Microbiology spectrum最新文献

Soil microbial communities are integral to ecosystem function but our understanding of how they respond to secondary succession in fragmented landscapes is limited, particularly in tropical dry forests. We used DNA metabarcoding to evaluate successional changes in soil bacteria and fungi, comparing land managed for cattle, young, and older secondary forests at moist and dry sites in the Republic of Panama. We highlight key functional groups of microbes that interact with plants, including arbuscular mycorrhizal fungi (AMF), nitrogen-fixing bacteria, and plant pathogenic fungi. Plant diversity was higher at the moist site and increased with succession as the plant communities changed at both sites. By contrast, bacterial diversity was similar across sites and successional stages, and while overall fungal diversity was higher at the moist site, it also showed no changes with succession at either site. However, microbial community composition did change, with pastures and older forests having distinct bacterial and fungal communities and young secondary forests often displaying transitional ones. Functional groups of microbes showed contrasting patterns between sites, with the dry forest having a higher diversity of Nitrogen-fixing bacteria despite lower densities of legumes, higher diversity and different communities of AMF, and a much lower incidence of putative fungal plant pathogens than the moist site. Our findings highlight the importance of looking at aboveground and belowground effects together and demonstrate that predictions generated for soil microbes in moist tropical forests may not apply to dry forests. These results may also inform the restoration of climate-resilient forests.

Importance: Secondary forests are important components of neotropical landscapes and soil microbes help to shape these forests and the ecosystem services that they provide. This study demonstrates that soil microbial communities in moist and dry tropical forests can recover and reassemble after only 20 years of natural succession following the removal of cattle. However, successional patterns that are seen in the plant community are not always seen belowground. These patterns were more predictable at the moist than the dry site where the patchiness of the landscape likely restricts dispersal of both plants and soil microbes. We highlight the importance of preserving remaining tropical dry forests as they host unique microbial biodiversity that may help forests respond to drought conditions. As community shifts in soil microbes influence plant establishment, forest productivity, and other aspects of ecosystem functioning during the succession of tropical forest communities, our results can inform the restoration of climate-resilient forests.

A temporary loop ileostomy is a routine procedure for protecting the anastomosis in patients undergoing radical resection of rectal cancer. Fecal diversion by a diverting ileostomy may induce microbiota dysbiosis in the defunctioned colon; however, data on temporal and spatial microbiome and metabolome changes in these patients are sparse. Thirty patients who underwent ileostomy closure were enrolled. Fecal and plasma samples were collected successively before ileostomy closure, at the first postoperative defecation, and 1 month postoperatively. The 16S rRNA gene sequencing was used to assess changes in gut microbes, and metabolic components in the plasma were analyzed using global untargeted metabolomics. Advanced data analysis methods were used to examine the differences and correlations between flora and metabolites. The gut microbiota in the ileostomy effluent and defunctioned colon had lesser species diversity and richness, with an abundance of aerobic, gram-negative, and potentially pathogenic bacteria. After the intestinal continuity was restored with routine meal feeding, the gut microbes recovered to a standard composition within 1 month. Moreover, xanthine, traumatic acid, L-glutamine, and norepinephrine levels increased markedly in patients with ileostoma. The ileostomy closure reversed the ileostomy-associated metabolic alterations, including an increased abundance of L-leucine, creatine, and 2-ketobutyric acid. Furthermore, Agathobacter and Peptostreptococcus were most closely associated with the reconstruction of postoperative gut microbes. We described a spatiotemporal map of the intestinal microbial ecological reconstruction and metabolic recovery before and after ileostomy reversal for perioperative intervention in patients with ileostomy closure surgery.

Importance: In this paper, the changes in the intestinal microbiome and plasma metabolome before and after temporary ileostomy were reported for the first time, and the dynamic changes in intestinal contents were described. At the same time, the key bacterial genera involved in the reestablishment of microflora after the restoration of intestinal continuity were found, and the key relationship between them and plasma metabolites was also found. More importantly, we found that patients with ileal fistula may be at risk of metabolic imbalance and that this particular metabolic state may potentially affect the course of tumor treatment. Finally, the samples in this study were obtained in their natural state and can be easily applied to the clinic to avoid unnecessary invasive examinations.

The lack of clinical breakpoints and epidemiological cut-off values (ECOFFs) for antifungals prescribed for vulvovaginal candidiasis (VVC) make interpretation of antifungal susceptibility data difficult. This leads to empirical prescribing, poor clinical management and emergence of resistance. The in vitro susceptibilities of 152 Candida albicans, 105 Candida parapsilosis, 31 Nakaseomyces glabratus, and 8 Pichia kudriavzevii VVC isolates against eight antifungals, were determined according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) E.Def 7.4. The minimum inhibitory concentration (MIC) distributions were analyzed and local ECOFFs were determined visually and statistically. The in vitro activity of azoles was correlated with fluconazole susceptibility and clinical data were evaluated. The MICs of various azoles showed a significant correlation with the MICs of fluconazole and fluconazole non-wild type (WT) isolates had significantly higher MICs for other azoles. The estimated local ECOFFs for C. albicans were 0.016 mg/L (ketoconazole, clotrimazole), 0.06 mg/L (miconazole, econazole, itraconazole), 1 mg/L (fenticonazole), and 3,200 mg/L (boric acid). For C. parapsilosis, local ECOFFs were 0.06 mg/L (ketoconazole, clotrimazole, itraconazole), 1 mg/L (miconazole, econazole), 2 mg/L (fenticonazole), and 3,200 mg/L (boric acid). For N. glabratus, they were 1 mg/L (ketoconazole, clotrimazole, miconazole, itraconazole), 2 mg/L (econazole, fenticonazole), and 12,800 mg/L (boric acid). Non-WT isolates were detected for azoles in N. glabratus (10%-35%), C. albicans (5%-16%), and C. parapsilosis (≤ 3%). All isolates were WT for boric acid. Local ECOFFs were established for three major Candida species causing VVC, guiding the identification of non-WT isolates potentially associated with treatment failure.IMPORTANCEThe interpretation of in vitro susceptibility data of Candida isolates from women with vulvovaginal candidiasis (VVC) is challenging due to the lack of clinical breakpoints (CBPs) and epidemiological cut-off values (ECOFFs) for drugs used in VVC. In the present study, local ECOFFs were established for three major Candida species causing VVC, guiding the identification of non-wild type isolates potentially associated with treatment failure. This paper provides the framework for developing ECOFFs and ultimately CBPs that would help guide antifungal therapy of VVC.

Signaling between rhizosphere microorganisms is crucial in bacteria interaction and communication, shaping the rhizomicrobiome. Plant growth-promoting bacterium Pseudomonas produces a spectrum of important antibiotics to inhibit plant pathogens, albeit with an associated metabolic burden. Antibiotics could function as intra- and interspecies signals at subinhibitory concentrations to coordinate gene expression and microbial behaviors. In this work, we characterized pyoluteorin as an interspecies signal that modulates the biosynthesis of 2,4-diacetylphloroglucinol (2,4-DAPG), a broad-spectrum biocontrol agent, in non-pyoluteorin-producing Pseudomonas fluorescens 2P24. We demonstrated that the key transcriptional repressor PhlF from the 2,4-DAPG biosynthetic gene cluster spontaneously senses pyoluteorin, enhancing repression of the phlA promoter activity and inhibiting 2,4-DAPG synthesis in P. fluorescens 2P24. Pyoluteorin also binds to another transcriptional repressor, PhlH, from the 2,4-DAPG biosynthetic gene cluster, subsequently releasing the transcription of phlG, which facilitates the hydrolysis of 2,4-DAPG. Both PhlF and PhlH are simultaneously involved in sensing exogenous pyoluteorin to regulate the 2,4-DAPG biosynthetic operon, playing a crucial role in controlling antibiotic metabolites in response to environmental changes. Further phylogenetic and structural analyses demonstrated that PhlH and PhlF are widely distributed across Pseudomonas spp. with conserved ligand-binding domains. The findings shed new light on the regulatory mechanism of 2,4-DAPG biosynthesis underlying interspecies signaling by pyoluteorin and provide invaluable clues for the rational design of co-inhabiting Pseudomonas spp. as biocontrol agents.

Importance: Rhizosphere microorganisms release vital signals that shape microbial communities, with antibiotics at low concentrations acting as intra- and interspecies signals. However, the mechanisms of these signals in coordinating gene expression are unclear. In non-pyoluteorin-producing Pseudomonas fluorescens 2P24, pyoluteorin was identified as an interspecies signal that regulates the phl biosynthesis gene cluster for 2,4-DAPG production. TetR family repressors PhlH and PhlF were found to positively regulate 2,4-DAPG hydrolysis and negatively regulate its synthesis in response to pyoluteorin. Structural modeling and docking analyses revealed the interactions between pyoluteorin and both PhlH and PhlF, modulating gene expression. Phylogenetic analyses showed a wide distribution of PhlH and PhlF across Pseudomonas spp. with conserved ligand-binding domains. These findings deepen our understanding of interspecies signaling mechanisms and highlight the potential for designing co-inhabiting Pseudomonas spp. as effective biocontrol agents.

Strongyloides stercoralis infection is a neglected tropical disease with a global distribution. Serodiagnosis is a sensitive method, but improving its performance and simplifying into a point-of-care test (POCT) are needed. This study aimed to improve the diagnostic performance of serological tests using partially purified Strongyloides ratti antigen in an enzyme-linked immunosorbent assay (ELISA) and an immunochromatographic test (ICT). Crude S. ratti antigen was purified by an IgG affinity column to partition the antigen into flow-through, washing fraction (WF), and elution fractions. Optimized ELISA and ICT using crude and antigen fractions were used to analyze sera from three groups of subjects. Group 1 comprised subjects with proven strongyloidiasis, Group 2 were subjects with other parasitic infections, and Group 3 were negative parasitic infections. The diagnostic performance and Kappa agreement of the serological tests were analyzed and compared, using larvae detection as the reference test (fecal examination). The results showed that the WF was the most efficient antigen in terms of sensitivity and specificity, as determined by the ELISA and ICT. Kappa's agreement between fecal examination and WF-ELISA was moderate (Kappa = 0.52), and WF-ICT was almost perfect (Kappa = 0.94). The WF antigen reduced cross-reactivity to other parasitic infections, that is, Opisthorchis viverrini, Taenia spp., and hookworms, compared to crude S. ratti antigen when assessed by ELISA and ICT. We concluded that the WF of purified S. ratti improved the ELISA and ICT diagnostic performance, and the latter assay format could be used as a POCT for screening and controlling strongyloidiasis.IMPORTANCEThis study aimed to improve the serological diagnosis of strongyloidiasis, a disease caused by infection with the intestinal nematode Strongyloides stercoralis, by evaluating the impact of Strongyloides ratti antigen purification using an IgG affinity column for detecting parasite-specific IgG in serum via enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test (ICT) formats. Compared to crude S. ratti antigen, the washing fraction (WF) of the purified antigen demonstrated significantly improved sensitivity and specificity in both ELISA and ICT, achieving strong diagnostic concordance with the gold-standard fecal examination. Furthermore, the WF antigen fraction exhibited reduced cross-reactivity with coinfections caused by the liver fluke (Opisthorchis viverrini), tapeworms (Taenia spp.), and hookworms. These findings underscore antigen purification as a promising strategy to enhance the accuracy of strongyloidiasis serodiagnosis.

The rational design of the antibiotic treatment of bacterial infections employs these drugs to reach concentrations that exceed the minimum needed to prevent the replication of the target bacteria. However, within a treated patient, spatial and physiological heterogeneity promotes antibiotic gradients such that the concentration of antibiotics at specific sites is below the minimum needed to inhibit bacterial growth. Here, we investigate the effects of sub-inhibitory antibiotic concentrations on three parameters central to bacterial infection and the success of antibiotic treatment, using in vitro experiments with Staphylococcus aureus and mathematical and computer-simulation models. Our results, using drugs of six different classes, demonstrate that exposure to sub-inhibitory antibiotic concentrations alters bacterial growth dynamics, increases the mutation rate to antibiotic resistance, and decreases the production of persister cells thereby reducing persistence levels. Understanding this trade-off between mutation rates and persistence levels resulting from sub-inhibitory antibiotic exposure is crucial for optimizing, and mitigating the failure of, antibiotic therapy.

Importance: Much of the research on antibiotics and antibiotic treatment has focused on drug concentrations sufficient to prevent the growth of bacteria. These concentrations, however, are not always reached everywhere in the body. Here, we look at the effects of exposure to these low concentrations of antibiotics on the common clinically important pathogen Staphylococcus aureus. We confirm a previous finding that sub-inhibitory antibiotic exposure decreases the total growth and the growth rate of the bacteria. Moreover, we demonstrate that the level of persistence, an important mechanism for bacteria to survive antibiotics, is decreased due to sub-inhibitory exposure. However, we find that the rate of generation of resistant mutants is substantially increased. Taken together, these results reveal an important trade-off that emerges as a consequence of bacteria being exposed to sub-inhibitory concentrations of antibiotics.

Prototheca are ubiquitous algae and occasional pathogens of humans and animals. While rare, the infection is often fatal and treatment options are limited to antifungals with low efficiency. Here, using growth curve assays, we demonstrate that five pathogenic species of Prototheca (P. blaschkeae, P. wickerhamii, P. cutis, P. ciferrii, P. bovis) were fully inhibited by 50-100 μg/mL of herbicide glyphosate, suggesting novel pathways that can be considered for anti-algal drug development.IMPORTANCEPrototheca are algae frequently found in the environment that occasionally cause infections in humans and animals. Although these infections are rare, they are often deadly for immunocompromised patients. Considering the rising ambient temperatures that promote algal bloom and a growing number of immunocompromised patients globally, such cases are likely to increase and will require efficient medications. Currently, the treatment is limited to antifungals that affect algal and animal membranes alike at concentrations close to toxic. Here, we hypothesized that targeting a pathway that is present in plants but not animals may be a new approach to the development of novel anti-algal compounds with high efficiency and lower toxicity. In this proof-of-principle study, we found that herbicide glyphosate, which targets the shikimate pathway found in plants but not in animals, efficiently inhibits all five tested pathogenic Prototheca, suggesting that the shikimate pathway may be a promising target for anti-algal drug development.

N-acetylcysteine (NAC) and ambroxol hydrochloride (AMB) are commonly prescribed alongside antibiotics to alleviate sputum retention in lower respiratory tract infections, which are often caused by bacterial pathogens. With the rising threat of antibiotic resistance, phage therapy has emerged as a promising alternative alongside. However, no studies have explored the potential interactions between phages and these mucoactive agents despite their frequent concurrent use during phage therapy. Therefore, investigating the potential synergy and its subsequent impact on phage infection dynamics could enhance clinical strategies for treating bacterial infections with phages. Our study utilized Pseudomonas aeruginosa strain ZS-PA-35 and Klebsiella pneumoniae strain Kp36, alongside their respective phages, to investigate their interactions in the presence of NAC or AMB. Our findings indicate that, under specific conditions, these mucoactive agents can function as adjuvants to lytic phages, enhancing bacterial susceptibility to phage infection and facilitating subsequent phage proliferation. Our study revealed that these synergistic interactions are strongly influenced by the physiological characteristics of the phages, the surrounding microenvironments, and the physiology of host tissues, as varying outcomes of phage-host interactions were observed among different phages and across distinct media. Taken together, our results emphasize the complexity of interactions between phages and NAC or AMB, underscoring the need for caution when using combination treatments.IMPORTANCEN-acetylcysteine (NAC) and ambroxol hydrochloride (AMB) are used in medical treatment of patients with acute and chronic bronchitis. Often, the choice of NAC or AMB is empirically determined by physicians. However, the potential impact of combining NAC or AMB with phage therapy remains unclear. To address this gap, a comprehensive understanding of their interplay is crucial to determine any potential synergistic effects. This study aims to elucidate how NAC or AMB influence phages targeting different receptors, thereby affecting their antibacterial activity against Pseudomonas aeruginosa and Klebsiella pneumoniae. Our results suggest that, under certain conditions, NAC or AMB provides an adjuvant effect by rendering the cells more susceptible to phage infection. These results contribute to advancing our understanding of the clinical combination of mucoactive agents and phage therapy, offering insights for optimizing treatment efficacy.