FEMS MICROBIOLOGY ECOLOGY
·
2014
·Vol. 87
·期 3
·576-585
·
IF 3.875
Liu Jing,Wang Jia-Kun,Zhu Wen,Pu Yi-Yi,Guan Le-Luo,Liu Jian-Xin
Treponema saccharophilum is a pectinolytic bacterium isolated from the bovine rumen. The abundance of this bacterium has not been well determined, reflecting the lack of a reliable and accurate detection method. To develop a rapid method for monitoring T. saccharophilum, we performed pyrosequencing of genomic DNA isolated from rumen microbiota to explore the 16S rRNA gene sequences of T. saccharophilum candidates. Species-specific primers were designed based on fifteen sequences of partial 16S rRNA genes generated through pyrosequencing with 97% or higher similarity with T. saccharophilumDSM2985 along with sequence from type strain. The relative abundance of T. saccharophilum was quantified in both in vitro and in vivo rumen systems with varied pectin-containing forages using real-time PCR. There was a clear association of T. saccharophilum with alfalfa hay, which contains more pectin than Chinese wild rye hay or corn stover. The relative abundance of T. saccharophilum was as high as 0.58% in vivo, comparable with the population density of other common rumen bacteria. It is recognized that T. saccharophilum plays an important role in pectin digestion in the rumen.
研究领域:
微生物学
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分子生物学
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动物科学
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PubMed
高影响因子
MOLECULES
·
2022
·Vol. 27
·期 19
·6461
·
IF 4.927
Luoyijun Xie,Qiyan Li,Yingying Liao,Zihua Huang,Yulin Liu,Chutong Liu,Leilei Shi,Qingjiao Li,Miaomiao Yuan
As a promising therapy, photothermal therapy (PTT) converts near-infrared (NIR) light into heat through efficient photothermal agents (PTAs), causing a rapid increase in local temperature. Considering the importance of PTAs in the clinical application of PTT, the safety of PTAs should be carefully evaluated before their widespread use. As a promising PTA, mesoporous polydopamine (MPDA) was studied for its clinical applications for tumor photothermal therapy and drug delivery. Given the important role that intestinal microflora plays in health, the impacts of MPDA on the intestine and on intestinal microflora were systematically evaluated in this study. Through biological and animal experiments, it was found that MPDA exhibited excellent biocompatibility, in vitro and in vivo. Moreover, 16S rRNA analysis demonstrated that there was no obvious difference in the composition and classification of intestinal microflora between different drug delivery groups and the control group. The results provided new evidence that MPDA was safe to use in large doses via different drug delivery means, and this lays the foundation for further clinical applications.Keywords:intestinal microflora;mesoporous polydopamine;toxicity analysis;16S rRNA gene sequencing
研究领域:
药学
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生物医学工程
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微生物学
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DOI
PubMed
高影响因子
Biosensors-Basel
·
2025
·Vol. 15
·期 12
·821
·
IF 5.6
Jie Chen,Shutao Liu,Sunyi Chen,Jingwen Mai,Maiwula Abudukadi,Yao Chen,Jie Lu,Guanglei Li,Chenchen Ge
Mycoplasma hominis (MH) is a prevalent opportunistic pathogen that is strongly associated with a wide range of urogenital tract infections and severe adverse pregnancy outcomes in clinical settings. Current MH detection methods, including microbial culture and qPCR, are time-consuming and rely on complex equipment, making them unsuitable for scenarios requiring rapid or simplified testing. In this study, we developed a visual readout biosensing platform by synergistically integrating recombinase polymerase amplification (RPA), CRISPR/Cas12a-mediated target nucleic acid recognition, and lateral flow biosensors for the rapid, sensitive, and specific identification of MH. The assay specifically targets the MH-specific 16S rRNA gene, achieving a limit of detection as low as 2 copies/reaction of recombinant plasmid containing the target gene with a total assay time of 60 min. Critical reaction parameters, including Cas12a-crRNA molar ratio, volume of RPA amplicon input, and Cas12a cleavage time, were systematically optimized to maximize the biosensor’s response efficiency and detection reliability. The platform exhibited exceptional specificity, with no cross-reactivity observed against common co-occurring urogenital pathogens, and effectively minimized aerosol contamination risks via a rigorous decontamination workflow. Furthermore, this work represents the first documented implementation of a contamination-control protocol for an MH-specific CRISPR-LFA assay. Notably, testing results from 18 clinical samples demonstrated the high specificity of this assay, highlighting its promising potential for clinical application.
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PubMed
高影响因子
Frontiers in Microbiology
·
2015
·
IF 3.989
Chen Lin,Xu Jianming,Feng Youzhi,Wang Juntao,Yu Yongjie,Brookes Philip C.
In soil microbiology, there is a “paradox” of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity, and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences), followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia, and uncultured Chytridiomycota) were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9 and 36.5% relative frequency, respectively), which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation.
研究领域:
土壤微生物学
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环境科学
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分子生态学
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PubMed
高影响因子
Frontiers in Medicine
·
2021
·
IF 5.093
Li Yujuan,Zhang Wencui,Sun Tainning,Liu Baowen,Manyande Anne,Xu Weiguo,Xiang Hong-Bing
The high incidence of patients with chronic itch highlights the importance of fundamental research. Recent advances in the interface of gut microbiota have shed new light into exploring this phenomenon. However, it is unknown whether gut microbiota plays a role in chronic itch in rodents with or without cognitive dysfunction. In this study, the role of gut microbiota in diphenylcyclopropenone (DCP)-evoked chronic itch was investigated in mice and hierarchical cluster analysis of novel object recognition test (ORT) results were used to classify DCP-evoked itch model in mice with or without cognitive dysfunction (CD)-like phenotype and 16S ribosomal RNA (rRNA) gene sequencing was used to compare gut bacterial composition between CD (Susceptible) and Non-CD phenotypes (Unsusceptible) in chronic itch mice. Results showed that the microbiota composition was significantly altered by DCP-evoked chronic itch and chronic itch induced novel object recognition-related CD. However, abnormal gut microbiota composition induced by chronic itch may not be correlated with novel object recognition-related CD.
研究领域:
神经科学
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微生物学
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行为科学
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PubMed
高影响因子
FOOD RESEARCH INTERNATIONAL
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2021
·
IF 6.475
Fengfei Gu,Shuling Liang,Senlin Zhu,Jianxin Liu,Hui-Zeng Sun
Cow’s milk is a highly-nutritious dairy product part of human diet worldwide. Rumen-protected methionine (RPM) is widely used to improve lactation performance of dairy cows, but understanding of the effects of RPM on milk nutrients composition are still limited. In this study, twenty mid-lactating dairy cows were supplemented with 20 gm/day RPM for 8 weeks to investigate the responses of milk nutritional composition to RPM. Metabolomics was applied for analyzing milk metabolites and 16S rRNA gene sequencing was used for analysis of rumen microbial composition. Milk fat content and yield were significantly increased after RPM supplementation. Totally 443 compounds belonging to 15 classes were identified, among which 15 metabolites were significantly changed. The functional nutrient α-ketoglutaric acid were significantly increased in the milk after RPM supplementation. We found 48 significantly differing bacterial genera in the rumen after supplementing RPM. Multi-omics integrated analysis revealed the higher abundance of Acetobacter , unclassified_f_Lachnospiraceae and Saccharofermentan contributed to the improved milk fat. In addition, the enriched abundance of Thermoactinomyces , Asteroleplasma , and Saccharofermentan showed positive correlations with higher α-ketoglutaric acid of milk. Our results uncover the metabolomic fingerprint and the key functional metabolites in the milk after supplementing RPM in dairy cows, as well as the key rumen bacteria associated with them. These findings provide novel insights into the development of functional dairy products that enriched the functional nutrient α-ketoglutaric acid or high milk fat.
研究领域:
动物营养学
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微生物学
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代谢组学
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乳品科学
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PubMed
高影响因子
CURRENT MICROBIOLOGY
·
2025
·Vol. 83
·期 2
·112
·
IF 2.6
Gao Peng,Lu Xie-Feng,Yao Ling,Xu Yuan-Jia,Zhang Shu-Yi,Liu Guo-Hong,Zhou Shun-Gui
Two novel aerobic, rod-shaped, motile bacterial strains, designated as strains sgz302251 T and sgz5001026 T , were both isolated from paddy soils. 16S rRNA gene sequences analysis revealed that strain sgz302251 T exhibited 98.3% similarity with its closest reference strain Paenibacillus vietnamensis N4 T , while strain sgz5001026 T had the highest similarity of 97.5% to Ectobacillus polymachus KACC 18242 T . The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains sgz302251 T , sgz5001026 T and their closest reference strains were 86.0% and 21.2%, 84.9% and 22.9%, respectively. The genomic DNA G + C contents of sgz302251 T and sgz5001026 T were 63.4% and 68.8%, respectively. Strain sgz302251 T grew at 20–37 °C (optimum 30 °C), pH 5.0–9.0 (optimum 6.5–7.5) and tolerated 0–1.0% NaCl (optimum 0.5%, w/v), while strain sgz5001026 T grew at 4–45 °C (optimum 37 °C), pH 5.0–9.0 (optimum 6.0) and 0–0.5% NaCl (optimum 0%). The quinone in both strains was MK-7 and major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The main fatty acids (> 5%) of strain sgz302251 T were anteiso-C 15:0 , anteiso-C 17:0 , and C 16:0 , whereas strain sgz5001026 T included anteiso-C 15:0 , iso-C 15:0 , iso-C 16:0 and iso-C 14:0 . Based on the above evidence, the proposed names of the two novel species are Paenibacillus praedii sp. nov. (type strain sgz302251 T = MCCC 1K09633 T = KCTC 43808 T ), Ectobacillus soli sp. nov. (type strain sgz5001026 T = MCCC 1K09373 T = KCTC 25903 T ), respectively.
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高影响因子
Gut Pathogens
·
2023
·Vol. 15
·期 1
·1-14
·
IF 4.2
Wang Shanshan,Wen Qiuyu,Qin Yan,Xia Quan,Shen Chenlin,Song Shuai
Background The pseudo germ-free (PGF) model has been widely used to research the role of intestinal microbiota in drug metabolism and efficacy, while the modelling methods and the utilization of the PGF model are still not standardized and unified. A comprehensive and systematic research of the PGF model on the composition and function of the intestinal microbiota, changes in host cytochrome P450 (CYP450) enzymes expression and intestinal mucosal permeability in four different modelling cycles of the PGF groups are provided in this paper.Results 16S rRNA gene amplicon sequencing was employed to compare and analyze the alpha and beta diversity, taxonomic composition, taxonomic indicators and predicted function of gut microbiota in the control and PGF groups. Bacterial richness and diversity decreased significantly in the PGF group beginning after the first week of establishment of the PGF model with antibiotic exposure. The PGF group exposed to antibiotics for 4-week-modelling possessed the fewest indicator genera. Moreover, increased intestinal mucosal permeability occurred in the second week of PGF model establishment, indicating that one week of antibiotic exposure is an appropriate time to establish the PGF model. The results of immunoblots revealed that CYP1A2, CYP2C19 and CYP2E1 expression was significantly upregulated in the PGF group compared with the control group, implying that the metabolic clearance of related drugs would change accordingly. The abundance of functional pathways predicted in the gut microbiota changed dramatically between the control and PGF groups.Conclusion sThis study provides information concerning the microbial and CYP450 enzyme expression profiles as a reference for evaluating drug metabolism differences co-affected by gut microbiota and host CYP450 enzymes in the PGF model.
研究领域:
药理学
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微生物学
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分子生物学
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胃肠病学
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DOI
PubMed
高影响因子
WATER AIR AND SOIL POLLUTION
·
2017
·Vol. 228
·期 2
·1-14
·
IF 1.702
Zhang Jing,Liu Shicheng,Li Lingling,Ren Yuan,Feng Chunhua,Wei Chaohai,Li Yipeng,Huang Zhili
Tetrachlorobisphenol A (TCBPA) is a widely used flame retardant and a potential endocrine disruptor. We estimated the role of the microbial community in degradation of TCBPA in river sediment from the vicinity of an E-waste processing facility. The effects of different anaerobic conditions on degradation efficiency of TCBPA were investigated, and differences in bacterial communities among these conditions were analyzed by 16S ribosomal RNA (rRNA) gene sequencing. The most effective dechlorination of TCBPA occurred under methanogenic conditions followed by electron donor-enhanced conditions and sulfate-reducing conditions with initial sulfate concentrations of 1, 10, and 20 mM. The extent of TCBPA removal under these conditions mentioned above was 65, 44, 43, 23, and 23%, respectively. 16S rRNA gene sequence analysis indicated that five dominant genera in the phylum Chloroflexi and another five species of Bacteroidetes , Chlorobi , and Firmicutes in these five systems were largely involved in TCBPA dechlorination. The initial sample had a total relative abundance of autochtonous potential dechlorinating bacteria of 12%. After 160 days, these values increased to 29–43% under above conditions. Addition of TCBPA decreased bacterial diversity. Efficiency of TCBPA degradation depends on the abundance and metabolism of dechlorinating bacterial guilds. The effectiveness of dechlorinating microbes in degradation of TCBPA was reduced by high sulfate concentrations.
研究领域:
环境微生物学
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生物修复
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生态毒理学
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高影响因子
ENVIRONMENTAL POLLUTION
·
2017
·
IF 5.099
Sisheng Wu,Cuiyuan Jin,Yueyi Wang,Zhengwei Fu,Yuanxiang Jin
Propamocarb (PM) is a widely used fungicide with property of affecting fatty acid and phospholipid biosynthesis in funguses. In this study, we explored its effects on mice gut microbiota and metabolism by exposing mice to 3, 30, and 300 mg/L PM through drinking water for a duration of 28 days. We observed that the transcription of hepatic genes related to regulate lipid metabolism were perturbed by PM exposure. The microbiota in the cecal contents and feces changed during or after PM exposure at phylum or genus levels. 16S rRNA gene sequencing for the cecal content revealed shifted in overall microbial structure after PM exposure, and operational taxonomic unit (OTU) analysis indicated that 32.2% of OTUs changed by 300 mg/mL PM exposure for 28 days. In addition, based on 1 H NMR analysis,a total of 20 fecal metabolites mainly including succinate, short chain fatty acids, bile acids and trimethylamine were found to be significantly influenced by exposure to 300 mg/L PM.,. These metabolites were tightly correlated to host metabolism. Our findings indicated that high doses of PM exposure could disturb mice metabolism through, or partly through, altering the gut microbiota and microbial metabolites.
研究领域:
毒理学
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微生物学
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代谢组学
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DOI
PubMed
高影响因子
Chinese Journal of Natural Medicines
·
2022
·
IF 3.887
Si-Li ZHENG,Dong-Ning ZHANG,Yan-Fen DUAN,Fang HUANG,Lin-Tao HAN,Guo-Yan MO
Ma-Mu-Ran Antidiarrheal Capsules (MMRAC) is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis (AE) and bacillary dysentery in Xinjiang (China) for many years. However, the potential therapeutic mechanism of MMRAC for AE and its regulatory mechanism on host metabolism is unclear. This study used fecal metabolomics profiling with GC/MS and 16S rRNA gene sequencing analysis to explore the potential regulatory mechanisms of MMRAC on a dextran sulfate sodium salt (DSS)-induced mouse model of AE. Fecal metabolomics-based analyses were performed to detect the differentially expressed metabolites and metabolic pathways. The 16S rRNA gene sequencing analysis was used to assess the altered gut microbes at the genus level and for functional prediction. Moreover, Pearson correlation analysis was used to integrate differentially expressed metabolites and altered bacterial genera. The results revealed that six intestinal bacteria and seven metabolites mediated metabolic disorders (i.e., metabolism of amino acid, carbohydrate, cofactors and vitamins, and lipid) in AE mice. Besides, ten altered microbes mediated the differential expression of eight metabolites and regulated these metabolisms after MMRAC administration. Overall, these findings demonstrate that AE is associated with metabolic disorders and microbial dysbiosis. Further, we present that MMRAC exerts protective effects against AE by improving host metabolism through the intestinal flora.
研究领域:
药理学
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微生物学
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代谢组学
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胃肠病学
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DOI
PubMed
高影响因子
Food Bioscience
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2020
·
IF 3.067
Zhaoxia Yang,Sasa Liu,Jing Lv,Zeping Sun,Wenhuan Xu,Chaofan Ji,Huipeng Liang,Shengjie Li,Chenxu Yu,Xinping Lin
Chouguiyu (stinky Mandarin fish), a traditional spontaneously fermented fish in China, is famous for its unique aroma and pleasant taste. However, the relationships between the succession of microorganisms during the fermentation and the formation of Chouguiyu 's unique aroma and taste remain to be characterized. In this study, 16S rRNA gene amplicon sequencing was done to investigate the evolving microbiota during Chouguiyu fermentation, and the volatile compounds and amino acids profiles were measured alongside with chemical characterization of the samples (e.g., determination of pH, TVB-N, TBARS , and TCA-soluble peptides). Based on the changes of the microbiota, the fermentation was categorized into two stages: early-fermentation, 1st-3rd days; and late-fermentation, 4th-7th days. Linalool, piperitone, anethole , 1-octen-3-ol, 2-methyl-3-octanone and indole were identified as characteristic volatile compounds in Chouguiyu . According to the sensory evaluation results, the flavor of the Chouguiyu was reinforced in the late-fermentation stage. Redundancy analysis showed the relationships between evolving microbiota and the formation of Chouguiyu 's aroma and taste, and Psychrilyobacter was identified to be the most important bacterial genus contributing to flavor and aroma development, followed by Fusobacterium , Arcobacter and O c eanisphaera . These genera were positively correlated with Glu, Met, Tyr, Pro, linalool, piperitone, indole, TBARS, TVB-N, and TCA , and influenced the flavor and aroma of the Chouguiyu . The results of this study provided a scientific basis to further improve Chouguiyu production.
研究领域:
食品科学
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微生物学
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化学分析
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高影响因子
危险品化学品经营许可证（带存储）