Antibiotics-Basel
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2019
·Vol. 8
·期 2
·45
·
IF 2.921
Bernardo Ribeiro da Cunha,Luís P. Fonseca,Cecília R. C. Calado
Given the increase in antibiotic-resistant bacteria, alongside the alarmingly low rate of newly approved antibiotics for clinical usage, we are on the verge of not having effective treatments for many common infectious diseases. Historically, antibiotic discovery has been crucial in outpacing resistance and success is closely related to systematic procedures—platforms—that have catalyzed the antibiotic golden age, namely the Waksman platform, followed by the platforms of semi-synthesis and fully synthetic antibiotics. Said platforms resulted in the major antibiotic classes: aminoglycosides, amphenicols, ansamycins, beta-lactams, lipopeptides, diaminopyrimidines, fosfomycins, imidazoles, macrolides, oxazolidinones, streptogramins, polymyxins, sulphonamides, glycopeptides, quinolones and tetracyclines. During the genomics era came the target-based platform, mostly considered a failure due to limitations in translating drugs to the clinic. Therefore, cell-based platforms were re-instituted, and are still of the utmost importance in the fight against infectious diseases. Although the antibiotic pipeline is still lackluster, especially of new classes and novel mechanisms of action, in the post-genomic era, there is an increasingly large set of information available on microbial metabolism. The translation of such knowledge into novel platforms will hopefully result in the discovery of new and better therapeutics, which can sway the war on infectious diseases back in our favor.Keywords:antibiotic discovery platforms;drug screening;semi-synthesis;fully synthetic antibiotics;genomics;proteomics;metabolomics;lipidomics;metagenomics
研究领域:
药理学
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微生物学
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基因组学
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生物信息学
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DOI
PubMed
高影响因子
Frontiers in Plant Science
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2023
·
IF 5.6
Chen Qingbing,Gao Kang,Xu YuRan,Sun YaHui,Pan Bo,Chen Dongliang,Luo Chang,Cheng Xi,Liu Hua,Huang Conglin
Chrysanthemums are one of the top ten most well-known traditional famous flowers in China and one of the top four cut flowers worldwide, holding a significant position in landscape gardening. The cold temperatures of winter restrict the cultivation, introduction, and application of chrysanthemum, resulting in high costs for year-round production. This severely impacts the ornamental and economic value of chrysanthemum. Therefore, research on cold tolerance is of vital importance for guiding chrysanthemum production and application. With the development of genomics, transcriptomics, metabolomics, and other omics approaches, along with high-throughput molecular marker technologies, research on chrysanthemum cold tolerance has been continuously advancing. This article provides a comprehensive overview of the progress in cold tolerance research from various aspects, including chrysanthemum phenotype, physiological mechanisms, the forward genetics, molecular mechanisms, and breeding. The aim is to offer insights into the mechanisms of cold tolerance in chrysanthemum and provide reference for in-depth research and the development of new cold tolerance chrysanthemum varieties.
研究领域:
植物学
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遗传学
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园艺学
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DOI
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
·
2024
·
IF 12.2
Qing Qiu,Han Li,Xuejian Sun,Kejian Tian,Jinming Gu,Fenglin Zhang,Dandan Zhou,Xinwen Zhang,Hongliang Huo
Faced with the escalating challenge of global plastic pollution, this study specifically addresses the research gap in the biodegradation of polystyrene (PS). A PS-degrading bacterial strain was isolated from the gut of Tenebrio molitor , and genomics, molecular docking, and proteomics were employed to thoroughly investigate the biodegradation mechanisms of Pseudomonas putida H-01 against PS. Using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (ATR-FTIR), and contact angle analysis, significant morphological and structural changes in the PS films under the influence of the H-01 strain were observed. The study revealed several potential degradation genes and ten enzymes that were specifically upregulated in the PS degradation environment. Additionally, a novel protein with laccase-like activity, LacQ1, was purified from this strain for the first time, and its crucial role in the PS degradation process was confirmed. Through molecular docking and molecular dynamics (MD) simulations, the interactions between the enzymes and PS were detailed, elucidating the binding and catalytic mechanisms of the degradative enzymes with the substrate. These findings have deepened our understanding of PS degradation.
研究领域:
环境生物学
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微生物学
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生物化学
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产品关联
DOI
PubMed
高影响因子
BMC GENOMICS
·
2017
·Vol. 18
·期 1
·1-15
·
IF 3.729
Lu Yuzhen,Luo Feifei,Cen Kai,Xiao Guohua,Yin Ying,Li Chunru,Li Zengzhi,Zhan Shuai,Zhang Huizhan,Wang Chengshu
Background Ascomycete Cordyceps species have been using as valued traditional Chinese medicines. Particularly, the fruiting bodies of Cordyceps cicadae (syn. Isaria cicadae ) have long been utilized for the treatment of chronic kidney disease. However, the genetics and bioactive chemicals in this fungus have been largely unexplored. Results In this study, we performed comprehensive omics analyses of C. cicadae , and found that, in contrast to other Cordyceps fungi, C. cicadae produces asexual fruiting bodies with the production of conidial spores instead of the meiotic ascospores. Genome sequencing and comparative genomic analysis indicate that the protein families encoded by C. cicadae are typical of entomopathogenic fungi, including the expansion of proteases and chitinases for targeting insect hosts. Interestingly, we found that the MAT1-2 mating-type locus of the sequenced strain contains an abnormally truncated MAT1-1-1 gene. Gene deletions revealed that asexual fruiting of C. cicadae is independent of the MAT locus control. RNA-seq transcriptome data also indicate that, compared to growth in a liquid culture, the putative genes involved in mating and meiosis processes were not up-regulated during fungal fruiting, further supporting asexual reproduction in this fungus. The genome of C. cicadae encodes an array of conservative and divergent gene clusters for secondary metabolisms. Based on our analysis, the production of known carcinogenic metabolites by this fungus could be potentially precluded. However, the confirmed production of oosporein raises health concerns about the frequent consumption of fungal fruiting bodies. Conclusions The results of this study expand our knowledge of fungal genetics that asexual fruiting can occur independent of the MAT locus control. The obtained genomic and metabolomic data will benefit future investigations of this fungus for medicinal uses.
研究领域:
真菌学
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遗传学
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生物信息学
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药理学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2022
·
IF 14.224
Huaxin Lei,Jiayu Zhang,Jin Huang,Dengjin Shen,Yin Li,Rui Jiao,Renxin Zhao,Xiaoyan Li,Lin Lin,Bing Li
The aerobic, lincomycin-degrading bacterial strain Conexibacter sp . LD01, belonging to the phylum Actinobacteria, was isolated from activated sludge . Both second- and third-generation sequencing technologies were applied to uncover the genomic characterization and high-quality genome with 99.2% completeness and 2.2% contamination was obtained. The biodegradation kinetics of lincomycin fit well with the modified Gompertz model ( R 2 > 0.97). Conexibacter sp . LD01 could subsist with lincomycin as the sole source of carbon, nitrogen, and energy. When 500 mg/L of glucose was added as a co-substrate, the biodegradation rate improved significantly, whereas the addition of 500 mg/L sodium pyruvate had a slight inhibitory effect. Ammonia nitrogen was the best nitrogen source for Conexibacter sp . LD01 when growing and degrading lincomycin. In total, 17 metabolic products consisting of nine novel products were detected, and five biodegradation pathways, including N-demethylation, breakage of the amido bond, sulfoxidation, and oxidation of the pyrrolidine ring and propylamino chain, were proposed. This study significantly expands our understanding of the functional microorganisms and mechanism involved in lincomycin biodegradation at the phylum level.
研究领域:
微生物学
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环境科学
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基因组学
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产品关联
DOI
PubMed
高影响因子
Food Chemistry-X
·
2025
·
IF 8.2
Zixi Yang,Yanxia Xie,Yuanmin Zhu,Mengjie Lei,Xuemin Chen,Wenwen Jin,Chunhua Fu,Longjiang Yu
Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes ( P < 0.05). The contents of free amino acids, L -theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea , Aspergillus , Brachybacterium , and Staphylococcus . By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium . This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters ( P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.
研究领域:
食品科学
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微生物学
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代谢组学
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产品关联
DOI
PubMed
高影响因子
WATER RESEARCH
·
2019
·
IF 7.913
Fang Zhang,Wei Zhang,Ding-Kang Qian,Kun Dai,Mark C.M. van Loosdrecht,Raymond Jianxiong Zeng
Sludge , of which alginate-like biomaterial is a major organic component, is an increasing environmental problem. Thus, efficient anaerobic degradation of alginate provides a new method for sludge utilization. In this study, anaerobic alginate hydrolytic bacteria (AHB) were proposed to enrich with methanogens synergetically to reduce the inhibition of intermediate metabolites. The COD of produced methane reached 80.7 ± 1.9% (n = 4) of initial alginate COD. After considering the microbial growth (8%–18% of COD), a good COD balance indicated that alginate was fully consumed and the main final metabolites were methane and CO 2 . Methanogenesis could promote alginate conversion by AHB. The enriched bacteria for alginate degradation in this study were different from that of former known AHB. The metabolic pathway of alginate degradation was revealed by metagenomics , in which oligo-alginate lyase was detected in twelve bacteria, and typical carbon metabolic pathways to convert alginate to methane were identified. More studies of bacterial isolation and biofuel production are still needed in the future.
研究领域:
环境科学
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微生物学
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生物技术
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产品关联
DOI
PubMed
高影响因子
Microbiology Research
·
2023
·Vol. 14
·期 1
·91-103
·
IF 1.5
Jinyan Liu,Zhisong Cui,Tong Hao,Yingchao Li,Xiao Luan,Ke Feng,Li Zheng
Increasing pollution has significantly threatened the Antarctic ecosystem. The contamination of hydrocarbons has drawn a considerable amount of attention owing to their toxicity, recalcitrance, and persistence. Considering the Antarctic Treaty, only indigenous species are allowed to bioremediate the contaminated environment. However, the knowledge of the ecological role, physiology, function, and genomics of endemic hydrocarbon consumers is still limited. Here, we investigated the dynamics of phenanthrene-consuming communities derived from the Antarctic soil and found thatVariovorax, Rhodocyclaceae, andHydrogenophagawere differentiated in all the phenanthrene-consuming subcultures. We isolated a pure culture of the key hydrocarbon consumerVariovoraxsp. strain N23. Moreover, the result of the polyphasic approach suggested that strain N23 represents a novel species of the genusVariovorax. In addition, the genomic characteristics of this strain revealed incomplete degradation pathways for diverse hydrocarbons. Overall, this study reveals the relatively weak hydrocarbon-degrading potential of the indigenous bacteria and suggests the need for more careful protection of the Antarctic ecosystem.Keywords:polycyclic aromatic hydrocarbons;psychrophilic bacteria;genomics;chemotaxis;biodegradation
研究领域:
环境科学
·
微生物学
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基因组学
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生物修复
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生态学
✓ 已验证
产品关联
DOI
高影响因子
Food Chemistry-X
·
2025
·
IF 8.2
Munguntsetseg Battur,Muhammad Aaqil,Jingchuan Zheng,Huang Xiao Lin,Bolormaa Chuluunotgon,Tserenkhand Zorigtbaatar,Cunchao Zhao,Yang Tian
This study investigates the impact of milk addition on the fermentation of walnut soy sauce, using Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) and metagenomics to analyze flavor profiles and microbial dynamics. GC-IMS analysis showed significant increases in volatile compounds such as esters (ethyl acetate), aldehydes (hexanal), and alcohols (isoamyl alcohol), enhancing the aroma and taste. Metagenomic analysis revealed that milk increased microbial diversity, with Weissella and Lactobacillus dominating early fermentation. The milk-enriched soy sauce (SYM) exhibited higher amino acid nitrogen (2.67 g/L), and total nitrogen (7.18 g/L) compared to the control, indicating improved nutritional quality. Protease activity peaked at 2438.5 U/g for neutral protease, supporting efficient protein hydrolysis. Relative Odor Activity Value (ROAV) analysis identified 29 key flavor compounds, including 3-methyl butanol and ethyl 2-methyl butyrate, which contributed fruity and buttery notes to SYM. These results suggest that milk enhances microbial growth and improves both flavor and nutritional quality of walnut soy sauce.
研究领域:
食品科学
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微生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
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2025
·
IF 4.1
Jinghua Lv,Shujia Zhang,Siqi He,Tianyu Shi,Yuge Liang,Yunbei Li,Kaili Ma
Antibiotics significantly impact the anaerobic fermentation of waste activated sludge (WAS). However, only a few studies have been conducted on the influence of ofloxacin (OFL) on the production of short-chain fatty acids (SCFAs) and its underlying mechanisms during WAS anaerobic fermentation. This study aimed to elucidate the impact of OFL on SCFA production from alkaline-pretreated WAS fermentation. The results showed that the addition of 10 mg OFL/kg SS led to a peak concentration of 2931.85 mg COD/L, resulting in a 1.1-fold increase in SCFA production compared to the control group. Further exploration revealed that OFL simultaneously promoted WAS solubilization, hydrolysis and acidification. Additionally, a low concentration of OFL increased the abundance of hydrolytic acidifying bacteria but decreased the abundance of SCFA-consuming bacteria. Metagenomic analysis revealed an enhanced abundance (103.76–134.56%) of critical genes related to extracellular hydrolysis (i.e., malZ , bglX , and degP ), membrane transport (i.e., msmX , gtsA , and gltI ), substrate metabolism (i.e., glk , glnA , and gdhA ), and SCFAs biosynthesis (i.e., ackA and fabG ) in the presence of low OFL concentration. These findings broadened our understanding regarding the influence exerted by OFL on WAS anaerobic fermentation.
研究领域:
环境科学
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微生物学
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生物技术
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产品关联
DOI
高影响因子
BIORESOURCE TECHNOLOGY
·
2024
·
IF 9.7
Qinglian Wu,Lin Deng,Tian Lan,Hui Wang,Kaiming Wang,Huacheng Zhu,Yanping Zhou,Wanqian Guo
The integration of biochar into microbial Chain Elongation (CE) proves to be an effective tool of producing high-value bio-based products. This study innovatively applied biochar fabricated under microwave irradiation with carbon fiber cloth assistance into CE system. Results highlighted that microwave biochar achieved maximal CE efficiency yielding 8 g COD/L, with 3-fold increase to the blank group devoid of any biochar. Microwave biochar also obtained the highest substrate utilization rate of 94 %, while conventional biochar group recorded 90 % and the blank group was of 74 %. Mechanistic insights revealed that the reductive surface properties facilitated CE performance, which is relevant to fostering dominant genera of Parabacteroides , Bacteroides , and Macellibacteroides . By metagenomics, microwave biochar up-regulated functional genes and enzymes involved in CE process including ethanol oxidation, the reverse β-oxidation pathway, and the fatty acid biosynthesis pathway. This study effectively facilitated caproate production by utilizing a new microwave biochar preparation strategy.
研究领域:
环境工程
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微生物学
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生物技术
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Scientific Reports
·
2025
·Vol. 15
·期 1
·1-13
·
IF 3.9
Wu Dan,Niu Jingjie,Hu Jianping,Wang Hao,Kuang Haixue
This study aimed to assess the anti-hyperuricemia efficacy of Zhejiang psyllium polysaccharides (ZPP) in rats and to explore its underlying mechanism. Hyperuricemia was induced by intragastric administration of potassium oxonate, hypoxanthine, and adenine. The serum levels of uric acid (UA), creatinine (Cr), and blood urea nitrogen (BUN) were measured, and kidney pathology was examined. Serum metabolomics was employed to monitor metabolic alterations following ZPP intervention. Metagenomic analysis was conducted to investigate the impact of ZPP on the intestinal flora of hyperuricemia rats. The results showed that ZPP could significantly reduce the serum UA level in hyperuricemia rats and exhibited a certain renal protective effect. The metabolomics results indicated that ZPP regulates uric acid levels in rats with hyperuricemia and ameliorates renal pathological changes by modulating biomarkers associated with purine metabolism, amino acid metabolism, and lipid metabolism. Metagenomic research also found that ZPP could increase the relative abundance of uric acid metabolism-related probiotics, such as Limosilactobacillus reuteri and Lactobacillus murinus , thereby improving intestinal flora imbalance in rats with hyperuricemia.
研究领域:
生物化学与分子生物学
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微生物学
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药理学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）