Frontiers in Microbiology最新文献

Maximizing saccharification efficiency of lignocellulose and minimizing the production costs associated with enzyme requirements are crucial for sustainable biofuel production. This study presents a novel semi-fed-batch saccharification method that uses a co-culture of Clostridium thermocellum and Thermobrachium celere strain A9 to efficiently break down high solid-loading lignocellulosic biomass without the need for any external enzymes. This method optimizes saccharification efficiency and enhances glucose production from alkaline-treated rice straw, a representative lignocellulosic biomass. Initially, a co-culture of C. thermocellum and T. celere strain A9 was established with a treated rice straw loading of 150 g/l, supplemented with Tween 20, which enhanced enzymes stability and prevented unproductive binding to lignin, achieving a remarkable glucose concentration of up to 90.8 g/l. Subsequently, an additional 100 g/l of treated rice straw was introduced, resulting in a total glucose concentration of up to 140 g/l, representing 70.1% of the theoretical glucose yield from the 250 g/l treated rice straw load. In contrast, batch saccharification using an initial substrate concentration of 250 g/l of alkaline-treated rice straw without Tween 20 resulted in a glucose concentration of 55.5 g/l, with a theoretical glucose yield of only 27.7%. These results suggest that the semi-fed-batch saccharification method using co-cultivation of C. thermocellum and T. celere strain A9, supplemented with Tween 20 is an efficient microbial method for saccharifying high-concentration biomass. Moreover, this approach effectively manages high solids loading, optimizes efficiency, and reduces the need for external enzymes, thus lowering production costs and simplifying the process for industrial applications.

Ensuring companion animal welfare is a top priority for the pet industry and owners alike. The health of the pets can be directly and effectively improved through diet. Chenpi includes beneficial ingredients with proven anti-inflammatory, antioxidant, and immunomodulatory properties. The present investigation involved feeding snacks infused with Chenpi powder (CPP) to dogs for 42 days to examine the potential health benefits of CPP. The research evidenced a notable increase in serum superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activity in dogs, accompanied by a decrease in malondialdehyde (MDA), interleukin-8 (IL-8), and interferon-gamma (IFN-γ) level. Additionally, CPP increased fecal scores and significantly reduced fecal odors due to inhibition of 3-methylindole, hydrogen sulfide (H₂S), and ammonia nitrogen (NH₄ ⁺-N), and also raised the levels of fecal secretory immunoglobulin A (SIgA). Analysis of the microbial composition via 16S rRNA sequencing showed that CPP increased Bacteroidota and decreased Firmicutes in the gut flora at the phylum level. Functional prediction study of microbial communities also showed that the CPP group enriched metabolic and genetic information processing pathways. In addition, there were significant correlations between serum indicators and several significantly altered microorganisms. These findings suggest that CPP can potentially enhance the overall health of dogs by reducing fecal odorants, enhancing antioxidant and immunological capabilities, and modulating intestinal flora. This study establishes a solid scientific foundation regarding the application of CPP in functional pet foods.

Monoterpene α-pinene exhibits significant potential as an alternative fuel, widely recognized for its affordability and eco-friendly nature. It demonstrates multiple biological activities and has a wide range of applications. However, the limited supply of pinene extracted from plants poses a challenge in meeting the needs of the aviation industry and other sectors. Considering this, the microbial cell factory is the only viable option for achieving sustainable pinene production. This study employed a rational design model to optimize the copy number and integration site for the heterogenous pinene expression pathway in Escherichia coli (E. coli). The integrated strain with the best pinene pathway PG1 was selected. Subsequently, the resulting strain, E. coli HSY009, accumulated 49.01 mg/L of pinene after 24 h fermentation in the flask culture. To further enhance production, pinene expression cassette PG1 was sequentially integrated into three non-essential regions (44th, 58th, 23rd), resulting in an improved pinene titer. Then, the fermentation process under optimized conditions enhanced the production of pinene to 436.68 mg/L in a 5 L batch fermenter with a mean productivity of 14.55 mg/L/h. To the best of our knowledge, this work represents the maximum mean pinene productivity based on the currently available literature. The findings of this work provide valuable insights for optimizing E. coli to produce other valuable terpenoids that share the same intermediates, IPP and DMAPP. Conclusively, this research validates the model's universality and highlights its potential for application as cutting-edge biofuel precursors.

H4Nx avian influenza viruses (AIVs) have been isolated from wild birds and poultry and can also cross the species barrier to infect mammals (pigs and muskrats). The widespread presence of these viruses in wild birds and poultry and their ability to be transmitted interspecies make them an undeniable hazard to the poultry farming industry. In the present study, we collected fecal and swab samples from wild birds and poultry in Guangdong Province from January 2019 to March 2024, and various subtypes of AIVs were isolated, including 19 strains of H4 subtype AIVs. Further analysis was conducted on the internal genes of the 19 strains. These strains clustered together with high homology to highly pathogenic avian influenza virus (HPAIV), suggesting that H4Nx AIV may be reassorted from HPAIV. Two H4N8 strains are phylogenetically related to the porcine H4N8 AIV. Molecular characterization revealed that all viruses in this study were less pathogenic but had potential mammalian-adapted mutations. The transmission dynamics of H4Nx AIVs revealed that Europe and Asia, especially the Netherlands and Bangladesh, may be the centers of transmission. This may be linked to the migration of wild birds. The high migration rates from Russia to the Netherlands and from Russia to Bangladesh may also play a role. Therefore, continuous and systematic monitoring of wild birds to clarify the spatial and temporal distribution and prevalence of influenza viruses in wild birds is significant for early warning of avian influenza outbreaks in poultry and for risk assessment for public health and safety.

Background: Colistin is an antibiotic used as a last resort to treat multidrug-resistant Gram-negative bacterial infections. Plasmid-mediated mobile colistin-resistant (mcr) genes in Escherichia coli (E. coli) are disseminated globally and are considered to be a major public health threat. This study aimed to determine the molecular characteristics of colistin-resistant Escherichia coli isolates in clinical settings in Pakistan.

Methods: A total of 240 clinical E. coli strains isolated from urine and pus cultures were collected from two hospitals in Faisalabad and analyzed for phenotypic resistance to colistin by cultivation on CHROMagar plates supplemented with colistin 2 ug/ml. Molecular characteristics of colistin-resistant isolates were analyzed using conventional PCR, whole genome sequencing, and bioinformatics analysis.

Results: PCR and whole genome analysis confirmed the presence of the mcr-1 gene in 10 E. coli isolates. The minimum inhibitory concentration for colistin ranged from 4 ug/ml to 32 ug/ml. ResFinder analysis revealed the presence of multiple resistance determinants conferring co-resistance to β-lactams, aminoglycosides, trimethoprim, sulfonamides, tetracycline, quinolones, florfenicol, and macrolides. Hybrid genomic assembly indicated that mcr-1 is carried on IncI2 plasmids. Plasmid replicon typing indicated that IncI2-type plasmids (n = 10) were the most prevalent plasmids in these strains, followed by IncFIB (n = 8), IncFIC (n = 7), IncFIA (n = 6), IncFII (4), IncQ1 (n = 3), IncI1 (n = 1), IncY (n = 1), and IncN (n = 1). The Achtman MLST typing scheme revealed a large diversity of STs among the mcr-1-positive E. coli. VirulenceFinder analysis revealed the presence of numerous virulence factors ranging from 4 to 19.

Conclusion: Our study revealed the emergence and dissemination of colistin-resistant E. coli isolates carrying mcr-1 in hospital settings, posing a potential risk to anti-infective therapy. More efforts should be taken to monitor the prevalence of mcr-1-carrying bacteria in Pakistan.

Bovine genital leptospirosis (BGL) is a silent and chronic reproductive syndrome associated with reproductive failures that result in animal suffering and substantial financial losses for farmers. Important aspects of the interactions between the host and the pathogen during chronic leptospirosis have been well described in the kidney, but little is known about the genital infection mechanisms. The present study sheds light on the pathophysiology of BGL based on comparative genomic analysis of renal versus genital isolates of Leptospira santarosai genomes, an endemic species on Latin America. A significant number of genes were exclusive of the genital strains, with emphasis on genes associated with cell wall/membrane/envelope biogenesis, mobilome: prophages and transposons, and signal transduction mechanisms. Overall, these gene clusters play crucial roles in bacterial colonization and evasion of the immune response, which can reflect leptospiral tissue tropism to the genital niche. We provide new insights into the pathophysiology of an important and neglected syndrome in bovine, helping to elucidate the evolution of adaptation of leptospires in the genital tract of cows.

Hydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yielded promising results in analyses of microbial ecosystems, such as the human gut microbiome. In this study, LoopSeq is used to obtain near-full length (approximately 1,400-1,500 nucleotides) bacterial 16S rRNA gene sequences from hydrothermal sediments in Guaymas Basin. Based on these sequences, high-quality alignments and phylogenetic analyses provided new insights into previously unrecognized taxonomic diversity of sulfur-cycling microorganisms and their distribution along a lateral hydrothermal gradient. Detailed phylogenies for free-living and syntrophic sulfur-cycling bacterial lineages identified well-supported monophyletic clusters that have implications for the taxonomic classification of these groups. Particularly, we identify clusters within Candidatus Desulfofervidus that represent unexplored physiological and genomic diversity. In general, LoopSeq-derived 16S rRNA gene sequences aligned consistently with reference sequences in GenBank; however, chimeras were prevalent in sequences as affiliated with the thermophilic Candidatus Desulfofervidus and Thermodesulfobacterium, and in smaller numbers within the sulfur-oxidizing family Beggiatoaceae. Our analysis of sediments along a well-documented thermal and geochemical gradient show how lineages affiliated with different sulfur-cycling taxonomic groups persist throughout surficial hydrothermal sediments in the Guaymas Basin.

[This corrects the article DOI: 10.3389/fmicb.2023.1252294.].

Background: Antibiotics, as the most commonly prescribed class of drugs in neonatal intensive care units, have an important impact on the developing neonatal gut microbiota. Therefore, comprehending the effects of commonly used antibiotic therapy on the gut microbiota and butyrate-producers in early infants could provide information for therapeutic decision-making in the NICU.

Objectives: To explore the effects of antibiotic therapy on the early development of gut microbiota and butyrate-producers in early infants.

Methods: A total of 72 infants were included in the study. We performed 16S rRNA sequencing on stool swab samples collected from neonatal intensive care unit patients who received amoxicillin-clavulanic acid (AC, n = 10), moxalactam (ML, n = 28) and non-antibiotics (NA, n = 34). We then compared the taxonomic composition between treatment regimens, focusing on differences in butyrate-producers.

Results: Our study showed that there were significant differences in Shannon index (p = 0.033) and Beta diversity (p = 0.014) among the three groups. At the family level, compared with the other two groups, the relative abundance of Clostridiaceae (p < 0.001) and Veillonellaceae (p = 0.004) were significantly higher, while the relative abundance of Enterococcidae (p < 0.001) was significantly lower in the NA group. The relative abundance of Enterobacteriaceae (p = 0.022) in the AC group was greater than that in the other two groups. Additionally, butyrate-producers (p < 0.001), especially Clostridiaceae (p < 0.001), were noticeably more abundant in the NA group. The relative abundance of Clostridiaceae and butyrate-producers were the lowest in the ML group (p < 0.001).

Conclusion: We found that antibiotic therapy had an adverse impact on the initial development of gut microbiota and leaded to a reduction in the abundance of butyrate-producers, particularly Clostridiaceae. Furthermore, moxalactam had a more pronounced effect on the gut microbiota compared to amoxicillin-clavulanic acid.

Oncogenic gamma herpesviruses, including Epstein-Barr Virus (EBV) and Kaposi's Sarcoma-associated Herpesvirus (KSHV), are opportunistic cancer-causing viruses and induces oncogenesis through complex mechanisms, which involves manipulation of cellular physiology as well as epigenetic and epitranscriptomic reprogramming. In this review, we describe the intricate processes by which these viruses interact with the epigenetic machinery, leading to alterations in DNA methylation, histone modifications, and the involvement of non-coding RNAs. The key viral proteins such as EBNA1 and LMP1 encoded by EBV; LANA and vGPCR encoded by KSHV; play pivotal roles in these modifications by interacting with host factors, and dysregulating signaling pathways. The resultant reprogramming can lead to activation of oncogenes, silencing of tumor suppressor genes, and evasion of the immune response, which ultimately contributes to the oncogenic potential of these viruses. Furthermore, in this review, we explore current therapeutic strategies targeting these epigenetic alterations and discuss future directions for research and treatment. Through this comprehensive examination of the epigenetic and epitranscriptomic reprogramming mechanisms employed by oncogenic gamma herpesviruses, we aim to provide valuable insights into potential avenues for novel therapeutic interventions.