Microorganisms最新文献

The genera Komagataeibacter and Novacetimonas comprise industrially important species that produce various foods, nanocellulose, acetan-like polysaccharides, enantioselective sugars, and other valuable products. Here, we describe two novel strains, Hr1 and Jurk4, isolated from pear and apple-grape organic vinegars that showed very high (≥99.39%) 16S rRNA gene sequence identities to species of the Komagataeibacter and Novacetimonas genera, respectively. However, analysis of the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences revealed only 92.6% sequence identity between the Hr1 strain and its closest relative, Komagataeibacter sucrofermentans LMG 18788^T, and 93.8% sequence identity between the Jurk4 strain and its closest relative, Novacetimonas cocois JCM 31140^T. Further whole-genome analysis showed for both strains an average nucleotide identity (ANI) below 94% and an in silico DNA-DNA hybridization (dDDH) value of less than 70% to their closest species, supporting their distinction as novel species. The strain Hr1 can be phenotypically differentiated from its closest Komagataeibacter species based on its ability to utilize (NH₄)₂SO₄ as the sole nitrogen source in Asai medium with D-glucose and its inability to grow with 1-propanol as a sole carbon source. The strain Jurk4 can be differentiated from other Novacetimonas type strains based on its ability to produce 5-keto-D-gluconic acid, its growth in a medium with glycerol as the sole carbon source, and its inability to grow in an Asai medium with D-glucose. Both strains produce cellulose and possess clusters for acetane-like polysaccharide production, although of different types, which makes them industrially relevant. Based on these findings, we propose Komagataeibacter piraceti sp. nov. Hr1^T (=ZIM B1167^T = LMG 33628^T) and Novacetimonas labruscae sp. nov. Jurk4^T (=ZIM B1166^T = LMG 33630^T) as two novel members of the acetic acid bacteria group.

The breast tissue microbiome has been increasingly recognized as a potential contributor to breast cancer development and progression. However, inconsistencies in microbial composition across studies have hindered the identification of definitive microbial signatures. We conducted a systematic review and meta-analysis of 11 studies using 16S rRNA sequencing to characterize the bacterial microbiome in 1260 fresh breast tissue samples, including normal, mastitis-affected, benign, cancer-adjacent, and cancerous tissues. Studies published until 31 December 2023 were included if they analyzed human breast tissue using Illumina short-read 16S rRNA sequencing with sufficient metadata, while non-human samples, non-breast tissues, non-English articles, and those lacking metadata or using alternative sequencing methods were excluded. We also incorporated microbiome data from The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort to enhance our analyses. Our meta-analysis identified Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota as the dominant phyla in breast tissue, with Staphylococcus and Corynebacterium frequently detected across studies. While microbial diversity was similar between cancer and cancer-adjacent tissues, they both exhibited a lower diversity compared to normal and mastitis-affected tissues. Variability in bacterial genera was observed across primer sets and studies, emphasizing the need for standardized methodologies in microbiome research. An analysis of TCGA-BRCA data confirmed the dominance of Staphylococcus and Corynebacterium, which was associated with breast cancer proliferation-related gene expression programs. Notably, high Staphylococcus abundance was associated with a 4.1-fold increased mortality risk. These findings underscore the potential clinical relevance of the breast microbiome in tumor progression and emphasize the importance of methodological consistency. Future studies to establish causal relationships, elucidate underlying mechanisms, and assess microbiome-targeted interventions are warranted.

Global climate change has accelerated the reduction of permafrost regions across different altitude gradients, shortening the duration of the freezing period to varying extents. However, the response of the soil microorganisms of frozen soils along altitude gradients remains unclear. In this study, we employed 16S rRNA sequencing and LC-MS metabolomics to investigate the response of soil microbial communities and soil metabolites to vertical stratification in the permafrost soils of the Qinghai Lake region. The results indicated that Proteobacteria, Firmicutes, and Actinobacteria were key soil bacterial phyla in the permafrost soils of Qinghai Lake during the freezing period, with Proteobacteria and Firmicutes showing significant sensitivity to vertical stratification (p < 0.05). The majority of the physicochemical factors exhibited a trend of initially increasing and then decreasing with increasing altitude, whereas pH showed the opposite trend. pH and moisture content were identified as the most important environmental factors influencing soil bacterial community structure. Deterministic processes dominated the assembly of bacterial communities of frozen soils in the Qinghai Lake basin. Co-occurrence network analysis showed that increasing altitude gradients led to a higher average degree of the bacterial network, while reducing network complexity and inter-species connectivity. Soil metabolomics analysis revealed that vertical stratification altered the metabolic profiles of 27 metabolites, with the significantly changed metabolites primarily associated with carbohydrate and amino acid metabolism. In conclusion, the characteristics of the Qinghai Lake permafrost were regulated by regional vertical stratification, which further influenced microbial community structure and soil metabolic characteristics, thereby altering carbon and nitrogen stocks. Specifically, higher altitudes were more favorable for the retention of the carbon and nitrogen stocks of frozen soils in the Qinghai Lake basin.

The copy number (CN) variant AMY1 encodes the salivary amylase enzyme which promotes starch digestion. Although this gene has been associated with dental caries and periodontal disease susceptibility, the impact of the interaction between AMY1 CN and starch on oral biofilms is unclear. We explored how oral microbiota communities shaped by AMY1 CN respond to starch by employing an in vitro model of biofilm formation. We cultured biofilms using saliva samples from 31 donors with a range of AMY1 CNs (between 2 and 20 copies) and self-reported gum disease states; we used media with and without starch. Many of the most prevalent genera in saliva were also prevalent in the derived biofilms. The presence of starch in the media was associated with lower biofilm alpha diversity. We found a significant interaction between AMY1 CN and the media carbohydrate content that influenced the proportions of Atopobium and Veillonella. Members of these genera have been associated with dental caries and periodontitis. These findings suggest that the effects of carbohydrates on oral microbiome composition depend on AMY1 CN and that human oral bacteria evolved in response to expansion of this host gene locus.

Volatile organic compound pollution caused by toluene has become a global issue. In order to solve this problem, biodegradation of toluene has been applied all over the world. This study investigated the effects of Fe³⁺ on toluene degradation by the Rhodococcus sp. TG-1. The results show that 1 mg L^-1 Fe³⁺ increased the degradation rate of 600 mg L^-1 toluene from 61.9% to 87.2% at 16 h. The acceleration mechanism of Fe³⁺ was explicated using transmission electron microscope (TEM) and energy-dispersive X-ray spectroscopy (EDX) analyses, coupled plasma optical emission spectroscopy, an enzyme activity assay, and transcriptome analysis. Four genes were detected to be significantly up-regulated under Fe³⁺ induction, suggesting that Fe³⁺ might be implicated in toluene degradation. Meanwhile, Fe³⁺ was a component of the active center of catechol 1,2-dioxygenase (C12O) and significantly improved the enzyme activity of C12O. The mechanism by which Fe³⁺ accelerates toluene degradation was proposed based on the transcription levels of degradation genes and the enzyme activity of C12O. This study provided an improved method for enhancing the degradation effect of toluene and furthered our comprehension of the mechanism of toluene degradation.

Munition disposal practices have significant effects on microbial composition and overall soil health. Explosive soil contamination can disrupt microbial communities, leading to microbial abundance and richness changes. This study investigates the microbial diversity of soils and roots from sites with a history of ammunition disposal, aiming to identify organisms that may play a role in bioremediation. Soil and root samples were collected from two types of ammunition disposal (through open burning and open detonation) and unpolluted sites in Machachi, Ecuador, over two years (2022 and 2023). High-throughput sequencing of the 16S rRNA gene (for bacteria) and the ITS region (for fungi and plants) was conducted to obtain taxonomic profiles. There were significant variations in the composition of bacteria, fungi, and plant communities between polluted and unpolluted sites. Bacterial genera such as Pseudarthrobacter, Pseudomonas, and Rhizobium were more abundant in roots, while Candidatus Udaeobacter dominated unpolluted soils. Fungal classes Dothideomycetes and Sordariomycetes were prevalent across most samples, while Leotiomycetes and Agaricomycetes were also highly abundant in unpolluted samples. Plant-associated reads showed a higher abundance of Poa and Trifolium in root samples, particularly at contaminated sites, and Alchemilla, Vaccinium, and Hypericum were abundant in unpolluted sites. Alpha diversity analysis indicated that bacterial diversity was significantly higher in unpolluted root and soil samples, whereas fungal diversity was not significantly different among sites. Redundancy analysis of beta diversity showed that site, year, and sample type significantly influenced microbial community structure, with the site being the most influential factor. Differentially abundant microbial taxa, including bacteria such as Pseudarthrobacter and fungi such as Paraleptosphaeria and Talaromyces, may contribute to natural attenuation processes in explosive-contaminated soils. This research highlights the potential of certain microbial taxa to restore environments contaminated by explosives.

The emergence of antibiotic-resistant food-borne pathogens, especially Escherichia coli O157:H7, highlights the urgent need for innovative treatment strategies, particularly in light of rising resistances and the ongoing controversy surrounding antibiotic use in response to E. coli O157:H7 infections. To address this issue, we explored the potential of single- and multi-strain probiotics, both independently and in combination with gentamicin, through a series of in vitro and in vivo experiments. In vitro, gentamicin alone produced a mean inhibition zone of 12.9 ± 2.27 mm against E. coli O157:H7. The combination of gentamicin with single-strain probiotics (P1) increased the inhibition zone to 16.5 ± 2.24 mm (p < 0.05), while the combination with multi-strain probiotics (P2) resulted in the largest inhibition zone of 19 ± 2.8 mm (p < 0.05). In vivo, mice infected with E. coli O157:H7 and treated with P2, gentamicin (G), or their combination (G+P2), achieved 100% survival, no pathological symptoms, and full weight recovery within seven days. Conversely, mice treated with P1 or G+P1 exhibited lower survival rates (71.4% and 85%, respectively) and slower weight recovery. Hematological parameters improved across all groups, but kidney function analysis showed significantly higher serum creatinine levels in the P1, G, G+P1, and G+P2 groups compared to the P2 group (P1: 0.63 ± 0.15 mg/dL; G: 0.34 ± 0.09 mg/dL; G+P1: 0.53 ± 0.19 mg/dL; G+P2: 0.5 ± 0.23 mg/dL vs. P2: 0.24 ± 0.2 mg/dL). Histological analysis showed better intestinal and kidney tissue recovery in the P2 group, while the P1 and G+P1 groups exhibited abnormal ileal structures and severe cortical bleeding. These findings highlight the promise of multi-strain probiotics, alone or in conjunction with antibiotics, as a therapeutic strategy for E. coli O157:H7 infections. However, the nephrotoxicity associated with gentamicin co-administration remains a limitation, warranting further studies to optimize this approach.

Storage reservoirs are crucial components of long-distance water diversion projects, where water diversion may lead to changes in microbial diversity and community structure. Seasonal variations also drive alterations in microbial communities. However, the way that microbes assemble under the combined effects of water diversion and seasonal variations in the storage reservoir has not been extensively studied. Jihongtan Reservoir is the terminal storage reservoir of the Yellow River to Qingdao Water Diversion Project (YQWD), which had an average annual water diversion period exceeding 290 days in recent years. In this study, 16S rDNA amplicon sequencing was used to investigate the seasonal dynamics and assembly of planktonic bacterial communities during the water diversion period in Jihongtan Reservoir. The results indicate that planktonic bacteria were able to maintain stable diversity across all four seasons, while the community structure underwent significant seasonal succession. Water temperature (WT) was found to be the primary driving environmental factor influencing the seasonal dynamic of planktonic bacterial communities. Co-occurrence network patterns of planktonic bacterial communities varied across different seasons, particularly in spring and winter. The spring network displayed the most complexity, showcasing the highest connectivity and greater stability. In contrast, the winter network was simpler, exhibiting lower local connectivity but higher global connectivity and lower stability. The analysis of the neutral community model and null model revealed that the relative importance of deterministic and stochastic processes in governing planktonic bacterial community assembly varies seasonally. Stochastic processes (dispersal limitation) are more prominent in spring, summer, and autumn, while deterministic processes (heterogeneous selection) play a greater role in winter. This study is essential for gaining a comprehensive understanding of the effects of water diversion projects and offers valuable references for the assessment of other similar projects.

Microorganisms play a crucial role in purifying aquaculture water bodies. However, there is limited understanding regarding the core species of bacterial communities in aquaculture ponds and their metabolic functions. Using 16S rRNA gene sequencing technology, network analysis, and Biolog EcoPlates, we identified keystone and core taxa of bacterial communities in Litopenaeus vannamei ponds and investigated their correlations with their community's carbon source utilization abilities based on Biolog EcoPlates. We found that keystone and core taxa in bacterial communities were significantly correlated with the carbon source utilization abilities of bacterial communities. The positively correlated core taxa include (1) Bacillus, Flavobacterium, Brevibacillus, and Paenibacillus, which are used as probiotics in aquaculture, and (2) Candidatus Aquiluna, Dechloromonas, Sulfurifustis, Terrimicrobium, Alsobacter, and Gemmobacter, which have been reported to play a role in nitrogen removal. Furthermore, the positively correlated Tropicimonas (Rhodobacterales: Rhodobacteraceae) in aquaculture has not yet been applied. By nitrogen degradation experiments in aquaculture wastewater, we confirmed the synergistic relationship between the genera Tropicimonas and Bacillus. The co-introduction of Tropicimonas sediminicola SDUM182003 and Priestia aryabhattai HG1802 or Bacillus subtilis XQ1804 into the aquaculture tailwater reduced the time required for the removal rates of nitrite nitrogen and nitrate nitrogen to reach over 90% by 24-48 h. Our research reveals the correlation between core taxa and community carbon source utilization, indicating that the core taxa of bacterial communities play a crucial role in the metabolic functions of the community, and offering a reference for exploring new bacterial genera with probiotic potential.

During human history, many pandemic events have threatened and taken many human lives over the years. The deadliest outbreaks were caused by bacteria such as Yersinia pestis. Nowadays, antimicrobial resistance (AMR) in bacteria is a huge problem for the public worldwide, threatening and taking many lives each year. The present work aimed to gather current evidence published in scientific literature that addresses AMR risks. A literature review was conducted using the following descriptors: antimicrobial resistance, AMR, bacteria, and Boolean operators. The results showed that antimicrobial-resistant genes and antibiotic-resistant bacteria in organisms cause critical infectious diseases and are responsible for the infections caused by antibiotic-resistant bacteria (ARB). This review emphasizes the importance of this topic. It sheds light on the risk of reemerging infections and their relationship with AMR. In addition, it discusses the mechanisms and actions of antibiotics and the mechanisms behind the development of resistance by bacteria, focusing on demonstrating the importance of the search for new drugs, for which research involving peptides is fundamental.