance remains unclear. This study aimed to evaluate the effect of OmpA expression on mycobacterial drug resistance. In this study, a Mycobacterium smegmatis (Ms) strain overexpressing OmpA (Ms-OmpA) and a Mycobacterium bovis (Mb) strain overexpressing OmpA (Mb-OmpA) were constructed, and their susceptibility to anti-TB drugs was determined by performing the minimal inhibitory concentrations (MICs), the plate assay and the macrophage infection assays.

Results: The streptomycin MIC of the overexpressing strain was 2-fold lower than those of the wide-type (Ms) and empty plasmid strains (pMV-261) as well as amikacin and gentamicin. Moreover, both the plate and the macrophage infection assays indicate that overexpression of OmpA increases streptomycin sensitivity in Mycobacteria. The other aminoglycosides like amikacin and gentamicin have the same phenotypes as streptomycin on the plates for the virulent strain Mb-OmpA. The porin inhibitor spermidine can increase streptomycin tolerance in the overexpressing strain, and overexpressing OmpA can increase the intracellular accumulation of hydrophilic ethidium bromide, which indicates that porin protein OmpA contributes to aminoglycosides sensitivity in Mycobacteria.

Conclusions: In this study, we have characterized the contribution of OmpA in the antimicrobial resistance phenotype of Mycobacteria, which may provide valuable insights for understanding antibiotic resistance and designing new strategies for TB treatment.

Background: American ginseng is an important herb crop and is widely cultivated in China. However, continuous cropping seriously affects the production of American ginseng, and the reason is still unclear and needs more research. We analyzed the soil microbial alpha diversity and community composition as well as soil physicochemical properties in bulk soils to assess the changes in soil associated with planting American ginseng.

Results: The cultivation of American ginseng resulted in a significant decrease in soil pH value. The alpha diversity of soil bacteria and fungi was significantly reduced with the increase of American ginseng planting years. Planting American ginseng also largely altered the community composition of soil bacteria and fungi, in particularly, increased the relative abundance of the pathogenic fungus Fusarium, and reduced the relative abundance of some beneficial microorganisms, such as KD4-96, RB41 and Sphingomonas.

Conclusions: Soil acidification, reduction of beneficial taxa and accumulation of fungal pathogens, therefore, may lead to the replantation problem of American ginseng.

In the context of food transition, the agrifood sector has experienced increasingly strong demand for horticultural products. Fresh fruits and vegetables are mainly vehicles of microorganisms, including pathogens that cause human infections. Food safety and compliance with health standards in the fruits and vegetable value chain are significant concerns and multiple challenges, given the prevalence of foodborne pathologies in Southern countries, particularly in Senegal. This study aimed to describe the bacterial community and assess the microbiological quality of a range of fruits and vegetables sold on street stalls and open-air markets in Dakar, the capital city of Senegal. Samples purchased in seven sites were analyzed to isolate Escherichia coli (E. coli), Salmonella spp. and Vibrio spp. Some primary samples with a positive microbiological culture were subjected to DNA extraction and subsequent metagenomic analysis. A total of 240 fresh fruit and vegetable samples were collected, including lettuce (n = 40), tomatoes (n = 40), mango slices (n = 40), onion slices (n = 40), mint leaves (n = 40), strawberries and grapes (each n = 20). Of these samples, 50.83% (122/240) and 60.41% (145/240) were contaminated with E. coli and Vibrio spp., respectively, while Salmonella was not isolated in any product. E. coli and Vibrio spp. contamination levels, 1.3 10³ to 6 10⁶ Colonies Forming Units per gram of sample (CFU/g) and 4.55 10² to 8.73 10⁶ CFU/g, respectively, were significantly above the thresholds acceptable for human consumption. The most contaminated samples were lettuce, with a prevalence of 98% (39/40) for E. coli and Vibrio spp. followed by mint leaves with 100% (40/40) and 93% (37/40) of the samples containing E. coli and Vibrio spp. respectively. Out of 46 samples sequenced, the metagenomic analysis revealed high contamination rates for E. coli, Vibrio spp. and Salmonella spp., with 100%, 67.39% and 93.47% of prevalence, respectively. On the other hand, the alpha diversity analysis shows high bacterial diversity in lettuce and mint leaf samples, while the beta diversity analysis highlighted the presence of two major clusters. Our results stress the need for a surveillance system that extends this investigation to a national scale while increasing the number of sampling sites and products analyzed.