BMC Microbiology最新文献

{"title":"Multi-omics analysis of host-microbiome interactions in a mouse model of congenital hepatic fibrosis.","authors":"Mengfan Jiao, Ye Sun, Zixing Dai, Xiaoxue Hou, Xizhi Yin, Qingling Chen, Rui Liu, Yuwen Li, Chuanlong Zhu","doi":"10.1186/s12866-025-03892-x","DOIUrl":"https://doi.org/10.1186/s12866-025-03892-x","url":null,"abstract":"<p><strong>Background: </strong>Congenital hepatic fibrosis (CHF) caused by mutations in the polycystic kidney and hepatic disease 1 (PKHD1) gene is a rare genetic disorder with poorly understood pathogenesis. We hypothesized that integrating gut microbiome and metabolomic analyses could uncover distinct host-microbiome interactions in CHF mice compared to wild-type controls.</p><p><strong>Methods: </strong>Pkhd1^{del3-4/del3-4} mice were generated using CRISPR/Cas9 technology. Fecal samples were collected from 11 Pkhd1^{del3-4/del3-4} mice and 10 littermate wild-type controls. We conducted a combined study using 16 S rDNA sequencing for microbiome analysis and untargeted metabolomics. The gut microbiome and metabolome data were integrated using Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO), which helped identify key microbial and metabolic features associated with CHF.</p><p><strong>Results: </strong>CHF mouse model was successfully established. Our analysis revealed that the genera Mucispirillum, Eisenbergiella, and Oscillibacter were core microbiota in CHF, exhibiting significantly higher abundance in Pkhd1^{del3-4/del3-4} mice and strong positive correlations among them. Network analysis demonstrated robust associations between the gut microbiome and metabolome. Multi-omics dimension reduction analysis demonstrated that both the microbiome and metabolome could effectively distinguish CHF mice from controls, with area under the curve of 0.883 and 0.982, respectively. A significant positive correlation was observed between the gut microbiome and metabolome, highlighting the intricate relationship between these two components.</p><p><strong>Conclusion: </strong>This study identifies distinct metabolic and microbiome profiles in Pkhd1^{del3-4/del3-4} mice. Multi-omics analysis effectively differentiates CHF mice from controls and identified potential biomarkers. These findings indicate that gut microbiota and metabolites are integral to the pathogenesis of CHF, offering novel insights into the disease mechanism.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"176"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of SepF in Streptococcus suis involving cell division.","authors":"Ting Gao, Tingting Li, Jiajia Zhu, Linlin Zheng, Mo Chen, Wei Liu, Keli Yang, Tengfei Zhang, Fangyan Yuan, Zewen Liu, Rui Guo, Chang Li, Qiong Wu, Yongxiang Tian, Rui Zhou, Danna Zhou","doi":"10.1186/s12866-025-03919-3","DOIUrl":"https://doi.org/10.1186/s12866-025-03919-3","url":null,"abstract":"<p><strong>Background: </strong>Streptococcus suis (S. suis) is a major zoonotic pathogen that infects humans and pigs. The increasing emergence and dissemination of antibiotic resistance bacteria accelerates the urgent need to develop novel drug targets. Bacterial cell divisome is attractive target. FtsZ, an essential tubulin-like protein, forms a Z-ring that executes the synthesis of the divisome. However, the exact division process of S. suis remains unknown.</p><p><strong>Results: </strong>here, we reported a SepF homolog from S. suis that modulated the function of FtsZ. sepF disruption was not lethal and its deletion mutant (∆sepF) displayed normal growth rate. ∆sepF exhibited long chains, occasionally anuclear daughter cells. Electron microscope revealed that the lack of SepF in cells led to abnormal septum which twisted out of shape, and disturbed cell division due to an increased length-width ratio and multiple septal peptidoglycan wall in a cell compared to the wild type strain. Mechanistic studies showed that SepF interacted with FtsZ to promote the bundling of FtsZ protofilaments. Furthermore, sub-cellular localization of FtsZ-GFP in ∆sepF also confirmed the abnormal septum and cell morphology.</p><p><strong>Conclusions: </strong>These results showed that SepF was a cell division protein in S. suis responsible for maintaining cell shape and regulating FtsZ localization.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"179"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intermittent fasting driven different adaptive strategies in Eothenomys miletus (Red-backed vole) at different altitudes: based on the patterns of variations in intestinal microbiota.","authors":"Ting Jia, Wei Zhang, Wanlong Zhu, Lixian Fan","doi":"10.1186/s12866-025-03934-4","DOIUrl":"https://doi.org/10.1186/s12866-025-03934-4","url":null,"abstract":"<p><p>In the face of global warming, the Eothenomys miletus (Red - backed vole), a species dwelling in highland mountainous regions, is likely to encounter difficulties. Given its restricted mobility, it may struggle with the uncertainty of food resources. In such circumstances, it becomes increasingly crucial for this species to adjust its diverse responses to fulfill its energy requirements. E. miletus specimens were gathered from different altitudes for intermittent fasting (IF) experiments. In these experiments, the specimens underwent random fasting for 3 days within a seven - day cycle. 16 S rDNA sequencing technology, combined with physiological and biochemical assessment methods, was employed to analyze the impacts of IF on gut microorganisms, physiological and biochemical indicators, and the interactions among them. By exploring the adaptive responses of E. miletus to uncertain food resources, which provides novel perspectives on the adaptive strategies of small rodents in the wild during food-scarce periods. The results showed that IF significantly reduced the body mass of E. miletus. Significant correlations were found between various gut microbes and physiological indicators. Under IF conditions, E. miletus at high altitudes experienced a smaller reduction in body mass compared to those at low altitudes. Moreover, the diversity of gut microbes and endemic bacteria in E. miletus at high altitudes varied more than that of low altitudes. The differential response in body mass reduction between high-altitude and low-altitude E. miletus under IF conditions indicated that altitude is an important factor influencing the physiological adaptation of this species to dietary changes. High-altitude E. miletus showed a relatively smaller decrease in body mass, potentially reflecting their better adaptation to environmental stressors over time. Additionally, the greater variation in gut microbe diversity and endemic bacteria in high-altitude E. miletus implied that altitude may shape the gut microbiota, which in turn could be related to their unique physiological adaptations at high altitudes. Overall, E. miletus at high altitude may possess more stable regulatory mechanisms, demonstrating better adaptation under IF conditions. These findings provide valuable insights into the complex interplay between diet, altitude, and gut microbiota in the context of E. miletus physiology, highlighting the importance of considering both environmental and microbial factors in understanding the species' responses to nutritional challenges.​.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"185"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phyllospheric application of Bacillus mucilaginosus mediates the recovery of tea plants exposed to low-temperature stress by alteration of leaf endophytic community and plant physiology.","authors":"Xiao Han, Yaozong Shen, Litao Sun, Jiazhi Shen, Yilin Mao, Kai Fan, Shuangshuang Wang, Zhaotang Ding, Yu Wang","doi":"10.1186/s12866-025-03880-1","DOIUrl":"https://doi.org/10.1186/s12866-025-03880-1","url":null,"abstract":"<p><strong>Background: </strong>In winter, tea plants are highly susceptible to low-temperature freezing damage. The rapid recovery of tea plant vigor in spring is crucial for tea yield and quality. Some studies have reported that Bacillus mucilaginosus could improve the stress resistance of plants. However, there were no reports on the effect of B. mucilaginosus on the recovery of tea plant vigor after low-temperature stress. This study firstly used different concentrations of B. mucilaginosus to spray tea leaves and used 16S rRNA high-throughput sequencing technology to study the impact of different treatments on tea leaf endophytic populations. Meanwhile, physiological indexes such as Soil and plant analyzer development values (SPAD), maximum photochemical quantum yield of PS II (Fv/Fm), and superoxide dismutase (SOD) were measured and analyzed in tea plant leaves of different treatments, and the correlation between them and the bacterial community was studied.</p><p><strong>Results: </strong>Microbial results showed that the diversity of leaf endophytic populations treated with different concentrations of Bacillus mucilaginosus (T1, T2, T3) was higher than that in control group (CK) leaves, and T2 treatment had the highest diversity. The dominant bacterial phyla of all samples were Proteobacteria, Actinobacteriota, Firmicutes, and Bacteroidota. At the phylum level, the relative abundance of Actinobacteriota, Firmicutes, and Bacteroidota in leaves treated with B. mucilaginosus was significantly higher than that in the control. At the genus level, the relative abundance of Paenibacillus, Nocardioides, and Marmoricola in leaves treated with B. mucilaginosus was significantly higher than that in the control. Different concentrations of B. mucilaginosus affected the distribution of leaf endophytic populations. At the level of bacterial function, abundant metabolic functional features were observed, including amino acid transport and metabolism, as well as energy production and conversion, indicating that bacterial metabolism in tea plant leaf samples tends to be vigorous. The treatment with B. mucilaginosus significantly increased the activity of antioxidant enzymes and osmolyte content, promoted the recovery of Fv/Fm in tea plants after low-temperature stress, and improved the resistance of tea leaves to low-temperature stress, thereby promoting recovery.</p><p><strong>Conclusions: </strong>This study showed that B. mucilaginosus could significantly change the community structure of leaf endophytic populations, and increase antioxidant enzyme activity and osmolyte content in tea plants after low-temperature stress, promoting the rapid recovery of photosynthesis, and thereby benefiting the recovery of tea plant leaves. This study provided a theoretical basis for the application of B. mucilaginosus in practical production and also provided new ideas for the recovery of tea plants exposed to low-temperature stress.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"177"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The continuous expansion and spread of human brucellosis in the Xinjiang Uygur Autonomous Region: evidence from epidemiological and strains' genotyping-based analysis.","authors":"Zhiguo Liu, Bo Li, Chuizhao Xue, Min Yuan, Zhenjun Li, Junling Sun, Canjun Zheng","doi":"10.1186/s12866-024-03731-5","DOIUrl":"https://doi.org/10.1186/s12866-024-03731-5","url":null,"abstract":"<p><p>Human brucellosis is a severe public health threat in Xinjiang; however, the epidemiological evolution and molecular correlation of strains are still unclear. In this study, join point regression analysis, spatiotemporal scan analysis, conventional biotyping approaches, and multiple locus variable-number tandem repeat analysis (MLVA) were applied to characterize the epidemiological landscape. A total of 78,689 cases were reported from 1957 to 2023. The average annual reported cases and incidence rates were 1174.46 and 5.28/100,000, respectively. Join point analysis revealed that disease incidence trends increased from 2004 (329, 1.77/100,000) to 2023 (9,334, 36.08/100,000) (AAPC = 17.26, P = 0.00), and affected counties expanded from 21 in 2004 to 100 in 2023, implying that human brucellosis continues to worsen. In 2023, the incidence rates in most counties in southern Xinjiang were higher than 2.0/100,000, and human brucellosis has become endemic in southern Xinjiang. These data demonstrate that human brucellosis is continuously spreading and expanding in Xinjiang. High incidence rate of clusters was detected in North Xinjiang from 2013 to 2023, involving 54 counties. The substantial increase in ruminant farming has increased the risk of infection in humans. A total of 28 Brucella strains were isolated in patients, all B. melitensis bv. 3. MLVA revealed that the dominant genotypes consisted of strains from different areas, hosts, and years; strains from a common original continuously spread, small ruminant trade and transfer contributed to the spread of strains in adjacent regions. Therefore, strengthening surveillance and control of animal brucellosis is vital for preventing its further spread.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"181"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial and anti-inflammatory effects of antimicrobial peptide Lf-KR against carbapenem-resistant Escherichia coli.","authors":"Jingchun Kong, Yue Wang, Yan Liu, Weijun Chen, Yijia Han, Huijing Zhou, Xiaodong Zhang, Beibei Zhou, Tieli Zhou, Jiayin Zheng","doi":"10.1186/s12866-025-03906-8","DOIUrl":"https://doi.org/10.1186/s12866-025-03906-8","url":null,"abstract":"<p><strong>Background: </strong>Carbapenem-resistant Escherichia coli (CREC) is one of the most significant clinical pathogens, primarily emerging owing to the widespread use of broad-spectrum antibiotics. Antimicrobial resistance is a major global health challenge that prolongs treatment duration and increases healthcare costs. This study evaluated the antibacterial and anti-inflammatory effects of the antimicrobial peptide Lf-KR against CREC.</p><p><strong>Methods: </strong>Broth microdilution method, growth curve analysis, and time-kill assays were performed to evaluate the antibacterial activity of Lf-KR against CREC. The working mechanism of Lf-KR was elucidated using N-phenyl-1-naphthylamine, propidium iodide fluorochrome, and lipopolysaccharide-binding assays. qRT-PCR was used to assess the peptide's effects on the expression of pro-inflammatory cytokines expression during infection. Furthermore, the safety and stability of Lf-KR were assessed by testing its cytotoxicity, hemolytic activity, and antibacterial stability under various conditions. The Galleria mellonella infection model was applied to evaluate the in vivo activity of Lf-KR.</p><p><strong>Results: </strong>In vitro tests showed that Lf-KR exhibited potent antibacterial activity against CREC, with the minimum inhibitory concentrations of ranging from 4-8 µg/mL and minimum bactericidal concentrations 4-16 µg/mL. Mechanistically, Lf-KR induced bacterial cell death by disrupting the bacterial membrane. Furthermore, Lf-KR significantly reduced the expression of pro-inflammatory cytokine genes, including IL-1β, IL-6, and TNF-α, in RAW 264.7 macrophage cells infected with CREC. Lf-KR concentrations < 128 µg/mL showed no significant cytotoxicity or erythrocyte hemolytic activity. Lf-KR antibacterial activity was stable across a wide temperature range (- 80 °C to 65 °C), although it was more susceptible to inhibition by fetal bovine serum. The G. mellonella infection model further demonstrated the robust antimicrobial activity of Lf-KR.</p><p><strong>Conclusions: </strong>This study demonstrated that the antimicrobial peptide Lf-KR is a highly promising antimicrobial and anti-inflammatory agent against CREC, with potential applications in combating multi drug-resistant bacterial infections.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"183"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria.","authors":"Samuel O Ajoseh, Abdul-Azeez A Anjorin, Wasiu O Salami, Hanka Brangsch, Heinrich Neubauer, Gamal Wareth, Kabiru O Akinyemi","doi":"10.1186/s12866-025-03917-5","DOIUrl":"https://doi.org/10.1186/s12866-025-03917-5","url":null,"abstract":"<p><strong>Background: </strong>Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of antimicrobial resistance determinants and virulence-related genes in whole-genome sequencing data of 189 Nigerian A. baumannii isolates deposited in public repositories. Genotypes were determined in-silico by multilocus sequence typing (MLST) and core genome MLST (cgMLST). Further, antimicrobial resistance (AMR) and virulence-related genes were analyzed.</p><p><strong>Results: </strong>Most isolates (57.67%) originated from South-west Nigeria. Isolates of human origin accounted for 33.86%, while environmental sources comprised 6.87%, and 59.27% lacked information on the source of isolation. The cgMLST analysis revealed a multitude of genomic lineages circulating in Nigeria. The MLST Oxford scheme identified 44 sequence types (STs) in 62.96% of strains, with ST1089 being the most prevalent. The MLST Pasteur could assign 95.77% of strains to 49 STs, with ST2(IC2) and ST85(IC9) being the most dominant. Antimicrobial resistance analysis detected 168 genes encoding resistance to 12 antibiotic classes, with cephalosporin, carbapenem, and aminoglycoside resistance genes being the most prevalent. Notably, bla_ADC-79 (23.81%), bla_OXA-23 (30.69%), and aph(3″)-Ib (30%) were frequent variants encountered. Seventeen multi-efflux system genes conferring resistance to multiple antibiotic classes were identified. Virulence gene analysis revealed 137 genes encoding six mechanisms, with genes for nutritional factors, effector delivery systems, and biofilm production being the most prevalent.</p><p><strong>Conclusion: </strong>This study highlights the diversity in AMR and virulence genes of A. baumannii in Nigeria, emphasizing the need for ongoing genomic surveillance to inform infection control and develop antibiotic resistance management strategies.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"178"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of ciprofloxacin and aminoglycoside susceptibility testing for ceftriaxone non-susceptible Enterobacterales by disk diffusion and VITEK 2 vs. broth microdilution using updated Clinical and Laboratory Standards Institute breakpoints.","authors":"Zahra N Sohani, Anthony Lieu, Makeda Semret, Matthew P Cheng, Nancy Simic, Reggie Bamba, Mina Patel, Alexander Lawandi, Todd C Lee","doi":"10.1186/s12866-025-03923-7","DOIUrl":"https://doi.org/10.1186/s12866-025-03923-7","url":null,"abstract":"<p><strong>Background: </strong>Fluoroquinolones and aminoglycosides are potential treatment choices in the setting of increasingly multi-drug resistant Enterobacterales. The Clinical & Laboratory Standards Institute (CLSI) breakpoints for fluoroquinolones and aminoglycosides in the Enterobacterales were revised in 2019 and 2022, respectively. However, performance of existing widely used automated systems, such as the VITEK 2 AST-N391 card, has not been extensively tested for MDR isolates at these new breakpoints.</p><p><strong>Objective: </strong>To assess performance of the new breakpoints for ciprofloxacin, gentamicin, and tobramycin on the VITEK 2 system (bioMérieux, France) and disk diffusion by comparing to broth microdilution for ceftriaxone nonsusceptible Enterobacterales.</p><p><strong>Methods: </strong>Ninety-four ceftriaxone non-susceptible Escherichia coli and Klebsiella pneumoniae isolates were identified between January 2021-June 2023. Broth microdilution was used as the reference standard against which disk diffusion and VITEK 2 susceptibility testing were compared. For the Vitek 2, we used the AST-N391 card and interpreted the results according to the updated CLSI breakpoints.</p><p><strong>Results: </strong>Overall, 22.3% of isolates were susceptible to ciprofloxacin by BMD. Compared to BMD, disk diffusion had an overall minor error rate of 7.4% (95%CI 3.0-14.7%) with 0 major or very major errors (97.5% CI 0-3.8%). For the VITEK 2, a minor error rate of 13.8% (95% CI 7.6-22.5%), major error rate 19.0% (95%CI 7.7-40.0%) and very major error rate 0% (97.5%CI 0-3.8%) was noted. By comparison, 69.1% and 56.4% of isolates were susceptible to gentamicin and tobramycin, respectively. Disk diffusion and the VITEK 2 system both correctly categorized 100% of gentamicin susceptible and non-susceptible isolates. For tobramycin, disk diffusion had a 3.2% rate of misclassification (all minor errors) and the VITEK 2 had 2.1% rate of misclassification (all minor errors). There were no major or very major errors.</p><p><strong>Conclusions: </strong>Our findings suggest that both disk diffusion and to a greater extent the AST-N391 card for the VITEK 2 system will overcall non-susceptibility according to current CLSI breakpoints for ciprofloxacin. By contrast, the existing AST-N391 VITEK 2 card can likely be used to correctly infer susceptibility to gentamicin and tobramycin.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"175"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling organohalide respiration potential in River Nile sediments via 16S rRNA gene amplicon sequencing of endogenous bacterial communities.","authors":"Hwayda Soliman, Mohamed Ismaeil, Hoda Soussa, Wael S El-Sayed","doi":"10.1186/s12866-025-03864-1","DOIUrl":"https://doi.org/10.1186/s12866-025-03864-1","url":null,"abstract":"<p><strong>Background: </strong>Industrial waste, agricultural runoff and untreated sewage contaminate the Nile, leaving a toxic legacy in its sediments. Organohalides-polluted sediment in particular poses serious public health risks and detrimental effects on aquatic life. Sediment microbiomes may harbor bacterial strains that could be utilized in bioremediation of such toxic pollutants.</p><p><strong>Material and methods: </strong>Two microbiomes from polluted River Nile sediments were analyzed by using 16S rRNA gene amplicon sequencing. In addition, PICRUSt analysis based on 16S rRNA data was used to explore the organohalide respiring bacteria (OHRB) genera and their corresponding organohalide respiration (OHR) activity. Microcosm studies were performed to validate the potential for dechlorination activity of River Nile sediment. Dechlorination of the parent chloroethenes into daughter end product were detected by gas chromatography coupled with flame ionization detection analysis.</p><p><strong>Results: </strong>Analysis of 16S rRNA gene amplicon sequences using the EZ-biocloud server identified Proteobacteria as the dominant phylum in both microbiomes, with Bacteroidetes and Chloroflexi prevalent in RNS1 sediment and Chlorobi in RNS2 sediment. EZ-biocloud and PCR analyses detected several potential OHRB genera, including Dehalococcoides, Dehalogenimonas, Desulfomonile, Desulfovibrio, and Geobacter, suggesting potential OHR activity. Further evidence for potential OHR activity was provided by PICRUSt functional prediction analysis, which suggested the presence of reductive dehalogenases as functional biomarkers associated with OHR in the sediment samples. Specifically, PICRUSt analysis predicted the presence of potential genes of tetrachloroethene reductive dehalogenase and 3-chloro-4-hydroxyphenylacetate reductive dehalogenase, previously linked to OHR. Microcosm studies confirmed the dechlorination potential of tetrachloroethene to dichloroethene.</p><p><strong>Conclusion: </strong>This study demonstrates that River Nile sediment in industrialized area harbors distinct microbiomes enclosing various OHRB genera, providing substantial evidence for potential reductive dechlorination activity. It also provides potential functional biomarkers for OHR activity.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"186"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of different fiber levels of energy feeds on rumen fermentation and the microbial community structure of grazing sheep.","authors":"Xiaoyun Zhang, Xulei Liu, Kaili Xie, Yueting Pan, Fuyao Liu, Fujiang Hou","doi":"10.1186/s12866-024-03644-3","DOIUrl":"https://doi.org/10.1186/s12866-024-03644-3","url":null,"abstract":"<p><strong>Background: </strong>Rumen microbial community structure and stability are very important for ruminant health, growth and development, and livestock product yield. Dietary composition and nutritional structure affect microbial diversity and richness. The purpose of this study was to evaluate the effects of different fiber levels of energy feed on the rumen microflora and fermentation function of grazing sheep in salinized sown pasture, to reveal the response of the main microflora of sheep rumen at the phylum and genus levels to different fiber levels of energy feed and to analyze the internal mechanism to provide a reference for the selection of energy feed and the improvement of the production performance of grazing livestock.</p><p><strong>Results: </strong>The fiber level of energy feed affects the rumen fermentation and rumen microbial community structure of grazing sheep. Low-fiber-energy feeds significantly increased the relative abundance of Actinobacteria, while the relative abundances of Cyanobacteria, Ruminococcaceae_UCG_010, Ruminococcaceae_NK4A214_group, and Elusimicrobium significantly decreased, adjusting the relationship between the flora toward cooperation. High-fiber-energy feeds significantly increased the concentration of VFAs, significantly decreased the relative abundances of Proteobacteria, Ruminococcaceae_NK4A214_group and Rikenellaceae_RC9_gut_group, adjusted the relationship between the flora to compete, and promoted the enrichment of metabolic pathways such as \"Protein Digestion and Absorption,\" \"Nitrogen Metabolism,\" \"Starch and Sucrose Metabolism,\" and \"Degradation of Other Sugars.\"</p><p><strong>Conclusions: </strong>Supplementary feeding of high and low fiber energy feeds reduced the pH value of rumen fluid and the richness and diversity of microorganisms in grazing sheep, reduced the relative abundance of some harmful microorganisms, affected the metabolic activities of some fiber-digesting bacteria, regulated the interaction and competition between bacteria, increased the content of volatile fatty acids (VFAs) and the relative abundance of metabolic-related microorganisms in the supplementary feeding group, and enriched the metabolic-related pathways. However, further understand the mechanism of the effect of fiber level on the rumen of sheep, it is necessary to conduct in-depth analysis using research methods such as transcriptomics, proteomics and metabolomics.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"180"},"PeriodicalIF":4.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}