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Xu N, Zuo J, Li C, Gao C, Guo M. Reconstruction and Analysis of a Genome-Scale Metabolic Model of Acinetobacter lwoffii. Int J Mol Sci 2024; 25:9321. [PMID: 39273268 PMCID: PMC11395192 DOI: 10.3390/ijms25179321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/31/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii.
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Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jiaojiao Zuo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Chenghao Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
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Karampatakis T, Tsergouli K, Behzadi P. Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove for Acinetobacter baumannii. Antibiotics (Basel) 2024; 13:257. [PMID: 38534692 DOI: 10.3390/antibiotics13030257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/17/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen responsible for a variety of community- and hospital-acquired infections. It is recognized as a life-threatening pathogen among hospitalized individuals and, in particular, immunocompromised patients in many countries. A. baumannii, as a member of the ESKAPE group, encompasses high genomic plasticity and simultaneously is predisposed to receive and exchange the mobile genetic elements (MGEs) through horizontal genetic transfer (HGT). Indeed, A. baumannii is a treasure trove that contains a high number of virulence factors. In accordance with these unique pathogenic characteristics of A. baumannii, the authors aim to discuss the natural treasure trove of pan-genome and virulence factors pertaining to this bacterial monster and try to highlight the reasons why this bacterium is a great concern in the global public health system.
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Affiliation(s)
| | - Katerina Tsergouli
- Microbiology Department, Agios Pavlos General Hospital, 55134 Thessaloniki, Greece
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran 37541-374, Iran
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de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. Genomic Signature in Evolutionary Biology: A Review. BIOLOGY 2023; 12:biology12020322. [PMID: 36829597 PMCID: PMC9953303 DOI: 10.3390/biology12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.
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Affiliation(s)
- Rebeca de la Fuente
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Correspondence:
| | - Wladimiro Díaz-Villanueva
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
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Li Z, Huang S, He X, Ma H, Zhou X, Lin H, Zhang S. Specific Enriched Acinetobacter in Camellia Weevil Gut Facilitate the Degradation of Tea Saponin: Inferred from Bacterial Genomic and Transcriptomic Analyses. Microbiol Spectr 2022; 10:e0227222. [PMID: 36413019 PMCID: PMC9769793 DOI: 10.1128/spectrum.02272-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/31/2022] [Indexed: 11/24/2022] Open
Abstract
Beneficial gut bacteria can enhance herbivorous arthropod adaptation to plant secondary compounds (PSMs), and specialist herbivores provide excellent examples of this. Tea saponin (TS) of Camellia oleifera is triterpenoids toxic to seed-feeding weevil pest, Curculio chinensis (CW). Previous studies disclosed that Acinetobacter, which was specific enriched in the CW's gut, was involved in helping CW evade TS toxicity of C. oleifera. However, it is still not clear whether Acinetobacter is associated with other anti-insect compounds, and the molecular mechanism of Acinetobacter degradation of TS has not been clarified. To address these questions, we explored the relationship between host plant toxin content and Acinetobacter of CW gut bacteria. Results demonstrated that TS content significantly affected the CW gut microbiome structure and enriched bacteria functional for TS degradation. We further isolated Acinetobacter strain and conducted its genome and transcriptome analyses for bacterial characterization and investigation on its role in TS degradation. Biological tests were carried out to verify the ability of the functional bacterium within CW larvae to detoxify TS. Our results showed that TS-degrading bacteria strain (Acinetobacter sp. AS23) genome contains 47 genes relating to triterpenoids degradation. The AS23 strain improved the survival rate of CW larvae, and the steroid degradation pathway could be the key one for AS23 to degrade TS. This study provides the direct evidence that gut bacteria mediate adaptation of herbivorous insects to phytochemical resistance. IMPORTANCE Microorganism is directly exposed to the plant toxin environment and play a crucial third party in herbivores gut. Although previous studies have proved the existence of gut bacteria that help CWs degrade TS, the specific core flora and its function have not been explored. In this study, we investigated the correlation between the larva gut microbiome and plant secondary metabolites. Acinetobacter genus was the target flora related to TS degradation. There were many terpenoids genes in Acinetobacter sp. AS23 genome. Results of transcriptome analysis and biological tests suggested that steroid degradation pathway be the key pathway of AS23 to degrade TS. This study not only provides direct evidence that gut microbes mediate the rapid adaptation of herbivorous insects to phytochemical resistance, but also provides a theoretical basis for further research on the molecular mechanism of intestinal bacteria cooperating with pests to adapt to plant toxins.
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Affiliation(s)
- Zikun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, People’s Republic of China
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, People’s Republic of China
| | - Suya Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, People’s Republic of China
- College of Horticulture Science, Zhejiang A & F University, Hangzhou, People’s Republic of China
| | - Xinghua He
- Zhoushan Academy of Forestry Science, Zhoushan, People’s Republic of China
| | - Haijie Ma
- College of Horticulture Science, Zhejiang A & F University, Hangzhou, People’s Republic of China
| | - Xudong Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, People’s Republic of China
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, People’s Republic of China
| | - Haiping Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, People’s Republic of China
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, People’s Republic of China
| | - Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, People’s Republic of China
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, People’s Republic of China
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Zhang S, Li Z, Shu J, Xue H, Guo K, Zhou X. Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense. MICROBIOME 2022; 10:97. [PMID: 35752840 PMCID: PMC9233397 DOI: 10.1186/s40168-022-01290-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Herbivorous insects acquire their gut microbiota from diverse sources, and these microorganisms play significant roles in insect hosts' tolerance to plant secondary defensive compounds. Camellia weevil (Curculio chinensis) (CW) is an obligate seed parasite of Camellia oleifera plants. Our previous study linked the CW's gut microbiome to the tolerance of the tea saponin (TS) in C. oleifera seeds. However, the source of these gut microbiomes, the key bacteria involved in TS tolerance, and the degradation functions of these bacteria remain unresolved. RESULTS Our study indicated that CW gut microbiome was more affected by the microbiome from soil than that from fruits. The soil-derived Acinetobacter served as the core bacterial genus, and Acinetobacter sp. was putatively regarded responsible for the saponin-degradation in CW guts. Subsequent experiments using fluorescently labeled cultures verified that the isolate Acinetobacter sp. AS23 can migrate into CW larval guts, and ultimately endow its host with the ability to degrade saponin, thereby allowing CW to subsist as a pest within plant fruits resisting to higher concentration of defensive chemical. CONCLUSIONS The systematic studies of the sources of gut microorganisms, the screening of taxa involved in plant secondary metabolite degradation, and the investigation of bacteria responsible for CW toxicity mitigation provide clarified evidence that the intestinal microorganisms can mediate the tolerance of herbivorous insects against plant toxins. Video Abstract.
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Affiliation(s)
- Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China
- College of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China
| | - Zikun Li
- College of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China
| | - Jinping Shu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, Hangzhou, 311400, People's Republic of China.
| | - Huaijun Xue
- College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Kai Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China
- College of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China
| | - Xudong Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China.
- College of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, Hangzhou, 311300, People's Republic of China.
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Tian H, Zhu Y, Dai M, Li T, Guo Y, Deng M, Sun B. Additives Altered Bacterial Communities and Metabolic Profiles in Silage Hybrid Pennisetum. Front Microbiol 2022; 12:770728. [PMID: 35069475 PMCID: PMC8767026 DOI: 10.3389/fmicb.2021.770728] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/25/2021] [Indexed: 01/05/2023] Open
Abstract
This study was conducted to investigate the effects of different additives on the fermentation quality, nutrient composition, bacterial communities, and metabolic profiles of the silage of hybrid Pennisetum. The experiment was conducted using five treatments, i.e., CK, control group, MA, 1% malic acid of fresh matter (FM) basis, GL, 1% glucose of FM basis, CE, 100 U/g FM cellulase, and BS, 106 cfu/g FM Bacillus subtilis, with six replicates each treatment. After a 120-day fermentation, 30 silage packages were opened for subsequent determination. As a result, all four additives had positive effects on the fermentation quality and nutrient composition of the silage of hybrid Pennisetum. The high-throughput sequencing of V3-V4 regions in 16S rRNA was performed, and results showed that Firmicutes and Proteobacteria were the dominant phyla and that Aquabacterium and Bacillus were the dominant genera. MA, GL, CE, and BS treatment resulted in 129, 21, 25, and 40 differential bacteria, respectively. The four additives upregulated Bacillus smithii but downregulated Lactobacillus rossiae. Metabolic profiles were determined by UHPLC-Q/TOF-MS technology and the differential metabolites caused by the four additives were 47, 13, 47, and 18, respectively. These metabolites played antioxidant, antibacterial, and anti-inflammatory functions and involved in pathways, such as the citrate cycle, carbon fixation in photosynthetic organisms, and glyoxylate and dicarboxylate metabolism. In conclusion, silage additives promoted fermentation quality and nutrient composition by altering bacterial communities and metabolic profiles. This study provided potential biomarkers for the improvement of silage quality.
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Affiliation(s)
| | | | | | | | | | | | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China
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