Microorganisms最新文献

Polyhydroxybutyrate (PHB) is a biodegradable natural polymer produced by different prokaryotes as a valuable carbon and energy storage compound. Its biosynthesis pathway requires the sole expression of the phaCAB operon, although auxiliary genes play a role in controlling polymer accumulation, degradation, granule formation and stabilization. Due to its biodegradability, PHB is currently regarded as a promising alternative to synthetic plastics for industrial/biotechnological applications. Azohydromonas lata strain H1 has been reported to accumulate PHB by using simple, inexpensive carbon sources. Here, we present the first de novo genome assembly of the A. lata strain H1. The genome assembly is over 7.7 Mb in size, including a circular megaplasmid of approximately 456 Kbp. In addition to the phaCAB operon, single genes ascribable to PhaC and PhaA functions and auxiliary genes were also detected. A comparative genomic analysis of the available genomes of the genus Azohydromonas revealed the presence of phaCAB and auxiliary genes in all Azohydromonas species investigated, suggesting that the PHB production is a common feature of the genus. Based on sequence identity, we also suggest A. australica as the closest species to which the phaCAB operon of the strain H1, reported in 1998, is similar.

Hadal zones account for the deepest 45% of oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, further investigation is still required to fully elucidate the microbial taxonomy, ecological significance, metabolic diversity, and adaptation in hadal environments. In this study, a novel strain Lsc_1132^T was isolated from sediment of the Mariana Trench at 10,954 m in depth. Strain Lsc_1132^T contains heterogenous 16S rRNA genes, exhibiting the highest sequence similarities to the type strains of Neobacillus drentensis LMG 21831^T, Neobacillus dielmonensis, Neobacillus drentensis NBRC 102427^T, Neobacillus rhizosphaerae, and Neobacillus soli NBRC 102451^T, with a range of 98.60-99.10% identity. The highest average nucleotide identity (ANI), the highest digital DNA-DNA hybridization (DDH) values, and the average amino acid identity (AAI) with Neobacillus sp. PS3-40 reached 73.5%, 21.4%, and 75.54%, respectively. The major cellular fatty acids of strain Lsc_1132^T included iso-C_15:0, Summed Feature 3 (C_16:1ω6c and/or C_16:1ω7c), iso-C_17:0, anteiso-C_15:0, and iso-C_17:1ω5c. The respiratory quinone of strains Lsc_1132^T was MK-7. The G + C content of the genomic DNA was 40.9%. Based on the GTDB taxonomy and phenotypic data, strain Lsc_1132^T could represent a novel species of a novel genus, proposed as Aliineobacillus hadale gen. nov. sp. nov. (type strain Lsc_1132^T = MCCC 1K09620^T). Metabolically, strain Lsc_1132^T demonstrates a robust carbohydrate metabolism with many strain-specific sugar transporters. It also has a remarkable capacity for metabolizing amino acids and carboxylic acids. Genomic analysis reveals a streamlined genome in the organism, characterized by a significant loss of orthologous genes, including those involved in cytochrome c synthesis, aromatic compound degradation, and polyhydroxybutyrate (PHB) synthesis, which suggests its adaptation to low oxygen levels and oligotrophic conditions through alternative metabolic pathways. In addition, the reduced number of paralogous genes in strain Lsc_1132^T, together with its high protein-coding gene density, may further contribute to streamlining its genome and enhancing its genomic efficiency. This research expands our knowledge of hadal microorganisms and their metabolic strategies for surviving in extreme deep-sea environments.

The rising burden of type 2 diabetes mellitus (T2DM) is a growing global public health problem, particularly prominent in developing countries. The early detection of T2DM and prediabetes is vital for reversing the outcome of disease, allowing early intervention. In the past decade, various microbiome-metabolome studies have attempted to address the question of whether there are any common microbial patterns that indicate either prediabetic or diabetic gut microbial signatures. Because current studies have a high methodological heterogeneity and risk of bias, we have selected studies that adhered to similar design and methodology. We performed a systematic review to assess if there were any common changes in microbiome belonging to diabetic, prediabetic and healthy individuals. The cross-sectional studies presented here collectively covered a population of 65,754 people, with 1800 in the 2TD group, 2770 in the prediabetic group and 61,184 in the control group. The overall microbial diversity scores were lower in the T2D and prediabetes cohorts in 86% of the analyzed studies. Re-programming of the microbiome is potentially one of the safest and long-lasting ways to eliminate diabetes in its early stages. The differences in the abundance of certain microbial species could serve as an early warning for a dysbiotic gut environment and could be easily modified before the onset of disease by changes in lifestyle, taking probiotics, introducing diet modifications or stimulating the vagal nerve. This review shows how metagenomic studies have and will continue to identify novel therapeutic targets (probiotics, prebiotics or targets for elimination from flora). This work clearly shows that gut microbiome intervention studies, if performed according to standard operating protocols using a predefined analytic framework (e.g., STORMS), could be combined with other similar studies, allowing broader conclusions from collating all global cohort studies efforts and eliminating the effect-size statistical insufficiency of a single study.

Free-of-charge hepatitis C virus antibody (HCV Ab) screening in some key populations and in 1969-1989 birth cohorts have been funded in Italy as the first step in confirming diagnosis in individuals who may be unaware of their infection. The purpose of this study is to leverage existing in-hospital routine screening data to better understand the distribution of HCV. A retrospective study of hospitalized patients (PTs) tested for HCV Ab for 5 years (from January 2017 to December 2022) in San Raffaele hospital was conducted according to age categories: birth year group before 1947 (patients older than 76 years old), birth year group 1947-1968, birth year group 1969-1989, and two other groups with birth year groups 1990-2000 and 2001-2022 (with patients younger than 33 years old) using the TriNetX platform. Among the 42,805 in-hospital PTs tested, 1297 (3.03%) were HCV Ab positive. The prevalence of HCV Ab was greater in PTs over the age of 76 (5.3%), whereas it was lower in the youngest birth year cohort (2000-2022, 0.16%). Among 1297 HCV Ab positive PTs, only 198 (15.3%) were tested for the presence of HCV RNA. The birth cohort 1969-1989 had a modest seroprevalence (1.5%), yet they were the most affected age group, with 44.4% being HCV RNA positive. The in-hospital HCV screening including birth year cohort 1947-1989 could be a more valuable option compared to the screening for birth year group 1969-1989 in the general population.

Vibrio vulnificus (V. vulnificus) is a Gram-negative, halophilic bacillus known for causing severe infections such as gastroenteritis, necrotizing fasciitis, and septic shock, with mortality rates exceeding 50% in high-risk individuals. Transmission occurs primarily through the consumption of contaminated seafood, exposure of open wounds to infected water, or, in rare cases, insect bites. The bacterium thrives in warm, brackish waters with high salinity levels, and its prevalence is rising due to the effects of climate change, including warming ocean temperatures and expanding coastal habitats. High-risk populations include individuals with underlying conditions such as chronic liver disease, diabetes, or immunosuppression, which heighten susceptibility to severe outcomes. The pathogenicity of V. vulnificus is mediated by an array of virulence factors, including hemolysins, proteases, and capsular polysaccharides, as well as mechanisms facilitating iron acquisition and immune system evasion. Clinical manifestations range from localized gastrointestinal symptoms to life-threatening systemic infections such as septicemia. Rare but severe complications, including pneumonia and meningitis, have also been reported. Treatment typically involves the use of doxycycline in combination with third-generation cephalosporins, although the emergence of multidrug-resistant strains is an escalating concern. Alternative therapeutic approaches under investigation include natural compounds such as resveratrol and the application of antimicrobial blue light. For necrotizing infections, prompt and aggressive surgical intervention remains essential to improving patient outcomes. As global temperatures continue to rise, understanding the epidemiology of V. vulnificus and developing innovative therapeutic strategies are critical to mitigating its growing public health impact.

Several studies have suggested that probiotics could play a role in the management of patients with chronic bacterial prostatitis (CBP). In this randomized, placebo-controlled clinical study, we evaluated the efficacy and safety of consumption of probiotics containing human Lactobacillus casei DG^® as an add-on treatment in patients with clinical recurrences of CBP, through gut microbiota modification analysis. Enrolled patients with CBP were randomized to receive for 3 months probiotics containing human Lactobacillus casei DG^® or placebo following 1 month treatment with ciprofloxacin. During the enrollment and follow-ups, urological examinations analyzed symptoms and quality of life, while microbiological tests analyzed gut and seminal microbiota. During the study, the development of adverse drug reactions was evaluated through the Naranjo scale. Twenty-four patients with CBP were recruited and treated for 3 months with placebo (n. 12) or with Lactobacillus casei DG^® (n. 12). Lactobacillus casei DG^® induced a significantly (p < 0.01) faster recovery of symptoms than placebo (2 days vs. 8 days) and an increased time free from symptoms (86 days vs. 42 days) without the occurrence of adverse events. In the probiotic group, the appearance of Lactobacilli after 30 days (T1) was higher vs. the placebo group, and a significant reduction in Corynebacterium, Peptoniphilus, Pseudomonas, Veillonella, Staphylococcus, and Streptococcus was also observed. These preliminary data suggest that in patients with CBP, the use of Lactobacillus casei DG after an antimicrobial treatment improves the days free of symptoms and the quality of life, without the development of adverse drug reactions.

Paenibacillus polymyxa strain PJH16, isolated and tested by our team, suppresses cucumber Fusarium wilt as an efficient biocontrol agent. For further investigation, the strain has been combined with two other Bacillus strains (Bacillus velezensis VJH504 and Bacillus subtilis JNF2) to enhance biocontrol ability, which formed high-efficiency microbial agents in the current study. The methodological target taken is based on achieving the optimal growth conditions of the combined microbial agents; hence, the medium composition and culture conditions were optimized through a single-factor test, orthogonal test and response surface methodology. Following this, the effectiveness of the microbial combination was assessed through pot experiments, which provided a theoretical foundation for the synthesis of microbial flora to significantly control cucumber Fusarium wilt. The results showed excellent compatibility, proving suitable for the proliferation and growth of Paenibacillus polymyxa PJH16, Bacillus velezensis VJH504, and Bacillus subtilis JNF2 strains together, specifically, when the inoculation amounts were adjusted to 4% of each. Using the single-factor test and orthogonal test analysis, the optimum composition of culture medium for the composite strain was identified as 3% glucose as the optimal carbon source, 2% yeast extract powder as the preferred nitrogen source, and 1% dipotassium hydrogen phosphate as the most suitable inorganic salt. Furthermore, the optical density (OD₆₀₀) of the composite strain solution reached its highest level at 3.16 under the following culture conditions: inoculation volume of 200 µL, 171 rpm culture speed, 21.6 h culture time, 30 °C cultural temperature, and an initial pH of 7.0. The pot experiment demonstrated that the mixed bacterial solution achieved a relative control efficacy of 93.4% against cucumber Fusarium wilt, which was significantly superior to that of single- strain or pesticide treatment, and also promoted cucumber growth. In summary, the microbial flora synthesized by the three Bacillus strains displayed a high bacterial concentration, following the optimization of culture conditions, and exerted remarkable control and growth-promoting effects on cucumber Fusarium wilt. This finding holds great significance for future developments of composite microbial agents.

Two extruded diets isoenergetic, isonitrogenous, and isolipidic were formulated with poultry meal (control diet) as the source of animal-origin proteins (160 g/kg of feed) or with 90 g/kg of poultry meal and 70 g/kg of hydrolyzed feather meal (treated diet) and were fed to eight dogs (four adult female and four adult male English Setters). Body condition, muscle condition, and fecal consistency scores and body weight were monitored at the beginning of the trial and after 3, 7, 15, and 45 days, and no significant differences (p > 0.05) were observed between diets and between sex. Fecal samples, collected at the same time points, were analyzed for microbiota composition. No significant difference was calculated for the alpha diversity index between control diet and treated diet, nor for the diets × times of sampling interaction and for sex. Beta diversity was different (p-value 0.001) between the control and treated groups. The beta diversity between sexes was significantly different (p-value = 0.047). Linear Discriminant analysis effect size analysis revealed significant differences between dietary groups, identifying Clostridiales, Coprococcus, Bacteroides plebeius, Eubacterium biforme, Catenibacterium, and Prevotella copri as more abundant in the CTR diet, while Fusobacterium, Bacteroides, Fusobacteriaceae, Paraprevotellaceae, Enterococcus, Faecalibacterium, Enterobacteriaceae, Peptostreptococcaceae, and Clostridium spiroforme were more abundant in the treated diet. Sex differences were also significant, with 25 taxa differing between male and female dogs. Overall, the study underscores the impact of HFM and sex on gut microbiota composition in dogs, with potential implications for dietary interventions and microbiome research.

The pancreas, previously considered a sterile organ, has recently been shown to harbor its own microbiota that may influence tumor biology and patient outcomes. Despite increasing interest in the impact of the microbiome on cancer, the relationship between pancreatic tissue and oral microbiomes in pancreatic ductal adenocarcinoma (PDAC) remains limited. In this study, the oral and pancreas tissue microbiomes of patients with PDAC were compared to patients with other periampullary cancers (DC/AC) and a healthy control group using 16S rRNA gene sequence analysis. The results showed a significant reduction in microbial diversity in the saliva of cancer patients compared to healthy controls, while the PDAC patients exhibited a distinct microbial profile in their pancreatic tissues, consisting predominantly of Firmicutes, Proteobacteria, and Actinobacter, after filtering the microbiome of the indoor environment. Notably, the presence of oral bacteria such as Anoxybacillus, Clostridium, and Bacillus in pancreatic tissues suggests potential translocation from the oral cavity. This study emphasizes the importance of understanding the role of body fluid and tissue microbiota in pancreatic cancer, proposing that oral dysbiosis may contribute to disease progression. Moreover, the results suggest that the microbiome of the indoor environment in which samples are collected and analyzed is also important in microbiota analysis studies.

Hepatitis B virus (HBV) infections remain a significant global health challenge, especially in low- and middle-income countries where access to healthcare services is often limited. This study aimed to assess the prevalence of hepatitis B virus (HBV), hepatitis delta virus (HDV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) co-infections in a cohort of 426,528 patients tested for HBsAg in Romania between 2018 and 2023. Of the 17,082 HBsAg-positive individuals (4.0% prevalence), the highest HBV positivity rates were observed in the 30-39 and over 60 age groups. Chronic HBV infection was identified in 13.2% of the cohort, with 3.6% testing positive for HBeAg, indicating active viral replication. Co-infection rates were 11.3% for HDV, 1.4% for HCV, and 0.45% for HIV. The incidence of HDV co-infection increased significantly from 2018 to 2023, particularly in older populations. HCV co-infection was more prevalent in individuals aged 50-59 and over 60, with a declining trend from 2020 onward. The study also revealed a weak correlation between liver enzyme levels (ALT and AST) and HBV viral load, suggesting that liver function tests may not fully reflect the severity of HBV infection. HIV co-infection was notably rare compared to other regions, likely due to regional healthcare interventions. The findings from our study highlight the need for targeted interventions, particularly for high-risk groups such as older adults and middle-aged individuals, to reduce the burden of chronic HBV and its complications.