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Wang J, Wang X, Liu L, Wang X, Wang J, Zheng Y, Wang L, Pan X. Analyzing the Interaction between Tetrahymena pyriformis and Bacteria under Different Physicochemical Conditions When Infecting Guppy Using the eDNA Method. Animals (Basel) 2024; 14:2194. [PMID: 39123720 PMCID: PMC11310954 DOI: 10.3390/ani14152194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
In the aquaculture system of ornamental fish, the interaction between bacterial microbiota and ciliate protozoa can prevent or promote disease outbreaks, and different physicochemical conditions will affect the relationships between them. We investigated the interaction between bacterial microbiota and the parasite Tetrahymena pyriformis when infecting Poecilia reticulata (guppy) under different physicochemical conditions. The abundance of T. pyriformis in water, the relative abundance of bacterial species, and histopathological observation were studied or monitored using environmental DNA (eDNA) extraction technology, the qPCR method, and 16s rRNA sequencing, respectively. The morphological identification and phylogenetic analysis of T. pyriformis were carried out. The infected guppy tissue was also stained by the hematoxylin and eosin methods. The results showed: (1) the bacterial communities of water samples were mainly composed of species assigned to Proteobacteria and Bacteroidetes, and Tabrizicola and Puniceicoccaceae were positively correlated with fish mortality, T. pyriformis abundance, and temperature. (2) Arcicella and Methyloversatilis universalis with different correlations between ciliates appeared in different treatment groups, the result of which proved that environmental factors affected the interaction between bacteria and T. pyriformis. (3) Lower temperatures and a higher pH were more beneficial for preventing disease outbreaks.
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Affiliation(s)
| | | | | | | | | | | | | | - Xuming Pan
- Laboratory of Protozoology, Harbin Normal University, Harbin 150025, China; (J.W.); (X.W.); (L.L.); (X.W.); (J.W.); (Y.Z.); (L.W.)
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2
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Li L, Bian D, Wang Q, Xue C, Zhang Q, Zhang SM. Performance of anammox enchanced by pulsed electric fields under added organic carbon sources using integrated network and metagenomics analyses. BIORESOURCE TECHNOLOGY 2023; 380:129116. [PMID: 37137447 DOI: 10.1016/j.biortech.2023.129116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
This paper aims to investigate the function of a pulsed electric field (PEF) in the anaerobic ammonia oxidation (anammox) process after adding certain chemical oxygen demand (COD) through integrated network and metagenomics analyses. The findings showed that the presence of COD was detrimental to anammox, but PEF could significantly reduce the adverse effect. The total nitrogen removal in the reactor for applying PEF was 16.99% higher on average than the reactor for only dosing COD. Additionally, PEF upgraded the abundance of anammox bacteria subordinate to the phylum Planctomycetes by 9.64%. The analysis of molecular ecological networks promulgated that PEF resulted in an increase in network scale and topology complexity, thereby boosting the potential collaboration of the communities. Metagenomics analyses demonstrated that PEF dramatically promoted anammox central metabolism in the presence of COD, specifically enhancing pivotal N functional genes (hzs, hdh, amo, hao, nas, nor and nos).
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Affiliation(s)
- Liang Li
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Di Bian
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China.
| | - Qichun Wang
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - ChengYao Xue
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Qiuying Zhang
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Shi Meng Zhang
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
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3
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Liu Z, Cai R, Chen YL, Zhuo X, He C, Zheng Q, He D, Shi Q, Jiao N. Direct Production of Bio-Recalcitrant Carboxyl-Rich Alicyclic Molecules Evidenced in a Bacterium-Induced Steroid Degradation Experiment. Microbiol Spectr 2023; 11:e0469322. [PMID: 36744924 PMCID: PMC10100752 DOI: 10.1128/spectrum.04693-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 02/07/2023] Open
Abstract
Carboxyl-rich alicyclic molecules (CRAM) are highly unsaturated compounds extensively distributed throughout aquatic environments and sediments. This molecular group is widely referred to as a major proxy of recalcitrant organic materials, but its direct biosynthesis remains unclear. Steroids are a typical anthropogenic contaminant and have been previously suggested to be precursors of CRAM; however, experimental evidence to support this hypothesis is lacking. Here, a steroid-degrading bacterium, Comamonas testosteroni ATCC 11996, was incubated in a liquid medium supplemented with testosterone (a typical steroid) as the sole carbon source for 90 days. Testosterone-induced metabolites (TIM) were extracted for molecular characterization and to examine the bioavailability during an additional 90-day incubation after inoculation with a natural coastal microbial assemblage. The results showed that 1,775 molecular formulas (MFs) were assigned to TIM using ultrahigh-resolution mass spectrometry, with 66.99% categorized as CRAM-like constituents. A large fraction of TIM was respired or transformed during the additional 90-day seawater incubation; nevertheless, 638 MFs of the TIM persisted or increased during incubation. Among the 638 MFs, 394 were commonly assigned in natural deep seawater samples (depths of 500 to 2,000 m) from the South China Sea. Compared to the catabolites of the well-established testosterone degradation pathway, we compiled a list of bio-refractory MFs and potential chemical structures, some of which shared structural homology with CRAM. These results demonstrated direct microbial production of bio-refractory CRAM from steroid hormones and indicated that some of the biogenic CRAM resisted microbial decomposition, potentially contributing to the aquatic refractory dissolved organic matter (DOM) pool. IMPORTANCE CRAM are an operationally defined DOM group comprising a complex mixture of carboxylated and fused alicyclic structures. This DOM group is majorly characterized as refractory DOM in the marine environment. However, the origins of the complex CRAM remain unclear. In this study, we demonstrated that testosterone (a typical steroid) could be transformed into bio-refractory CRAM by a single bacterial strain and observed that some of the CRAM highly resisted microbial degradation. Through molecular comparison and screening, potential chemical structures of steroid-induced CRAM were suggested. This study established the biological connection between steroids and bio-refractory CRAM, and it provides a novel perspective explaining the fate of terrestrial contaminants in aquatic environments.
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Affiliation(s)
- Zijing Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yi-Lung Chen
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ding He
- Department of Ocean Science and the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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4
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Isolation and Characterization of Bacteria and Fungi Associated with Agarwood Fermentation. Curr Microbiol 2022; 79:313. [DOI: 10.1007/s00284-022-02999-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/14/2022] [Indexed: 11/03/2022]
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5
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Ibero J, Rivero-Buceta V, García JL, Galán B. Polyhydroxyalkanoate Production by Caenibius tardaugens from Steroidal Endocrine Disruptors. Microorganisms 2022; 10:706. [PMID: 35456754 PMCID: PMC9027588 DOI: 10.3390/microorganisms10040706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/10/2022] Open
Abstract
The α-proteobacterium Caenibius tardaugens can use estrogens and androgens as the sole carbon source. These compounds are steroidal endocrine disruptors that are found contaminating soil and aquatic ecosystems. Here, we show that C. tardaugens, which has been considered as a valuable biocatalyst for aerobic steroidal hormone decontamination, is also able to produce polyhydroxyalkanoates (PHA), biodegradable and biocompatible polyesters of increasing biotechnological interest as a sustainable alternative to classical oil-derived polymers. Steroid catabolism yields a significant amount of propionyl-CoA that is metabolically directed towards PHA production through condensation into 3-ketovaleryl-CoA, rendering a PHA rich in 3-hydroxyvalerate. To the best of our knowledge, this is the first report where PHAs are produced from steroids as carbon sources.
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Affiliation(s)
| | | | | | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, 28040 Madrid, Spain; (J.I.); (V.R.-B.); (J.L.G.)
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6
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Liu S, Cao R, Liu L, Lv Y, Qi X, Yuan Z, Fan X, Yu C, Guan Q. Correlation Between Gut Microbiota and Testosterone in Male Patients With Type 2 Diabetes Mellitus. Front Endocrinol (Lausanne) 2022; 13:836485. [PMID: 35399957 PMCID: PMC8990747 DOI: 10.3389/fendo.2022.836485] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/18/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE This study aimed at investigating the association between testosterone levels and gut microbiota in male patients with type 2 diabetes mellitus (T2DM) and providing a new strategy to elucidate the pathological mechanism of testosterone deficiency in T2DM patients. METHODS In an observational study including 46 T2DM male patients, the peripheral venous blood and fecal samples of all subjects were collected. The V3-V4 regions of bacterial 16S rDNA were amplified and sequenced. Alpha and beta diversities were calculated by QIIME software. The possible association between gut microbial community and clinical indicators was assessed using the Spearman correlation coefficient. The association between the relative abundance of bacteria and testosterone levels was discovered using linear regression analysis in R language. RESULTS There was no substantial difference in alpha and beta diversity. Blautia and Lachnospirales were significantly much higher in the testosterone deficiency group. Linear regression analysis showed that the abundance of Firmicutes at the phylum level and Lachnospirales at the order level were negatively correlated with testosterone level. After correcting for C-reactive protein (CRP) and homeostatic model assessment of insulin resistance (HOMA-IR), the relative abundance of Lachnospirales still had a significant negative correlation with testosterone level. Meanwhile, at the genus level, Lachnoclostridium, Blautia, and Bergeyella had a statistically significant negative association with testosterone level, respectively. Blautia was positively associated with FPG and total cholesterol level. Streptococcus was found positively associated with insulin, connecting peptide, and index of homeostatic model assessment of insulin resistance. CONCLUSION T2DM patients with testosterone deficiency have different gut microbiota compositions compared with T2DM patients alone. Low serum testosterone patients tend to have an increased abundance of opportunistic pathogens, which may be related to the occurrence and development of testosterone deficiency.
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Affiliation(s)
- Shuang Liu
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Ruying Cao
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Endocrinology, ChangQing People’s Hospital, Jinan, China
| | - Luna Liu
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Youyuan Lv
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Xiangyu Qi
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiude Fan
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Chunxiao Yu
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Chunxiao Yu, ; Qingbo Guan,
| | - Qingbo Guan
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Chunxiao Yu, ; Qingbo Guan,
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Kangale LJ, Raoult D, Fournier PE, Ghigo E. Culturomics revealed the bacterial constituents of the microbiota of a 10-year-old laboratory culture of planarian species S. mediterranea. Sci Rep 2021; 11:24311. [PMID: 34934139 PMCID: PMC8692324 DOI: 10.1038/s41598-021-03719-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/06/2021] [Indexed: 11/09/2022] Open
Abstract
The planarian species Schmidtea mediterranea is a flatworm living in freshwater that is used in the research laboratory as a model to study developmental and regeneration mechanisms, as well as antibacterial mechanisms. However, the cultivable microbial repertoire of the microbes comprising its microbiota remains unknown. Here, we characterized the bacterial constituents of a 10-year-old laboratory culture of planarian species S. mediterranea via culturomics analysis. We isolated 40 cultivable bacterial species, including 1 unidentifiable species. The predominant phylum is Proteobacteria, and the most common genus is Pseudomonas. We discovered that parts of the bacterial flora of the planarian S. mediterranea can be classified as fish pathogens and opportunistic human pathogens.
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Affiliation(s)
- Luis Johnson Kangale
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée-Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France. .,IHU-Méditerranée-Infection, Marseille, France.
| | - Eric Ghigo
- IHU-Méditerranée-Infection, Marseille, France. .,TechnoJouvence, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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8
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Aksu D, Diallo MM, Şahar U, Uyaniker TA, Ozdemir G. High expression of ring-hydroxylating dioxygenase genes ensure efficient degradation of p-toluate, phthalate, and terephthalate by Comamonas testosteroni strain 3a2. Arch Microbiol 2021; 203:4101-4112. [PMID: 34057546 DOI: 10.1007/s00203-021-02395-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Para-toluic acid, a major pollutant in industrial wastewater, is hazardous to human health. It has been demonstrated that Gram-negative bacteria are among the most effective degraders of para-toluic acid. In this study, the ability of Comamonas testosteroni strain 3a2, isolated from a petrochemical industry wastewater, to degrade para-toluic acid was investigated. The effect of different carbon (glucose and ethylene glycol) and nitrogen sources (urea, yeast extract, peptone, NaNO3, NH4NO3) on the biodegradation of para-toluic acid by the isolate 3a2 was evaluated. Furthermore, ring hydroxylating dioxygenase genes were amplified by PCR and their expression was evaluated during the biodegradation of para-toluic acid. The results indicated that strain 3a2 was able to degrade up to 1000 mg/L of para-toluic acid after 14 h. The highest degradation yield was recorded in the presence of yeast extract as nitrogen source. However, the formation of terephthalic acid and phthalic acid was noted during para-toluic acid degradation by the isolate 3a2. Toluate 1,2-dioxygenase, terephthalate 1,2 dioxygenase, and phthalate 4,5 dioxygenase genes were detected in the genomic DNA of 3a2. The induction of ring hydroxylating dioxygenase genes was proportional to the concentration of each hydrocarbon. This study showed that the isolate 3a2 can produce terephthalate and phthalate during the para-toluic acid biodegradation, which were also degraded after 24 h.
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Affiliation(s)
- Didem Aksu
- Application and Research Center for Testing and Analysis, Ege University, Izmir, Turkey.
| | | | - Umut Şahar
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
| | | | - Guven Ozdemir
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
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9
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Li X, Cheng W, Shang H, Wei H, Deng C. The Interplay between Androgen and Gut Microbiota: Is There a Microbiota-Gut-Testis Axis. Reprod Sci 2021; 29:1674-1684. [PMID: 34037957 DOI: 10.1007/s43032-021-00624-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
The gut microbiota, a large ecosystem interacting with the host, has been shown to affect the health and fitness of the host-microbial superorganism. Increasing evidence suggests that the gut microbiota communicates with distal organs of the host including the brain, liver, and muscle, as well as testis, through various complex mechanisms. So far, we know that the androgen can markedly remodel the gut microbiota and has initiated an interdisciplinary field termed "microgenderome." More recently, the gut microbiota has been found as a major regulator of androgen production and metabolism in turn and even could trespass the blood-testis barrier (BTB) to regulate spermatogenesis, which largely updates the current knowledge on male reproduction. In this review, we provided a brief overview of the context of the gender bias of diseases related to gut microbiota, the sex dimorphism of gut microbiota, and their relationships with androgen. We also summarized the known interaction between the testis and gut microbiota based on published animal studies and tentatively discussed the hypothesis of microbiota-gut-testis axis. Finally, we highlighted the opportunities and challenges underlying the ongoing research. This knowledge may extend our understanding of the role of gut microbiota in male health and microbiota-related diseases.
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Affiliation(s)
- Xiangping Li
- Department of Urology and Andrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wei Cheng
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Shang
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chunhua Deng
- Department of Urology and Andrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
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10
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Guo X, Wang Q, Xu H, He X, Guo L, Liu S, Wen P, Gou J. Emergence of IMP-8-Producing Comamonas thiooxydans Causing Urinary Tract Infection in China. Front Microbiol 2021; 12:585716. [PMID: 33790873 PMCID: PMC8005532 DOI: 10.3389/fmicb.2021.585716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
The emergence of carbapenem resistance (CR) caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. So far, CR genes have been widely detected in various bacteria. However, there is no report of CR gene harboring Comamonas thiooxydans. We first isolated a strain of an IMP-8-producing C. thiooxydans from a patient with urinary tract infection in China. Species identity was determined using MALDI-TOF MS analysis and carbapenemase-encoding genes were detected using PCR. The complete genomic sequence of C. thiooxydans was identified using Illumina Novaseq and Oxford Nanopore PromethION. Antimicrobial susceptibility analysis indicated that the C. thiooxydans strain ZDHYF418 was susceptible to imipenem, intermediate to meropenem, and was resistant to aztreonam, fluoroquinolones, and aminoglycosides. The blaIMP–8 gene was chromosomally located, and was part of a Tn402-like class 1 integron characterized by the following structure: DDE-type integrase/transposase/recombinase-tniB-tniQ-recombinase family protein-aac(6′)-Ib-cr-blaIMP–8-intI1. Phylogenetic analysis demonstrated that the closest relative of ZDHYF418 is C. thiooxydans QYY (accession number: CP053920.1). We detected 330 SNP differences between ZDHYF418 and C. thiooxydans QYY. Strain QYY was isolated from activated sludge in Jilin province, China in 2015. In summary, we isolated a strain of C. thiooxydans that is able to produce IMP-8 and a novel blaOXA. This is the first time that a CR gene has been identified in C. thiooxydans. The occurrence of the strain needs to be closely monitored.
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Affiliation(s)
- Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qian Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohong He
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
| | - Lihua Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuxiu Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Peipei Wen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjun Gou
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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11
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Kraigher B, Mandic-Mulec I. Influence of Diclofenac on Activated Sludge Bacterial Communities in Fed-Batch Reactors. Food Technol Biotechnol 2021; 58:402-410. [PMID: 33505203 PMCID: PMC7821779 DOI: 10.17113/ftb.58.04.20.6424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Research background The occurrence and environmental toxicity of pharmaceuticals have recently attracted increasing attention. Diclofenac is a highly consumed non-steroidal anti-inflammatory drug, which is often detected in wastewaters, but investigations of its influence on bacteria are scarce. Experimental approach We investigated the influence of this pharmaceutical on bacterial community in activated sludge exposed to increasing concentrations of diclofenac in fed-batch reactors over 41 days. Nitrification activity of the activated sludge was measured and changes in bacterial community structure were followed using culture-independent molecular method (terminal restriction fragment length polymorphism, T-RFLP) and by the cultivation approach. Results and conclusions Nitrification activity was not detectably influenced by the addition of diclofenac, while the main change of the bacterial community structure was detected only at the end of incubation (after 41 days) when diclofenac was added to artificial wastewater as the only carbon source. Changes in community composition due to enrichment were observed using cultivation approach. However, taxonomic affiliation of isolates did not match taxons identified by T-RFLP community profiling. Isolates obtained from activated sludge used as inoculum belonged to five genera: Comamonas, Arthrobacter, Acinetobacter, Citrobacter and Aeromonas, known for their potential to degrade aromatic compounds. However, only Pseudomonas species were isolated after the last enrichment step on minimal agar plates with diclofenac added as the sole carbon source. Novelty and scientific contribution Our results suggest that the selected recalcitrant and commonly detected pharmaceutical does not strongly influence the sensitive and important nitrification process of wastewater treatment. Moreover, the isolated strains obtained after enrichment procedure that were able to grow on minimal agar plates with diclofenac added as the only carbon source could serve as potential model bacteria to study bacterial diclofenac degradation.
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Affiliation(s)
- Barbara Kraigher
- University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Microbiology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Microbiology, Večna pot 111, 1000 Ljubljana, Slovenia
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12
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Expanding the Application Range of Microbial Oxidoreductases by an Alcohol Dehydrogenase from Comamonas testosteroni with a Broad Substrate Spectrum and pH Profile. Catalysts 2020. [DOI: 10.3390/catal10111281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Alcohol dehydrogenases catalyse the conversion of a large variety of ketone substrates to the corresponding chiral products. Due to their high regio- and stereospecificity, they are key components in a wide range of industrial applications. A novel alcohol dehydrogenase from Comamonas testosteroni (CtADH) was identified in silico, recombinantly expressed and purified, enzymatically and biochemically investigated as well as structurally characterized. These studies revealed a broad pH profile and an extended substrate spectrum with the highest activity for compounds containing halogens as substituents and a moderate activity for bulky–bulky ketones. Biotransformations with selected ketones—performed with a coupled regeneration system for the co-substrate NADPH—resulted in conversions of more than 99% with all tested substrates and with excellent enantioselectivity for the corresponding S-alcohol products. CtADH/NADPH/substrate complexes modelled on the basis of crystal structures of CtADH and its closest homologue suggested preliminary hints to rationalize the enzyme’s substrate preferences
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Wojcieszyńska D, Marchlewicz A, Guzik U. Suitability of Immobilized Systems for Microbiological Degradation of Endocrine Disrupting Compounds. Molecules 2020; 25:molecules25194473. [PMID: 33003396 PMCID: PMC7583021 DOI: 10.3390/molecules25194473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
The rising pollution of the environment with endocrine disrupting compounds has increased interest in searching for new, effective bioremediation methods. Particular attention is paid to the search for microorganisms with high degradation potential and the possibility of their use in the degradation of endocrine disrupting compounds. Increasingly, immobilized microorganisms or enzymes are used in biodegradation systems. This review presents the main sources of endocrine disrupting compounds and identifies the risks associated with their presence in the environment. The main pathways of degradation of these compounds by microorganisms are also presented. The last part is devoted to an overview of the immobilization methods used for the purposes of enabling the use of biocatalysts in environmental bioremediation.
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Whittington HD, Singh M, Ta C, Azcárate-Peril MA, Bruno-Bárcena JM. Accelerated Biodegradation of the Agrochemical Ametoctradin by Soil-Derived Microbial Consortia. Front Microbiol 2020; 11:1898. [PMID: 32982997 PMCID: PMC7477900 DOI: 10.3389/fmicb.2020.01898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/20/2020] [Indexed: 01/25/2023] Open
Abstract
Pesticide-resistant plant pathogens are an increasing threat to the global food supply and have generated a need for novel, efficacious agrochemicals. The current regulatory process for approving new agrochemicals is a tedious but necessary process. One way to accelerate the safety evaluation process is to utilize in vitro systems to demonstrate pesticide degradation by soil microbes prior to ex vivo soil evaluations. This approach may have the capability to generate metabolic profiles free of inhibitory substances, such as humic acids, commonly present in ex vivo soil systems. In this study, we used a packed-bed microbial bioreactor to assess the role of the natural soil microbial community during biodegradation of the triazolopyrimidine fungicide, ametoctradin. Metabolite profiles produced during in vitro ametoctradin degradation were similar to the metabolite profiles obtained during environmental fate studies and demonstrated the degradation of 81% of the parent compound in 72 h compared to a half-life of 2 weeks when ametoctradin was left in the soil. The microbial communities of four different soil locations and the bioreactor microbiome were compared using high throughput sequencing. It was found that biodegradation of ametoctradin in both ex vivo soils and in vitro in the bioreactor correlated with an increase in the relative abundance of Burkholderiales, well characterized microbial degraders of xenobiotic compounds.
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Affiliation(s)
- Hunter D Whittington
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Mahatam Singh
- BASF Corporation, Research Triangle Park, NC, United States
| | - Chanh Ta
- BASF Corporation, Research Triangle Park, NC, United States
| | - M Andrea Azcárate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - José M Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Chiang Y, Wei ST, Wang P, Wu P, Yu C. Microbial degradation of steroid sex hormones: implications for environmental and ecological studies. Microb Biotechnol 2020; 13:926-949. [PMID: 31668018 PMCID: PMC7264893 DOI: 10.1111/1751-7915.13504] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022] Open
Abstract
Steroid hormones modulate development, reproduction and communication in eukaryotes. The widespread occurrence and persistence of steroid hormones have attracted public attention due to their endocrine-disrupting effects on both wildlife and human beings. Bacteria are responsible for mineralizing steroids from the biosphere. Aerobic degradation of steroid hormones relies on O2 as a co-substrate of oxygenases to activate and to cleave the recalcitrant steroidal core ring. To date, two oxygen-dependent degradation pathways - the 9,10-seco pathway for androgens and the 4,5-seco pathways for oestrogens - have been characterized. Under anaerobic conditions, denitrifying bacteria adopt the 2,3-seco pathway to degrade different steroid structures. Recent meta-omics revealed that microorganisms able to degrade steroids are highly diverse and ubiquitous in different ecosystems. This review also summarizes culture-independent approaches using the characteristic metabolites and catabolic genes to monitor steroid biodegradation in various ecosystems.
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Affiliation(s)
- Yin‐Ru Chiang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
| | | | - Po‐Hsiang Wang
- Biodiversity Research CenterAcademia SinicaTaipei115Taiwan
- Present address:
Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - Pei‐Hsun Wu
- Graduate Institute of Environmental EngineeringNational Taiwan UniversityTaipei106Taiwan
| | - Chang‐Ping Yu
- Graduate Institute of Environmental EngineeringNational Taiwan UniversityTaipei106Taiwan
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Dynamic changes in bacterial communities in the recirculating nutrient solution of cucumber plug seedlings cultivated in an ebb-and-flow subirrigation system. PLoS One 2020; 15:e0232446. [PMID: 32353053 PMCID: PMC7192414 DOI: 10.1371/journal.pone.0232446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/14/2020] [Indexed: 12/04/2022] Open
Abstract
Ebb-and-flow subirrigation systems are highly efficient, water-saving and environmentally friendly. However, one concern with these recirculating systems is the possible transmission of plant pathogens. Here, through 16S rRNA-targeted Illumina sequencing, the bacterial dynamics in a recirculating nutrient solution were characterized for cucumber plug seedlings cultivated in an ebb-and-flow system in summer and winter. Both the bacterial number and diversity in the nutrient solution increased immediately after the first irrigation cycle; then, these values were gradually stable with recirculating irrigation. In summer and winter, different bacterial compositions and changing patterns were observed. In summer, the predominant genera in the nutrient solution included Comamonas, Pseudomonas, Acinetobacter, Reyranella, Sphingobium, Bradyrhizobium, Sphingomonas, and Acidovorax. Of those genera, during recirculating irrigation, the relative abundance of Bradyrhizobium gradually decreased, whereas those of Pseudomonas, Reyranella, Sphingobium, Sphingomonas, and Acidovorax gradually increased. In winter, the bacterial communities were mainly composed of Nevskia, Bosea, Sphingobium, Acidovorax, Pseudomonas, and Hydrocarboniphaga. Of those genera, the relative abundance of Bosea, Sphingobium, and Acidovorax showed an increasing trend, whereas those of Nevskia and Hydrocarboniphaga decreased overall. Furthermore, in both summer and winter, no plant pathogenic bacteria on cucumber could be detected; however, some potentially beneficial bacteria, including Comamonas testosteroni, Acinetobacter baumannii, Pseudomonas aeruginosa, P. koreensis and Sphingobium yanoikuyae, colonized the nutrient solution and exhibited increased relative abundances during irrigation. The colonization of these bacteria might facilitate the plant growth promotion. Inoculation of the microbes from the effluent nutrient solution also promoted the growth of cucumber seedlings, but did not lead to any disease. The present data elucidate the bacterial dynamics in a cucumber cultivation ebb-and-flow system and provide useful information for biological control during cucumber seedling production.
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Liu C, Liu K, Zhao C, Gong P, Yu Y. The characterization of a short chain dehydrogenase/reductase (SDRx) in Comamonas testosteroni. Toxicol Rep 2020; 7:460-467. [PMID: 32215256 PMCID: PMC7090274 DOI: 10.1016/j.toxrep.2020.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
C. testosteroni is a research topic that can degrade steroid hormones into water and carbon dioxide through a series of enzymes in the body. Short-chain dehydrogenase (SDR) are a class of NAD (P) H-dependent oxidoreductases in C. testosteroni. Its main function is catalyzing the redox of the hydroxyl/ketone group of the hormone. In this paper, a SDR gene(SDRx) is cloned from C. testosteroni ATCC11996 and expressed. The polyclonal antibody was prepared and the SDRx gene knocked out by homologous recombination. Wild type and mutant C. testosteroni induced by testosterone, estradiol, estrone and estriol. The growth curves of the bacteria were measured by spectrophotometer. ELISA established the expression of SDRx protein, and high-performance liquid chromatography(HPLC) detected the contents of various hormones. The results show that the growth of wild type was faster than mutant type induced by testosterone. The concentration of SDRx is 0.318 mg/ml under testosterone induction. It has a great change in steroid hormones residue in culture medium measured by HPLC: Testosterone residue in the mutant type group was 42.4 % more than the wild type in culture medium. The same thing happens with induced by estrone. In summary, this SDRx gene involved in the degradation of testosterone and estradiol, and effects the growth of C. testosteroni.
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Affiliation(s)
- Chuanzhi Liu
- School of Life Science and Technology, Changchun University of Science and Technology, Weixing Road 7989, Changchun, Jilin Province, 130022, PR China
| | - Kai Liu
- School of Life Science and Technology, Changchun University of Science and Technology, Weixing Road 7989, Changchun, Jilin Province, 130022, PR China
| | - Chunru Zhao
- School of Life Science and Technology, Changchun University of Science and Technology, Weixing Road 7989, Changchun, Jilin Province, 130022, PR China
| | - Ping Gong
- School of Life Science and Technology, Changchun University of Science and Technology, Weixing Road 7989, Changchun, Jilin Province, 130022, PR China
| | - Yuanhua Yu
- School of Life Science and Technology, Changchun University of Science and Technology, Weixing Road 7989, Changchun, Jilin Province, 130022, PR China
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Qurbani K, Hamzah H. Intimate communication between Comamonas aquatica and Fusarium solani in remediation of heavy metal-polluted environments. Arch Microbiol 2020; 202:1397-1406. [DOI: 10.1007/s00203-020-01853-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 12/28/2022]
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19
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Pratush A, Ye X, Yang Q, Kan J, Peng T, Wang H, Huang T, Xiong G, Hu Z. Biotransformation strategies for steroid estrogen and androgen pollution. Appl Microbiol Biotechnol 2020; 104:2385-2409. [PMID: 31993703 DOI: 10.1007/s00253-020-10374-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 12/21/2022]
Abstract
The common steroid hormones are estrone (E1), 17β-estradiol (E2), estriol (E3), 17α-ethinylestradiol (EE2), and testosterone (T). These steroids are reported to contaminate the environment through wastewater treatment plants. Steroid estrogens are widespread in the aquatic environment and therefore pose a potential risk, as exposure to these compounds has adverse impacts on vertebrates. Excessive exposure to steroid estrogens causes endocrine disruption in aquatic vertebrates, which affects the normal sexual life of these animals. Steroid pollutants also cause several health problems in humans and other animals. Microbial degradation is an efficient method for removing hormone pollutants from the environment by remediation. Over the last two decades, microbial metabolism of steroids has gained considerable attention due to its higher efficiency to reduce pollutants from the environment. The present review is focused on the major causes of steroid pollution, concentrations of these pollutants in surface water, groundwater, drinking water, and wastewater, their effect on humans and aquatic animals, as well as recent efforts by various research groups that seek better ways to degrade steroids by aerobic and anaerobic microbial systems. Detailed overview of aerobic and anaerobic microbial biotransformation of steroid estrogens and testosterone present in the environment along with the active enzyme systems involved in these biotransformation reactions is described in the review article, which helps readers to understand the biotransformation mechanism of steroids in depth. Other measures such as co-metabolic degradation, consortia degradation, algal, and fungal steroid biotransformation are also discussed in detail.
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Affiliation(s)
- Amit Pratush
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Xueying Ye
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Qi Yang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jie Kan
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Tao Peng
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Tongwang Huang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Guangming Xiong
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School, Schleswig-Holstein, Campus Kiel, Brunswiker Str. 10, 24105, Kiel, Germany
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China.
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20
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Testosterone Degradative Pathway of Novosphingobium tardaugens. Genes (Basel) 2019; 10:genes10110871. [PMID: 31683600 PMCID: PMC6895838 DOI: 10.3390/genes10110871] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/16/2019] [Accepted: 10/28/2019] [Indexed: 01/25/2023] Open
Abstract
In this work, we have shown that Novosphingobium tardaugens NBRC 16725 (strain ARI-1), a bacterial strain that was isolated due to its capacity to mineralize the estrogenic endocrine compound 17β-estradiol, is also able to mineralize testosterone, the androgenic endocrine compound. Using in silico analysis, we predicted a new putative steroid degradation (SD) gene cluster in strain ARI-1, which resembles genes involved in testosterone degradation in Comamonas testosteroni and other testosterone degrading bacteria like Actinobacteria (like Rhodococcus and Mycobacteria genera) although with significant differences in gene organization. A whole transcriptomic analysis of N. tardaugens revealed that testosterone produces a limited induction of the genes of the SD cluster that show a high basal expression in its absence. The 3β/17β-hydroxysteroid dehydrogenase involved in the first metabolic step of testosterone degradation was identified by using genetic and biochemical approaches. The construction of knockout mutant strains in the genes of the SD cluster together with in silico analyses suggests the existence of gene redundancy in the genome of N. tardaugens. This work will expand the knowledge about the metabolic pathways and biotransformation capabilities of a Gram-negative bacterium that could become a new model system in the bacterial steroid degradation field.
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Olivera ER, Luengo JM. Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways. Genes (Basel) 2019; 10:E512. [PMID: 31284586 PMCID: PMC6678751 DOI: 10.3390/genes10070512] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Steroids are perhydro-1,2-cyclopentanophenanthrene derivatives that are almost exclusively synthesised by eukaryotic organisms. Since the start of the Anthropocene, the presence of these molecules, as well as related synthetic compounds (ethinylestradiol, dexamethasone, and others), has increased in different habitats due to farm and municipal effluents and discharge from the pharmaceutical industry. In addition, the highly hydrophobic nature of these molecules, as well as the absence of functional groups, makes them highly resistant to biodegradation. However, some environmental bacteria are able to modify or mineralise these compounds. Although steroid-metabolising bacteria have been isolated since the beginning of the 20th century, the genetics and catabolic pathways used have only been characterised in model organisms in the last few decades. Here, the metabolic alternatives used by different bacteria to metabolise steroids (e.g., cholesterol, bile acids, testosterone, and other steroid hormones), as well as the organisation and conservation of the genes involved, are reviewed.
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Affiliation(s)
- Elías R Olivera
- Departamento Biología Molecular (Área Bioquímica y Biología Molecular), Universidad de León, 24007 León, Spain.
| | - José M Luengo
- Departamento Biología Molecular (Área Bioquímica y Biología Molecular), Universidad de León, 24007 León, Spain
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Imperato V, Portillo-Estrada M, McAmmond BM, Douwen Y, Van Hamme JD, Gawronski SW, Vangronsveld J, Thijs S. Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland). Genes (Basel) 2019; 10:genes10060443. [PMID: 31212674 PMCID: PMC6628094 DOI: 10.3390/genes10060443] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up.
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Affiliation(s)
- Valeria Imperato
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Miguel Portillo-Estrada
- Centre of Excellence PLECO, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
| | - Breanne M McAmmond
- Department of Biology Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada.
| | - Yorben Douwen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Jonathan D Van Hamme
- Department of Biology Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada.
| | - Stanislaw W Gawronski
- Warsaw University of Life Sciences, Faculty of Horticulture, Biotechnology and Landscape Architecture, Nowoursynowska Road 159, 02-776 Warsaw, Poland.
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Skłodowska-Curie University, 20-950 Lublin, Poland.
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
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Metagenomes Reveal Global Distribution of Bacterial Steroid Catabolism in Natural, Engineered, and Host Environments. mBio 2018; 9:mBio.02345-17. [PMID: 29382738 PMCID: PMC5790920 DOI: 10.1128/mbio.02345-17] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroids are abundant growth substrates for bacteria in natural, engineered, and host-associated environments. This study analyzed the distribution of the aerobic 9,10-seco steroid degradation pathway in 346 publically available metagenomes from diverse environments. Our results show that steroid-degrading bacteria are globally distributed and prevalent in particular environments, such as wastewater treatment plants, soil, plant rhizospheres, and the marine environment, including marine sponges. Genomic signature-based sequence binning recovered 45 metagenome-assembled genomes containing a majority of 9,10-seco pathway genes. Only Actinobacteria and Proteobacteria were identified as steroid degraders, but we identified several alpha- and gammaproteobacterial lineages not previously known to degrade steroids. Actino- and proteobacterial steroid degraders coexisted in wastewater, while soil and rhizosphere samples contained mostly actinobacterial ones. Actinobacterial steroid degraders were found in deep ocean samples, while mostly alpha- and gammaproteobacterial ones were found in other marine samples, including sponges. Isolation of steroid-degrading bacteria from sponges confirmed their presence. Phylogenetic analysis of key steroid degradation proteins suggested their biochemical novelty in genomes from sponges and other environments. This study shows that the ecological significance as well as taxonomic and biochemical diversity of bacterial steroid degradation has so far been largely underestimated, especially in the marine environment. Microbial steroid degradation is a critical process for biomass decomposition in natural environments, for removal of important pollutants during wastewater treatment, and for pathogenesis of bacteria associated with tuberculosis and other bacteria. To date, microbial steroid degradation was mainly studied in a few model organisms, while the ecological significance of steroid degradation remained largely unexplored. This study provides the first analysis of aerobic steroid degradation in diverse natural, engineered, and host-associated environments via bioinformatic analysis of an extensive metagenome data set. We found that steroid-degrading bacteria are globally distributed and prevalent in wastewater treatment plants, soil, plant rhizospheres, and the marine environment, especially in marine sponges. We show that the ecological significance as well as the taxonomic and biochemical diversity of bacterial steroid degradation has been largely underestimated. This study greatly expands our ecological and evolutionary understanding of microbial steroid degradation.
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Shih CJ, Chen YL, Wang CH, Wei STS, Lin IT, Ismail WA, Chiang YR. Biochemical Mechanisms and Microorganisms Involved in Anaerobic Testosterone Metabolism in Estuarine Sediments. Front Microbiol 2017; 8:1520. [PMID: 28848528 PMCID: PMC5554518 DOI: 10.3389/fmicb.2017.01520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/28/2017] [Indexed: 11/13/2022] Open
Abstract
Current knowledge on the biochemical mechanisms underlying microbial steroid metabolism in anaerobic ecosystems is extremely limited. Sulfate, nitrate, and iron [Fe (III)] are common electron acceptors for anaerobes in estuarine sediments. Here, we investigated anaerobic testosterone metabolism in anaerobic sediments collected from the estuary of Tamsui River, Taiwan. The anaerobic sediment samples were spiked with testosterone (1 mM) and individual electron acceptors (10 mM), including nitrate, Fe3+, and sulfate. The analysis of androgen metabolites indicated that testosterone biodegradation under denitrifying conditions proceeds through the 2,3-seco pathway, whereas testosterone biodegradation under iron-reducing conditions may proceed through an unidentified alternative pathway. Metagenomic analysis and PCR-based functional assays suggested that Thauera spp. were the major testosterone degraders in estuarine sediment samples incubated with testosterone and nitrate. Thauera sp. strain GDN1, a testosterone-degrading betaproteobacterium, was isolated from the denitrifying sediment sample. This strain tolerates a broad range of salinity (0-30 ppt). Although testosterone biodegradation did not occur under sulfate-reducing conditions, we observed the anaerobic biotransformation of testosterone to estrogens in some testosterone-spiked sediment samples. This is unprecedented since biotransformation of androgens to estrogens is known to occur only under oxic conditions. Our metagenomic analysis suggested that Clostridium spp. might play a role in this anaerobic biotransformation. These results expand our understanding of microbial metabolism of steroids under strictly anoxic conditions.
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Affiliation(s)
- Chao-Jen Shih
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan.,Bioresource Collection and Research Center, Food Industry Research and Development InstituteHsinchu, Taiwan
| | - Yi-Lung Chen
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | | | - Sean T-S Wei
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | - I-Ting Lin
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | - Wael A Ismail
- Environmental Biotechnology Program, Department of Life Sciences, College of Graduate Studies, Arabian Gulf UniversityManama, Bahrain
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
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