Frontiers in Microbiology最新文献

Background: Maintaining good oral and gut health is essential for the wellbeing of animals, and fungi are key components of the oral and gut microbiota. This study aims to explore the diversity and seasonal dynamics of oral and gut fungal communities in captive giant pandas, with a focus on their potential functional roles in health and digestion.

Methods: In the study, we collected saliva and fecal samples from 60 captive giant pandas were collected in different seasons, oral and gut fungi were analyzed using internal transcribed spacer (ITS) amplicon sequencing. We used α and β diversity analyses to examine the differences in species diversity and composition among the different seasons. Furthermore, we validated the ITS amplicon sequencing results through fungal isolation and identification.

Results: Analyses of α and β diversity revealed both the differences and similarities between the fungal communities in the oral and gut microbiomes of giant pandas. Ascomycota and Basidiomycota were predominant in both oral and gut groups, while the dominant genera in the four seasons were Cutaneotrichosporon, and unidentified_Chaetothyriales_sp. Additionally, Cladosporium and Candida were predominant in the oral and gut fungus, respectively, across all four seasons. Notably, fungal abundance and diversity in the oral microbiome were significantly higher than in the gut microbiome, a pattern observed throughout most seasons. Several potentially pathogenic fungi, such as Fusarium, Candida and Aspergillus, were detected in healthy giant pandas, with most showing increased abundance during winter. It is worth mentioning that we found a distinct bias in the functional communities of oral and gut fungi. The abundance of saprophytic fungi in the gut is relatively high, which may be related to their role in cellulose digestion.

Conclusion: The abundance and diversity of fungal communities in the oral cavity and gut of giant pandas exhibit significant seasonal variations. While the oral cavity hosts a higher abundance and diversity of fungi, the species composition of fungal community composition is similar to that of the intestines. The majority of gut fungi are likely derived from the oral cavity or diet, the significant seasonal variation in gut fungal community structure further suggests that long-term resident fungi may not be present in the gut.

Increasing concerns about chemical fungicides require sustainable alternatives for crop protection. Microbe-mediated synthesis of metal nanoparticles offers a sustainable, eco-friendly and highly effective strategy for plant disease management. This study investigates the mycosynthesis of zinc oxide nanoparticles (ZnO NPs) using the culture filtrate of Trichoderma harzianum and their antifungal activity against Alternaria brassicae. Nanoparticles were synthesized under optimized conditions of cell-free culture filtrate (CFCF) concentration, substrate concentration, pH and temperature. Ultraviolet-visible (UV-Vis) spectroscopy confirmed an absorption peak between 200 and 400 nm, while X-ray diffraction (XRD) confirms the hexagonal crystal structure with an average size of 29 nm. Dynamic light scattering (DLS) and zeta potential analysis revealed a hydrodynamic size of 50.79 nm and a surface charge of -17.49 mV, indicating good stability. Fourier transform infrared (FTIR) spectroscopy analysis identified functional groups (C=O, N-O, and O-H) that are crucial for nanoparticles stabilization. Scanning electron microscopy (SEM) and High-resolution transmission electron microscopy (HR-TEM) analysis revealed spherical, rod-shaped and hexagonal nanoparticles with sizes between 12 and 41 nm. Mycogenic-zinc oxide nanoparticles (M-ZnO NPs) significantly inhibited the mycelial growth of A. brassicae by 91.48% at 200 μg/mL, compared to chemically synthesized ZnO NPs at 200 μg/mL (79.62%) and mancozeb 0.2% (82.96%). SEM-EDX analysis revealed deformations and absorption of M-ZnO NPs in fungal hyphae, while confocal laser scanning microscopy (CLSM) showed increased reactive oxygen species (ROS) formation and impaired membrane integrity in treated fungal cells. Stress enzyme analysis confirmed increased superoxide dismutase (SOD) and catalase (CAT) activity by 44.2 U/mol and 39.6 U/mol at 200 μg/mL M-ZnO NPs. Our studies suggest that the M-ZnO NPs synthesized with T. harzianum culture filtrate have increased antifungal activity even at lower doses and can be used as an alternative to traditional fungicides without affecting environment.

Because of growing inequalities, more than one-third of the worldwide population is expected to live in slums by 2050. Although slum dwellers are at increased risk of infectious diseases, this population may have been overlooked with respect to the sustainability of virus evolution. In this study, we aimed to analyze the genetic diversity and evolution of SARS-CoV-2 in the Complexo de Favelas da Maré slum, Rio de Janeiro, Brazil, and assess its impact on the global spread of the virus. We found that this slum harbored multiple strains of SARS-CoV-2, and its amplification and genetic diversity connected with the global circulation from 2020 to 2022. Thus, enhancing surveillance in slums could be important for future epidemic/pandemic preparedness by connecting virus genetic diversity in this region with its circulation at divergent locations.

Background: Our study examined the composition of the intestinal microflora in a hospitalized patient with AP symptoms treated several months earlier for diverticulitis. The therapeutic intervention necessitated Hartmann's procedure, culminating in colostomy creation.

Aims: Employing a thorough microbiological analysis we attempted to demonstrate whether the microflora isolated from the peripancreatic fluid exhibited a stronger correlation with the contents of the stoma or with the rectal swab. Additionally, we sought to determine the association between later onset of AP and diverticulitis.

Methods: Following clinical materials from the patient in the initial phase of AP were collected: rectal swab, colostomy bag contents (in the publication referred to as stoma content/stool) and peripancreatic fluid. Microbiological analysis was performed, including classic culture methodology, NGS techniques, and genotyping methodologies. Furthermore, the effect of bile on the shift in the population of selected bacterial species was examined.

Results: The NGS technique confirmed greater consistency in bacteria percentage (phyla/family) between stoma content and peripancreatic fluid. In both samples, a clear dominance of the Proteobacteria phyla (over 75%) and the Enterobacteriaceae family was demonstrated. Moreover, NGS verified the presence of the Fusobacteriota phylum and Fusobacteriaceae family only in rectal swabs, which may indicate a link between this type of bacteria and the etiology of diverticulitis. We observed that Escherichia coli 33 isolated from stool exhibited active gaseous metabolite production (mainly hydrogen).

Conclusions: The abundant production of hydrogen may substantially impact enzymatic processes, inducing specific alterations in disulfide bonds and trypsin inactivation. Our investigation alludes to the conceivable active involvement of bile in effecting qualitative and quantitative modifications in the peripancreatic microbiota composition, establishing a correlation between released bile and bacterial generation of gaseous metabolites.

Gut microbiota has been increasingly linked to metabolic health and diseases over the past few decades. Bile acids (BAs), the major components of bile, are bidirectionally linked to intestinal microbiota, also known as the gut microbiome-BA metabolic axis. Gut microbiota-derived bile salt hydrolase (BSH, EC 3.5.1.24), which catalyzes the "gateway" reaction in a wider pathway of bile acid modification, not only shapes the bile acid landscape, but also modulates the crosstalk between gut microbiota and host health. Therefore, microbial BSHs exhibit the potential to directly or indirectly influence microbial and host physiologies, and have been increasingly considered as promising targets for the modulation of gut microbiota to benefit animal and human health. However, their physiological functions in bacterial and host physiologies are still controversial and not clear. In this review, we mainly discuss the current evidence related to the physiological roles that BSHs played in gut microbiota and human health, and the possible underlying mechanisms. Meanwhile, we also present the potential applications of BSHs and BSH-producing probiotics in various fields. Finally, we describe several important questions that need to be addressed by further investigations. A detailed exploration of the physiological significance of BSHs will contribute to their future diagnostic and therapeutic applications in improving animal and human health.

Desulfurella acetivorans is a strictly anaerobic sulfur-reducing deltaproteobacterium that can grow heterotrophically by oxidation of acetate or autotrophically with molecular hydrogen. Here we show that D. acetivorans possesses a putative operon encoding enzymes of the methylcitrate cycle of propionate oxidation and demonstrate that this bacterium is capable of propionate growth. However, activities of the methylcitrate cycle enzymes could not be detected in extracts of propionate-grown cells, and experiments with [U-¹³C₃]propionate and comparative proteomic analysis of acetate- and propionate-grown cells suggested that the methylcitrate cycle is not active during propionate growth. Instead, propionyl-CoA assimilation proceeds via its carboxylation to methylmalonyl-CoA, which is further converted to succinyl-CoA. The latter is directed to the tricarboxylic acid (TCA) cycle, where it is converted to oxaloacetate and condenses with acetyl-CoA (produced by decarboxylation of another oxaloacetate molecule) to form citrate, which is oxidized in the TCA cycle. These results highlight the uncertainty of genomic predictions in the analysis of microbial metabolic pathways and the need for their experimental confirmation.

Background: Despite the extensive research conducted on heat responses of Lentinula edodes heterokaryotic cells, the responses of the two sexually compatible monokaryons to heat stress (HS) remain largely unknown.

Methods: To bridge this gap, we examined the nucleus-specific (SP3 and SP30) heat resistant mechanisms using an integrated physiological, metabolomic and transcriptomic approach.

Results: The results showed that HS elicited the boost of ROS and hampered mycelium growth for both monokaryons. Metabolome and transcriptome analysis demonstrated that the two sexually compatible monokaryons responded differently to HS. For SP3, the differentially expressed genes (DEGs) were significantly enriched in Mitogen-Activated Protein Kinase (MAPK) signaling, cell cycle and sugar metabolism, whereas those DEGs for SP30 were enriched in glyoxylate and dicarboxylate metabolism, and protein processing. The differentially accumulated metabolites (DAMs) of both strains were enriched in the glycerophospholipid metabolism, alpha-linolenic acid metabolism, biosynthesis of cofactors, etc, but were regulated differently in each strain. The enriched KEGG pathways for SP3 tend to be downregulated, whereas those in SP30 exhibited a contrary trend. The genes in MAPK signaling pathway were associated with the glycerophospholipid metabolism in SP3, but not in SP30. Omics-integration analysis revealed distinguishing regulatory networks and identified completely different hub genes for the two strains.

Discussion: Our findings revealed, for the first time, the different heat-resistance mechanisms of the two compatible nuclei and provided candidate metabolites, responsive genes and regulatory pathways for further experimental validation.

Soil microbial communities are integral to almost all terrestrial biogeochemical cycles, which are essential to coastal wetland functioning. However, how soil bacterial community assembly, composition, and structure respond to native and non-native plant invasions in coastal wetlands remains unclear. In this study of the coastal wetlands of the Yellow River Delta in China, the assembly, community composition, and diversity of soil bacterial communities associated with four wetland plant species (Phragmites australis, Spartina alterniflora, Suaeda salsa, and Tamarix chinensis) and four soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm) were characterized using high-throughput sequencing. Plant species identity, as well as environmental factors, rather than soil depth, was found to play predominant roles in shaping the diversity and structure of wetland soil bacterial communities. S. alterniflora invasion altered bacterial community structure and increased bacterial diversity. Phragmites australis-associated bacterial communities were enriched with sulfate-reducing bacteria such as Desulfurivibrio and Desulfuromonas. In comparison, S. alterniflora-associated bacterial communities were enriched with both sulfate-reducing bacteria (SEEP-SRB1) and sulfate-oxidizing bacteria (Sulfurimonas), which maintained a dynamic balance in the local sulfur-cycle, and thereby enhanced S. alterniflora growth. In addition, stochastic processes dominated the assembly of soil bacterial communities associated with all four plant species, but were most important for the S. alterniflora community. The S. alterniflora-associated bacterial community also showed stronger interactions and more extensive connections among bacterial taxa; a co-occurrence network for this community had the greatest average clustering coefficient, average degree, modularity, and number of links and nodes, but the lowest average path length. Altogether, individual plant species had distinct effects on soil bacterial community assembly and structure, with the invasive species having the strongest impact. These results provide insights into microbial ecology and inform management strategies for coastal wetland restoration.

Background: Mastitis is a widespread disease on a global scale, significantly impacting the dairy industry. Mastitis in dairy cattle is caused by over 150 different bacteria, with Staphylococcus aureus (S. aureus) playing a significant role in financial losses, problems with animal welfare, and challenges with food safety. Phage treatment is thus being investigated as an effective replacement for reducing contaminants and illnesses caused by bacteria. In this study, we identified a phage UHP46, that effectively targets mastitis-causing S. aureus.

Methods: S. aureus S46 was used to screen for the wastewater lytic phages. The isolated lytic phage UHP46, which formed clear plaques and spots, was further characterized.

Results: Phage UHP46, belonging to the Herelleviridae family, forms clear, circular plaques in bacterial lawn. UHP46 showed stability under various range of temperature and pH levels, with maximum activity observed at pH 7 and temperature 37°C. Genomic analysis revealed that phage UHP46 is a dsDNA virus with an approximate genome size of 139,731 bp, and it encodes 72 proteins with known functions and 136 hypothetical proteins. One-step growth curve analysis indicated latent period of approximately 20 mins and burst size of about 27 progeny/cell. In organic stability test, UHP46 showed stability in DMSO and acetone. Furthermore, it effectively inhibited S. aureus growth for up to 16 h, suggesting its suitability for therapeutic applications against S. aureus infections.

Conclusion: These findings suggest that phage UHP46 could serve as a promising alternative to antibiotics for managing S. aureus- induced mastitis, contributing to dairy production and improved animal health.

Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi), based on catalytically dead Cas9 nuclease of Streptococcus pyogenes, is a programmable and highly flexible tool to investigate gene function and essentiality in bacteria due to its ability to block transcription elongation at nearly any desired DNA target. In this study, I assess how CRISPRi can be programmed to control the life cycle and infectivity of Escherichia coli bacteriophage T7, a highly virulent and obligatory lytic phage. This is achieved by blocking the expression of critical host-dependent promoters and genes that are required for T7 genome translocation and lifecycle progression. Specifically, I focus on the promoters within the non-coding internalisation signal region and the E. coli-recognised promoter C controlling T7 RNA polymerase (T7 RNAP) expression. Fluorescent reporter assays reveal that CRISPRi targeting of promoters in the internalisation signal is only moderately effective, whereas the downregulation of the phage's own T7 RNAP occurs very efficiently. Effects on the time to lysis were strongest when the left-most promoter on the leading end of the T7 genome or T7 RNAP was targeted. The stringency of the CRISPRi approach further improved when using multiplex sgRNAs to target multiple phage regions simultaneously, resulting in a 25% increase in the time to lysis and up to an 8-fold reduction in plaque size. Overall, this study expands dCas9-dependent CRISPRi as a flexible tool to non-invasively manipulate and probe the lifecycle and infectivity of otherwise native T7 phage.