1
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Zhou YM, Yuan JJ, Xu YQ, Gou YH, Zhu YYX, Chen C, Huang XX, Ma XM, Pi M, Yang ZX. Fecal microbiota as a predictor of acupuncture responses in patients with postpartum depressive disorder. Front Cell Infect Microbiol 2023; 13:1228940. [PMID: 38053532 PMCID: PMC10694210 DOI: 10.3389/fcimb.2023.1228940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023] Open
Abstract
Background There are several clinical and molecular predictors of responses to antidepressant therapy. However, these markers are either too subjective or complex for clinical use. The gut microbiota could provide an easily accessible set of biomarkers to predict therapeutic efficacy, but its value in predicting therapy responses to acupuncture in patients with depression is unknown. Here we analyzed the predictive value of the gut microbiota in patients with postpartum depressive disorder (PPD) treated with acupuncture. Methods Seventy-nine PPD patients were enrolled: 55 were treated with acupuncture and 24 did not received any treatment. The 17-item Hamilton depression rating scale (HAMD-17) was used to assess patients at baseline and after eight weeks. Patients receiving acupuncture treatment were divided into an acupuncture-responsive group or non-responsive group according to HAMD-17 scores changes. Baseline fecal samples were obtained from the patients receiving acupuncture and were analyzed by high-throughput 16S ribosomal RNA sequencing to characterize the gut microbiome. Results 47.27% patients responded to acupuncture treatment and 12.5% patients with no treatment recovered after 8-week follow-up. There was no significant difference in α-diversity between responders and non-responders. The β-diversity of non-responders was significantly higher than responders. Paraprevotella and Desulfovibrio spp. were significantly enriched in acupuncture responders, and these organisms had an area under the curve of 0.76 and 0.66 for predicting responder patients, respectively. Conclusions Paraprevotella and Desulfovibrioare may be useful predictive biomarkers to predict PPD patients likely to respond to acupuncture. Larger studies and validation in independent cohorts are now needed to validate our findings.
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Affiliation(s)
- Yu-Mei Zhou
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Jin-Jun Yuan
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Yu-Qin Xu
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Yan-Hua Gou
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Yannas Y. X. Zhu
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Chen Chen
- Department of Acupuncture and Tuina, Shenzhen Maternal and Child Health Care Hospital, Shenzhen, China
| | - Xing-Xian Huang
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Xiao-Ming Ma
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Min- Pi
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Zhuo-Xin Yang
- Department of Acupuncture, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
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2
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Liu F, Nong X, Qu W, Li X. Weikangling capsules combined with omeprazole ameliorates ethanol-induced chronic gastritis by regulating gut microbiota and EGF-EGFR-ERK pathway. Life Sci 2023; 315:121368. [PMID: 36623766 DOI: 10.1016/j.lfs.2023.121368] [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: 10/19/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/09/2023]
Abstract
AIMS Weikangling capsules (WKLCs) have been widely used in the treatment of chronic gastritis. Whether used alone or combined with omeprazole (OME), it shows a significant effect. However, the mechanisms haven't been established. The study aimed to explore the mechanisms of WKLCs and its combination with OME on chronic gastritis. MAIN METHODS The components of WKLCs and EA (the ethyl acetate extraction extracted from WKLCs) fraction were analyzed. Then chronic gastritis model rats were induced by 56 % ethanol and treated with OME, low dose of WKLCs (WKL), high dose of WKLCs (WKH), WKLCs combined with OME (WO), and EA fraction (EA) to evaluate the mechanisms of WKLCs, drug combination and EA fraction. KEY FINDINGS A total of 22 components of WKLCs were quantified, among them 18 were enriched in EA fraction. WKLCs alleviated the morphology and inflammation of gastric mucosa and downregulated the levels of inflammatory factors (IL-1β, TNF-α, IL-6) and epidermal growth factor (EGF) in serum by inhibiting the EGF-EGFR-ERK pathway, regulating gut microbiota composition and SCFAs contents in feces. WKLCs plus OME was better than OME. EA fraction improved digestive function by increasing pepsin activity and decreasing gastrointestinal hormones (GAS and VIP) compared with WKLCs. SIGNIFICANCE This study elucidated that the effect of WKLCs and its combination with OME in the treatment of chronic gastritis was attributed to regulating the composition of the gut microbiota and inhibiting the EGF-EGFR-ERK pathway. The EA fraction is an inseparable effective substance of WKLCs. This study provides scientific evidence for clinical application.
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Affiliation(s)
- Feng Liu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaojing Nong
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wenhua Qu
- Heilongjiang Sunflower Pharmaceutical Co. Ltd., Heilongjiang 150070, China
| | - Xiaobo Li
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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3
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Kalvandi S, Garousin H, Pourbabaee AA, Farahbakhsh M. The release of petroleum hydrocarbons from a saline-sodic soil by the new biosurfactant-producing strain of Bacillus sp. Sci Rep 2022; 12:19770. [PMID: 36396722 PMCID: PMC9672099 DOI: 10.1038/s41598-022-24321-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Adsorption of old-aged petroleum hydrocarbons to the soil solid phase, which causes biosurfactant loss of performance, is among the limiting factors for the remediation of the saline-sodic soils contaminated with petroleum. Therefore, to find a functional biosurfactant in oil-contaminated saline-sodic soils, the efficiency of 39 bacteria isolated from petroleum-contaminated soils was evaluated. The strains were cultured in the Bushnell-Haas medium, and the produced biosurfactants and bioemulsifiers in this medium were extracted using chloroform/methanol and ethyl acetate extraction methods, respectively. Their partial purification was performed by column chromatography, and eventually, their performance in releasing TPH from the contaminated soil was evaluated. The soil test results revealed that the highest TPH releases due to the effects of the biosurfactants and bioemulsifier produced from SHA302, SH21, and SH72 isolates were 42.4% ± 0.2, 21.6% ± 0.15 and 24.3% ± 0.91, respectively. Based on the 16S rRNA gene sequence, the SHA302 strain showed 93.98% phylogenetic similarity with Bacillus pumilus strain ATCC 7061. The Fourier transform infrared spectroscopy and thin-layer chromatography results proved that the biosurfactants produced by isolates SHA302, SH21 and SH72 showed lipopeptide, glycolipoprotein and glycoprotein natures, respectively. The performance of the biosurfactant produced by SHA302 isolate indicated that it could be used as a good candidate for releasing TPH from saline-sodic soils with old contamination and facilitating the degradation of hydrocarbons.
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Affiliation(s)
- Sahar Kalvandi
- grid.46072.370000 0004 0612 7950Biology and Biotechnology Lab, Department of Soil Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hamidreza Garousin
- grid.46072.370000 0004 0612 7950Biology and Biotechnology Lab, Department of Soil Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ahmad Ail Pourbabaee
- grid.46072.370000 0004 0612 7950Biology and Biotechnology Lab, Department of Soil Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mohsen Farahbakhsh
- grid.46072.370000 0004 0612 7950Biology and Biotechnology Lab, Department of Soil Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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4
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Han D, Zhen H, Liu X, Zulewska J, Yang Z. Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model. Appl Microbiol Biotechnol 2022; 106:5715-5728. [PMID: 35896837 DOI: 10.1007/s00253-022-12083-x] [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: 04/13/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
High-throughput sequencing of ribosomal RNA (rRNA) amplicons has served as a cornerstone in microbiome studies. Despite crucial implication of organelle 16S rRNA measurements to host gut microbial activities, genomic DNA (gDNA) was overwhelmingly targeted for amplicon sequencings. Although gDNA could be a reliable resource for gene existing validation, little information is revealed in regard to the activity of microorganisms owing to the limited changes gDNA undertaken in inactive, dormant, and dead bacteria. We applied both rRNA- and gDNA-derived sequencings on mouse cecal contents. Respective experimental designs were verified to be suitable for nucleic acid (NA) purification. Via benchmarking, mainstream 16S rRNA hypervariable region targets and reference databases were proven adequate for respective amplicon sequencing study. In phylogenetic studies, significant microbial composition differences were observed between two methods. Desulfovibrio spp. (an important group of anaerobic gut microorganisms that has caused analytical difficulties), Pediococcus spp., and Proteobacteria were drastically lower as represented by gDNA-derived compositions, while microbes like Firmicutes were higher as represented by gDNA-derived microbiome compositions. Also, using PICRUSt2 as an example, we illustrated that rRNA-derived sequencing might be more suitable for microbiome function predictions since pathways like sugar metabolism were lower as represented by rRNA-derived results. The findings of this study demonstrated that rRNA-derived amplicon sequencing could improve identification capability of specific gut microorganisms and might be more suitable for in silico microbiome function predictions. Therefore, rRNA-derived amplicon sequencings, preferably coupled with gDNA-derived ones, could be used as a capable tool to unveil active microbial components in host gut. KEY POINTS: • Conventional pipelines were adequate for the respective amplicon sequencing study • Groups, such as Desulfovibrio spp., were differently represented by two methods • Comparative amplicon sequencings could be useful in host active microbiota studies.
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Affiliation(s)
- Dong Han
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China.,Key Laboratory of Food Bioengineering, (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hongmin Zhen
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Xiaoyan Liu
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Justyna Zulewska
- Department of Dairy Science and Quality Management, Faculty of Food Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Zhennai Yang
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China.
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5
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Stein N, Podder A, Lee Weidhaas J, Goel R. Simultaneous reduction of perchlorate and nitrate using fast-settling anoxic sludge. CHEMOSPHERE 2022; 286:131788. [PMID: 34375826 DOI: 10.1016/j.chemosphere.2021.131788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Fast-settling, anoxic sludge (FAS) was cultivated and utilized in this study to simultaneously reduce elevated levels of perchlorate and nitrate in an anaerobic sequencing batch reactor (AnSBR). Average perchlorate and nitrate removal efficiencies of 96.5 ± 8.44 % and 99.8 ± 0.32 %, respectively, were achieved from an average perchlorate and nitrate loading rate of 159 ± 101 g ClO4-/m3·d and 10.8 ± 7.25 g NO3--N/m3·d, respectively, throughout long-term operation (>500-d). Batch activity tests revealed a preferential utilization of nitrate over perchlorate, where significant perchlorate reduction inhibition occurred when nitrate was present as a competing electron acceptor under carbon-limiting conditions. Specific perchlorate and nitrate reduction rates were shown to increase as the hydraulic retention time (HRT) of the AnSBR was step-wise decreased and subsequently the perchlorate and nitrate loading rates were step-wise increased. Functional, mRNA-based expression of the nitrite reductase (nirS and nirK), nitrous oxide reductase (nosZ), perchlorate reductase subunit A (pcrA), and the chlorite dismutase (cld) genes illustrated the simultaneous activity of heterotrophic denitrification and perchlorate reduction occurring throughout a complete standard reactor operational cycle, and allowed for expression trends to be documented as the HRT of the AnSBR was reduced from 5-d to 1.25-d. Nitrous oxide (N2O) production was detected as a result of incomplete denitrification, where the largest N2O production occurred at the highest nitrate loading rates investigated in this study. Thauera species were heavily enriched at a longer HRT of 5-d, but were out-competed by Dechloromonas species as the HRT of the AnSBR was step-wise reduced to 1.25-d.
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Affiliation(s)
- Nathan Stein
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Aditi Podder
- Department of Civil, Environmental and Construction Engineering, University of Central Florida, Orlando, FL, 32816, USA
| | - Jennifer Lee Weidhaas
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, 84112, USA.
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6
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Wenbo L, Qiyan F, Haoqian L, Di C, Xiangdong L. Passive treatment test of acid mine drainage from an abandoned coal mine in Kaili Guizhou, China. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 84:1981-1996. [PMID: 34695025 DOI: 10.2166/wst.2021.405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Discharge of acid mine drainage (AMD) from abandoned coal mines of the YuDong catchment in Kaili City, Guizhou Province, China, has severely damaged local ecological environments. In this study, a laboratory-scale dispersed alkaline substrate (DAS) was studied for the treatment of simulated AMD. The experimental conditions and reaction mechanisms were preliminarily explored. The treatment effect and variation law of vertical effluent water quality of the experimental conditions were thoroughly analysed. The results indicated that small-sized limestone (diameter 5-7 mm) having a 20:1 mixture ratio with shavings and minimum HRT of 20 hours result in increasing effluent pH from 3.5 to 6.6, achieving 66.2% and 99.1% removal of Fe and Al, respectively. There were obvious differences in each reaction layer for the removal of various pollutants from AMD along the depth by DAS, the main reaction zone was first 20-30 cm of the reaction column. The removal process of metal ions and sulfate was accompanied by bio-mineralization reaction. This test provided a valuable support for the local practical engineering applications, enriched the AMD processing technology experimental cases, and provided reference for the treatment technology of similar polluted areas.
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Affiliation(s)
- Li Wenbo
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China E-mail: ; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Feng Qiyan
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China E-mail: ; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Liang Haoqian
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China E-mail: ; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Chen Di
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China E-mail: ; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Li Xiangdong
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China E-mail: ; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
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7
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Paenibacillus albiflavus sp. nov., a bacterium isolated from soil. Arch Microbiol 2021; 203:4973-4979. [PMID: 34269834 DOI: 10.1007/s00203-021-02476-3] [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: 08/29/2020] [Revised: 06/19/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Strain 18JY21-1T, a Gram-positive, endospore-forming, motile, and rod-shaped bacterium, was isolated from soil in South Korea and was characterised to determine its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence of strain 18JY21-1T revealed that the strain 18JY21-1T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain 18JY21-1T was found with Paenibacillus doosanensis CAU 1055T (97.7%) and Paenibacillus protaetiae KACC 19327T (94.4%). In genome analysis, the calculated average nucleotide identity (ANI) and the digital DNA-DNA hybridization (DDH) values between strain 18JY21-1T and Paenibacillus protaetiae KACC 19327T were 66.3% and 22.8%, respectively. Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C15:0 (38.7%) and C16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG). The cell wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-7. Based on the phylogenetic, chemotaxonomic, and phenotypic data, strain 18JY21-1T (= KCTC 3396T = JCM 33183T) should be classified as a type strain of a novel species, for which the name Paenibacillus albiflavus sp. nov. is proposed.
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8
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Gilmour CC, Soren AB, Gionfriddo CM, Podar M, Wall JD, Brown SD, Michener JK, Urriza MSG, Elias DA. Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 33570484 DOI: 10.1099/ijsem.0.004697] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sulfate-reducing, mercury-methylating strain ND132T was isolated from the brackish anaerobic bottom sediments of Chesapeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132T has been widely used as a model strain to study the process and to determine the genetic basis of Hg methylation. Originally called Desulfovibrio desulfuricans ND132T on the basis of an early partial 16S rRNA sequence, the strain has never been formally described. Phylogenetic and physiological traits place this strain within the genus Pseudodesulfovibrio, in the recently reclassified phylum Desulfobacterota (formerly Deltaproteobacteria). ND132T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1T and Pseudodesulfovibrio indicus J2T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88 % ANI between P. hydrargyri BerOc1T and ND132T, and 84 % similarity between ND132T and P. indicus J2T. These cut-off scores <95 %, along with a multi-gene phylogenetic analysis of members of the family Desulfovibrionacea, and differences in physiology indicate that all three strains represent separate species. The Gram-stain-negative cells are vibrio-shaped, motile and not sporulated. ND132T is a salt-tolerant mesophile with optimal growth in the laboratory at 32 °C, 2 % salinity, and pH 7.8. The DNA G+C content of the genomic DNA is 65.2 %. It is an incomplete oxidizer of short chain fatty acids, using lactate, pyruvate and fumarate with sulfate or sulfite as the terminal electron acceptors. ND132T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c and anteiso-C17 : 0. We propose the classification of strain ND132T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.
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Affiliation(s)
| | | | - Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Steven D Brown
- Present address: LanzaTech, Skokie, Illinois, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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9
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Tran TTT, Kannoorpatti K, Padovan A, Thennadil S. A study of bacteria adhesion and microbial corrosion on different stainless steels in environment containing Desulfovibrio vulgaris. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201577. [PMID: 33614090 PMCID: PMC7890485 DOI: 10.1098/rsos.201577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Stainless steel is an important material used in many applications due to its mechanical strength and corrosion-resistant properties. The high corrosion resistance of stainless steel is provided by the passive film. Different stainless steels have different alloy elements and surface properties which could have a significant influence on bacterial attachment to the surface and thus might result in different microbial corrosion behaviours. In this study, the effect of adhesion of sulfate-reducing bacteria (SRB) on corrosion behaviour in artificial seawater on different stainless steels was investigated. Stainless steel materials used were SS 410, SS 420, SS 316 and DSS 2205 and pure chromium. The contact angle was measured to study the effect of surface properties of materials. Adhesion was measured by counting cells attached to the surface of materials. The corrosion behaviour of the materials was measured by electrochemical testing including measuring open circuit potential, electrochemical impedance spectroscopy and potentiodynamic behaviour. The long-term corrosion behaviour of each material was studied after six months of exposure by measuring weight loss and surface analysis with scanning electron microscope with energy-dispersive X-ray analysis. Hydrophobicity had a strong effect on bacterial attachment. Alloying elements e.g. nickel also had shown its ability to attract bacteria to adhere on the surface. However, the corrosion rate of different materials is determined not only by bacterial attachment but also by the stability of the passive film which is determined by the alloying elements, such as Mo and Cr. Chromium showed high resistance to corrosion, possibly due to toxicity on bacterial attachment. The nature of bacterial attachment and corrosion behaviour of the materials are discussed.
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Affiliation(s)
- T. T. T. Tran
- Energy and Resources Institute, College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, Northern Territory 0909, Australia
| | - K. Kannoorpatti
- Energy and Resources Institute, College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, Northern Territory 0909, Australia
| | - A. Padovan
- Research Institute for the Environment and Livelihoods, College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, Northern Territory 0909, Australia
| | - S. Thennadil
- Energy and Resources Institute, College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, Northern Territory 0909, Australia
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10
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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Wang C, Yu G, Yang F, Wang J. Formation of anaerobic granules and microbial community structure analysis in anaerobic hydrolysis denitrification reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:139734. [PMID: 32526572 DOI: 10.1016/j.scitotenv.2020.139734] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/19/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
An anaerobic hydrolysis denitrification (AnHD) process was developed to pretreat municipal wastewater for integrating partial nitration/anammox process. The results indicated that the carbon to nitrogen (C/N) ratio of municipal wastewater changed from 4.4 ± 0.3 to 2.2 ± 0.2 after pretreatment by AnHD process, which was favorable to the partial nitration/anammox process. The influent C/N ratio had influence on the formation of anaerobic granules. Two intrinsic factors, cyclic diguanylic acid (c-di-GMP) concentration and core bacterial community, were mainly responsible for the anaerobic granular formation. The higher c-di-GMP content increased the extracellular polymeric substances and decreased the motility of the bacteria, which was beneficial for the formation of anaerobic granules. The microbial community analysis showed that the lactic acid bacteria (Lactococcus) was the core bacteria during anaerobic hydrolysis process, while the denitrifying bacteria (Denitratisoma and unclassified Comamonadaceae) were the core bacterial community during AnHD process, which were responsible for nitrogen removal and anaerobic granular formation.
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Affiliation(s)
- Chao Wang
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China; Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environment Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Guoce Yu
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China
| | - Fenglin Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environment Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Jianlong Wang
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China.
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12
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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13
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Thiel J, Spring S, Tindall BJ, Spröer C, Bunk B, Koeksoy E, Ngugi DK, Schink B, Pester M. Desulfolutivibrio sulfoxidireducens gen. nov., sp. nov., isolated from a pyrite-forming enrichment culture and reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov. Syst Appl Microbiol 2020; 43:126105. [DOI: 10.1016/j.syapm.2020.126105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
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14
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Albonico F, Barelli C, Albanese D, Manica M, Partel E, Rosso F, Ripellino S, Pindo M, Donati C, Zecconi A, Mortarino M, Hauffe HC. Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet. PLoS One 2020; 15:e0237262. [PMID: 32760129 PMCID: PMC7410245 DOI: 10.1371/journal.pone.0237262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.
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Affiliation(s)
- Francesca Albonico
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Department of Veterinary Medicine, Universiy of Milan, Milan, Italy
| | - Claudia Barelli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Mattia Manica
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Erika Partel
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Fausta Rosso
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Silvia Ripellino
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Massimo Pindo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all’ Adige (TN), Trento, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Alfonso Zecconi
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Heidi C. Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
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15
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Damodara Kannan A, Evans P, Parameswaran P. Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations. BIORESOURCE TECHNOLOGY 2020; 310:123425. [PMID: 32361646 DOI: 10.1016/j.biortech.2020.123425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
This study evaluates the microbial community development in the suspended sludge within a pilot-scale gas sparged Anaerobic membrane bioreactor (AnMBR) under ambient conditions, as well as understand the influence of microbial signatures in the influent municipal wastewater on the bioreactor using amplicon sequence analysis. The predominant bacterial phyla comprised of Bacteroidetes, Proteobacteria, Firmicutes, and Chloroflexi demonstrated resiliency with ambient temperature operation over a period of 472 days. Acetoclastic Methanosaeta were predominant during most of the AnMBR operation. Beta diversity analysis indicated that the microbial communities present in the influent wastewater did not affect the AnMBR core microbiome. Syntrophic microbial interactions were evidenced by the presence of the members from Synergistales, Anaerolineales, Clostridiales, and Syntrophobacterales. The proliferation of sulfate reducing bacteria (SRB) along with sulfate reduction underscored the competition of SRB in the AnMBR. Operational and environmental variables did not greatly alter the core bacterial population based on canonical correspondence analysis.
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Affiliation(s)
- Arvind Damodara Kannan
- Department of Civil Engineering, Kansas State University, Fiedler Hall, 1701C Platt Street, Manhattan, KS 66506, USA
| | - Patrick Evans
- CDM Smith, 14432, SE Eastgate Way, Suite 100, Bellevue, WA 98007, USA
| | - Prathap Parameswaran
- Department of Civil Engineering, Kansas State University, Fiedler Hall, 1701C Platt Street, Manhattan, KS 66506, USA.
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16
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Han K, Yoon J, Yeum Y, Park S, Kim HK, Kim M, Chung HM, Kwon S, Yun ST, Kim Y. Efficacy of in situ well-based denitrification bio-barrier (WDB) remediating high nitrate flux in groundwater near a stock-raising complex. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 258:110004. [PMID: 31929050 DOI: 10.1016/j.jenvman.2019.110004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/14/2019] [Accepted: 12/15/2019] [Indexed: 06/10/2023]
Abstract
This study assessed the feasibility of an in situ well-based denitrification bio-barrier (WDB) for managing groundwater contaminated with high-strength nitrate. To evaluate the efficacy of WDB using fumarate as a carbon source and/or electron donor, three sequential single-well push-pull tests (SWPPTs) were conducted at six test sites. The values of the isotope enrichment factor (ɛ) ranging from -6.5‰ to -22.6‰ and the detection and degradation of nitrite and nitrous oxide confirmed complete in situ denitrification of nitrate to nitrogen gas. The ratio of the first-order rate coefficient of fumarate to nitrate (k1,fum/k1,NO3) was obtained to estimate the amount and frequency of fumarate injection for the effective design of WDB. At three sites, the ratios ranged from 0.67 to 0.80, while the other two sites showed higher ratios of 2.97 and 2.20 than the theoretical values and significant amounts of sulfate reduction, theoretically equivalent to 6.5% of total fumarate consumption. Considering the theoretical mole ratio of fumarate to nitrate of 0.98, the amount and frequency of fumarate injection is site specific. During the operating WDB, the average annual nitrate mass degraded (95% CI) was 2.2 ± 1.0 kg N/yr/well. The amount of N reduced by one well of WDB is equivalent to treating 110 m3 of groundwater at 30 mg N/L to the level of 10 mg N/L for one year. WDB would be an effective remediation option for managing high nitrate flux in groundwater.
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Affiliation(s)
- Kyungjin Han
- Department of Environmental Engineering, Korea University, Sejong, 30019, Republic of Korea
| | - Jonghyun Yoon
- National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Yuhoon Yeum
- Program in Environmental Technology and Policy, Korea University, Sejong, 30019, Republic of Korea
| | - Sunhwa Park
- National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Hyun-Koo Kim
- National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Moonsu Kim
- National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Hyen Mi Chung
- National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Sooyoul Kwon
- Department of Environmental Health, Korea National Open University, Seoul, 03087, Republic of Korea
| | - Seong-Taek Yun
- Department of Earth and Environmental Sciences and KU-KIST Green School, Korea University, Seoul, 02841, Republic of Korea
| | - Young Kim
- Department of Environmental Engineering, Korea University, Sejong, 30019, Republic of Korea; Program in Environmental Technology and Policy, Korea University, Sejong, 30019, Republic of Korea.
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17
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Ding H, Yu X, Chen L, Han J, Zhao Y, Feng J. Tolerable upper intake level of iron damages the intestine and alters the intestinal flora in weaned piglets. Metallomics 2020; 12:1356-1369. [DOI: 10.1039/d0mt00096e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Iron is an indispensable element for animal growth but become toxic at high concentrations, while tolerable upper intake level of iron shows adverse effect in the intestine.
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Affiliation(s)
- Haoxuan Ding
- College of Animal Science
- Zhejiang University
- Key Laboratory of animal feed and nutrition of Zhejiang Province
- Hangzhou
- China
| | - Xiaonan Yu
- College of Animal Science
- Zhejiang University
- Key Laboratory of animal feed and nutrition of Zhejiang Province
- Hangzhou
- China
| | - Lingjun Chen
- College of Animal Science
- Zhejiang University
- Key Laboratory of animal feed and nutrition of Zhejiang Province
- Hangzhou
- China
| | - Jianan Han
- College of Animal Science
- Zhejiang University
- Key Laboratory of animal feed and nutrition of Zhejiang Province
- Hangzhou
- China
| | - Yang Zhao
- College of Animal Science
- Zhejiang University
- Key Laboratory of animal feed and nutrition of Zhejiang Province
- Hangzhou
- China
| | - Jie Feng
- College of Animal Science
- Zhejiang University
- Key Laboratory of animal feed and nutrition of Zhejiang Province
- Hangzhou
- China
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18
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Recovery of Metals from Waste Lithium Ion Battery Leachates Using Biogenic Hydrogen Sulfide. MINERALS 2019. [DOI: 10.3390/min9090563] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lithium ion battery (LIB) waste is increasing globally and contains an abundance of valuable metals that can be recovered for re-use. This study aimed to evaluate the recovery of metals from LIB waste leachate using hydrogen sulfide generated by a consortium of sulfate-reducing bacteria (SRB) in a lactate-fed fluidised bed reactor (FBR). The microbial community analysis showed Desulfovibrio as the most abundant genus in a dynamic and diverse bioreactor consortium. During periods of biogenic hydrogen sulfide production, the average dissolved sulfide concentration was 507 mg L−1 and the average volumetric sulfate reduction rate was 278 mg L−1 d−1. Over 99% precipitation efficiency was achieved for Al, Ni, Co, and Cu using biogenic sulfide and NaOH, accounting for 96% of the metal value contained in the LIB waste leachate. The purity indices of the precipitates were highest for Co, being above 0.7 for the precipitate at pH 10. However, the process was not selective for individual metals due to simultaneous precipitation and the complexity of the metal content of the LIB waste. Overall, the process facilitated the production of high value mixed metal precipitates, which could be purified further or used as feedstock for other processes, such as the production of steel.
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19
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Zhu N, Yu N, Zhu Y, Wei Y, Hou Y, Zhang H, Sun AD. Identification of spoilage microorganisms in blueberry juice and their inactivation by a microchip pulsed electric field system. Sci Rep 2018; 8:8160. [PMID: 29802290 PMCID: PMC5970226 DOI: 10.1038/s41598-018-26513-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/11/2018] [Indexed: 01/08/2023] Open
Abstract
Blueberry juice is a healthy and nutritious food that has become increasingly popular worldwide. However, little is known about the microbial groups of this juice that can cause its spoilage. This study aimed to identify the main spoilage microorganisms in blueberry juice and explore whether a microchip pulsed electric field (MPEF) can effectively inactivate them. We performed polymerase chain reaction (PCR) amplification, as well as 16S rDNA, 18S rDNA, internal transcribed spacer (ITS), and 26S rDNA gene sequence analyses. Nine species belonging to eight genera, including Pantoea, Burkholderia, Pichia, Meyerozyma, Cryptococcus, Aureobasidium, Cladosporium, and Penicillium were identified as spoilage microorganisms. Cryptococcus sp., Meyerozyma sp., and Pichia sp. were specific spoilage organisms (SSO) owing to their rising numbers throughout spoilage progression. The effect of MPEF on the potential inactivation of these microorganisms was to induce significant inactivation of viable Cryptococcus sp., Meyerozyma sp., and Pichia sp. This research provides a theoretical basis for the application of MPEF in improving the quality of blueberry juice.
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Affiliation(s)
- Ning Zhu
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ning Yu
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yue Zhu
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yulong Wei
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanan Hou
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Haiping Zhang
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ai-Dong Sun
- Department of Food Science and Engineering, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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20
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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21
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Ritz NL, Lin DM, Wilson MR, Barton LL, Lin HC. Sulfate-reducing bacteria slow intestinal transit in a bismuth-reversible fashion in mice. Neurogastroenterol Motil 2017; 29. [PMID: 27477318 DOI: 10.1111/nmo.12907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/21/2016] [Indexed: 12/25/2022]
Abstract
BACKGROUND Hydrogen sulfide (H2 S) serves as a mammalian cell-derived gaseous neurotransmitter. The intestines are exposed to a second source of this gas by sulfate-reducing bacteria (SRB). Bismuth subsalicylate binds H2 S rendering it insoluble. The aim of this study was to test the hypothesis that SRB may slow intestinal transit in a bismuth-reversible fashion. METHODS Eighty mice were randomized to five groups consisting of Live SRB, Killed SRB, SRB+Bismuth, Bismuth, and Saline. Desulfovibrio vulgaris, a common strain of SRB, was administered by gavage at the dose of 1.0 × 109 cells along with rhodamine, a fluorescent dye. Intestinal transit was measured 50 minutes after gavage by euthanizing the animals, removing the small intestine between the pyloric sphincter and the ileocecal valve and visualizing the distribution of rhodamine across the intestine using an imaging system (IVIS, Perkin-Elmer). Intestinal transit (n=50) was compared using geometric center (1=minimal movement, 100=maximal movement). H2 S concentration (n=30) was also measured when small intestinal luminal content was allowed to generate this gas. KEY RESULTS The Live SRB group had slower intestinal transit as represented by a geometric center score of 40.2 ± 5.7 when compared to Saline: 73.6 ± 5.7, Killed SRB: 77.9 ± 6.9, SRB+Bismuth: 81.0 ± 2.0, and Bismuth: 73.3 ± 4.2 (P<.0001). Correspondingly, the Live SRB group had the highest luminal H2 S concentration of 4181.0 ± 968.0 ppb compared to 0 ± 0 ppb for the SRB+Bismuth group (P<.0001). CONCLUSIONS & INFERENCES Live SRB slow intestinal transit in a bismuth-reversible fashion in mice. Our results demonstrate that intestinal transit is slowed by SRB and this effect could be abolished by H2 S-binding bismuth.
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Affiliation(s)
- N L Ritz
- Section of Gastroenterology, New Mexico VA Health Care System, Albuquerque, NM, USA.,Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - D M Lin
- Section of Gastroenterology, New Mexico VA Health Care System, Albuquerque, NM, USA
| | - M R Wilson
- Section of Gastroenterology, New Mexico VA Health Care System, Albuquerque, NM, USA
| | - L L Barton
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - H C Lin
- Section of Gastroenterology, New Mexico VA Health Care System, Albuquerque, NM, USA.,Department of Medicine, University of New Mexico, Albuquerque, NM, USA
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22
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Cao J, Gayet N, Zeng X, Shao Z, Jebbar M, Alain K. Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio. Int J Syst Evol Microbiol 2016; 66:3904-3911. [PMID: 27392787 DOI: 10.1099/ijsem.0.001286] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to Desulfovibrio portus MSL79T (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2T (96.11 %), Desulfovibrio piezophilus C1TLV30T (96.04 %) and Desulfovibrio profundus DSM 11384T (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6×0.4-0.6 µm). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5-7) and at temperatures between 9 and 40 °C (optimum 30-35 °C). J2T was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C17 : 0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T represents a novel species of a novel genus in the family Desulfovibrionaceae, for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.
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Affiliation(s)
- Junwei Cao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Collaborative Innovation Center of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China.,School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, PR China.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Nicolas Gayet
- Ifremer, Centre de Brest, REM EEP LEP, Institut Carnot Ifremer EDROME, F-29280 Plouzané, France
| | - Xiang Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Collaborative Innovation Center of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Collaborative Innovation Center of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Mohamed Jebbar
- Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - Karine Alain
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
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Ma X, Hu X, Liu L, Li X, Ma Z, Chen J, Wei X. The quality changes and microflora analysis of commercial instant soya milk. Food Sci Nutr 2016; 5:123-130. [PMID: 28070323 PMCID: PMC5217880 DOI: 10.1002/fsn3.371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/19/2016] [Indexed: 12/15/2022] Open
Abstract
Soya milk can be easily contaminated because of its rich nutritional profile and simple package form, which thus may lead to short shelf life and has been considered as a public health concern. The objective of this study is to investigate the changes of sensory quality, viscosity, pH values, bacteria, and protein denaturation in soya milk samples which were stored for 0, 4, 8, 12, and 24 h at 25 ± 2°C. The results showed that the sensory properties were on the decline along with the storage time. The viscosity value increased from 1.61 Pa.s to 2.50 Pa.s, while the pH value decreased from 6.87 to 6.61. In addition, the number of total bacteria and Lactobacillus increased and the protein in soya milk denatured continually. The 16S rDNA sequence analysis indicated that the main microbial strains were Rummeliibacillus, Acinetobacter, Enterobacter, Phyllanthus, Bergia, Zhihengliuella, and Nesterenkonia. In this study, statistics in producing, packaging, and stocking process of soya milk were given, which provided experience to controlling soya milk.
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Affiliation(s)
- Xiaohong Ma
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Xinzhong Hu
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Liu Liu
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Xiaoping Li
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Zhen Ma
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Jiahui Chen
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Xue Wei
- College of food engineering and nutritional science Shaanxi Normal University Xi'an Shaanxi 710119 China
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Barton LL, Lyle DA, Ritz NL, Granat AS, Khurshid AN, Kherbik N, Hider R, Lin HC. Bismuth(III) deferiprone effectively inhibits growth of Desulfovibrio desulfuricans ATCC 27774. Biometals 2016; 29:311-9. [PMID: 26896170 DOI: 10.1007/s10534-016-9917-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 11/28/2022]
Abstract
Sulfate-reducing bacteria have been implicated in inflammatory bowel diseases and ulcerative colitis in humans and there is an interest in inhibiting the growth of these sulfide-producing bacteria. This research explores the use of several chelators of bismuth to determine the most effective chelator to inhibit the growth of sulfate-reducing bacteria. For our studies, Desulfovibrio desulfuricans ATCC 27774 was grown with nitrate as the electron acceptor and chelated bismuth compounds were added to test for inhibition of growth. Varying levels of inhibition were attributed to bismuth chelated with subsalicylate or citrate but the most effective inhibition of growth by D. desulfuricans was with bismuth chelated by deferiprone, 3-hydroxy-1,2-dimethyl-4(1H)-pyridone. Growth of D. desulfuricans was inhibited by 10 μM bismuth as deferiprone:bismuth with either nitrate or sulfate respiration. Our studies indicate deferiprone:bismuth has bacteriostatic activity on D. desulfuricans because the inhibition can be reversed following exposure to 1 mM bismuth for 1 h at 32 °C. We suggest that deferiprone is an appropriate chelator for bismuth to control growth of sulfate-reducing bacteria because deferiprone is relatively nontoxic to animals, including humans, and has been used for many years to bind Fe(III) in the treatment of β-thalassemia.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Daniel A Lyle
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nathaniel L Ritz
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Medicine, University of New Mexico and New Mexico VA Health Care System, Albuquerque, NM, 87018, USA
| | - Alex S Granat
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ali N Khurshid
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nada Kherbik
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Robert Hider
- Medicinal Chemistry, Institute of Pharmaceutical Science, King's College, London, London, SE1 9NH, UK
| | - Henry C Lin
- Department of Medicine, University of New Mexico and New Mexico VA Health Care System, Albuquerque, NM, 87018, USA
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25
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Rout NP, Khandual S, Gutierrez-Mora A, Ibarra-Montoya JL, Vega-Valero G. Divergence in three newly identified Arthrospira species from Mexico. World J Microbiol Biotechnol 2015; 31:1157-65. [DOI: 10.1007/s11274-015-1865-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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26
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346-351. [PMID: 24505072 DOI: 10.1099/ijs.0.059774-0] [Citation(s) in RCA: 2074] [Impact Index Per Article: 207.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA-DNA hybridization (DDH) technique. An ANI threshold range (95-96%) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65% 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2-99.0%) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.
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Affiliation(s)
- Mincheol Kim
- School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyun-Seok Oh
- Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sang-Cheol Park
- Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea.,School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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28
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Liu Q, Sun S, Piao M, Yang JY. Purification and Characterization of a Protease Produced by a Planomicrobium sp. L-2 from Gut of Octopus vulgaris. Prev Nutr Food Sci 2014; 18:273-9. [PMID: 24551830 PMCID: PMC3925218 DOI: 10.3746/pnf.2013.18.4.273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/26/2013] [Indexed: 12/04/2022] Open
Abstract
Protease widely exists in the digestive tract of animals and humans, playing a very important role in protein digestion and absorption. In this study, a high protease-producing strain Planomicrobium sp. L-2 was isolated and identified from the digestive tract of Octopus variabilis. The strain was identified by physiological and biochemical experiments and 16S rDNA sequences analysis. A protease was obtained from the strain Planomicrobium sp. L-2 through ammonium sulfate precipitation, dialysis and enrichment, DEAE-Sephadex A50 anion-exchange chromatography, and Sephadex G-100 gel chromatography. The molecular weight and properties of the protease were characterized, including optimum temperature and pH, thermal stability, protease inhibitions and metal ions. According to our results, the protease from Planomicrobium sp. L-2 strain designated as F1-1 was obtained by three-step separation and purification from crude enzyme. The molecular weight of the protease was 61.4 kDa and its optimum temperature was 40°C. The protease F1-1 showed a broad pH profile for casein hydrolysis between 5.0~11.0. No residual activity was observed after incubation for 40 min at 60°C and 60 min at 50°C. F1-1 protease was inhibited by Mn2+, Hg2+, Pb2+, Zn2+, and Cu2+ ions, as well as PMSF, indicating that the protease F1-1 was a serine protease. Additionally, research basis provided by this study could be considered for industrial application of octopus intestinal proteases.
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Affiliation(s)
- Qing Liu
- Department of Food Science and Technology, College of Fisheries Sciences, Pukyong National University, Busan 608-737, Korea
| | - Shujing Sun
- Department of Food Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Meizi Piao
- Department of Food Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Ji Young Yang
- Department of Food Science and Technology, College of Fisheries Sciences, Pukyong National University, Busan 608-737, Korea
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29
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Abstract
We report the draft genome sequence of Bacillus sp. strain FJAT-14515. The genome is 5.44 Mb in length. It covers 5,263 genes with an average length of 791 bp, has a G+C value of 37.06%, and contains 67 tRNAs, 31 small RNAs, and 5 rRNA loci.
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Vasaï F, Brugirard Ricaud K, Bernadet MD, Cauquil L, Bouchez O, Combes S, Davail S. Overfeeding and genetics affect the composition of intestinal microbiota in Anas platyrhynchos (Pekin) and Cairina moschata (Muscovy) ducks. FEMS Microbiol Ecol 2013; 87:204-16. [PMID: 24102552 DOI: 10.1111/1574-6941.12217] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/30/2013] [Accepted: 09/09/2013] [Indexed: 01/10/2023] Open
Abstract
To investigate the effect of overfeeding on the ileal and cecal microbiota of two genotypes of ducks (Pekin and Muscovy), high-throughput 16S rRNA gene-based pyrosequencing was used. The ducks were overfed for 12 days with 58% maize flour and 42% maize grain. Samples were collected before the overfeeding period (at 12 weeks), at 13 weeks, at 14 weeks, and 3 h after feeding. In parallel, ducks fed ad libitum were killed at the same ages. Whatever the digestive segment, the genotype, and the level of intake, Firmicutes and Bacteroidetes are the dominant phyla in the bacterial community of ducks (at least 80%). Before overfeeding, ileal samples were dominated by Bacilli, Clostridia, and Bacteroidia classes (≥ 70%), and cecal samples, by Bacteroidia and Clostridia classes (around 90%) in both Pekin and Muscovy ducks. The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding triggers major changes in the ileum, whereas the ceca are less affected. Overfeeding increased the relative abundance of Clostridiaceae, Lactobacillaceae, Streptococcaceae, and Enterococcaceae families in the ileum, whereas genotype affects particularly three families: Lachnospiraceae, Bacteroidaceae, and Desulfovibrionaceae in the ceca.
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Affiliation(s)
- Florian Vasaï
- IUT des Pays de l'Adour, IPREM-EEM UMR 5254, Mont de Marsan, France
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Prevost S, Cayol JL, Zuber F, Tholozan JL, Remize F. Characterization of clostridial species and sulfite-reducing anaerobes isolated from foie gras with respect to microbial quality and safety. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii. PLoS One 2013; 8:e62091. [PMID: 23630625 PMCID: PMC3632597 DOI: 10.1371/journal.pone.0062091] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/16/2013] [Indexed: 02/07/2023] Open
Abstract
Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ 15N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.
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33
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Zhao C, Gao Z, Qin Q, Li F, Ruan L. Desulfobaculum xiamenensis gen. nov., sp. nov., a member of the family
Desulfovibrionaceae
isolated from marine mangrove sediment. Int J Syst Evol Microbiol 2012; 62:1570-1575. [DOI: 10.1099/ijs.0.036632-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain P1T, which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, that were motile, with a single polar flagellum. The strain was non-spore-forming with a cell size of 0.6×1.5–2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22–44 °C (optimum, 35–40 °C) and pH range 5.5–8.5 (optimum, pH 7.0). NaCl was required for growth and tolerated at up to 3.5 % (w/v) (optimum, 0.5 %). Strain P1T utilized hydrogen, succinate, l-malate, citrate, oxalate, dl-lactate, pyruvate, or cysteine as electron donors, and sulfate or sulfite as electron acceptors. Fermentation products from pyruvate were acetate, H2 and CO2. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P1T formed a distinct evolutionary lineage within the family
Desulfovibrionaceae
. Strain P1T was most closely related to members of the genera
Desulfovibrio
(92.0–94.3 % 16S rRNA gene sequence similarity),
Desulfocurvus
(91.1 %),
Bilophila
(87.9 %) and
Lawsonia
(86.0 %) of the family
Desulfovibrionaceae
. The DNA G+C content of strain P1T was 64.5 mol% and the major cellular fatty acids were iso-C15 : 0 (18.8 %), anteiso-C15 : 0 (5.0 %), C16 : 0 (14.2 %) and iso-C17 : 1ω9c (24.4 %). The predominant menaquinone was MK-7 (97 %). Major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Strain P1T was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P1T represents a novel species of a new genus, for which the name Desulfobaculum xiamenensis gen. nov., sp. nov. is proposed. The type strain of Desulfobaculum xiamenensis is P1T ( = CGMCC 1.5166T = DSM 24233T).
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Affiliation(s)
- Chao Zhao
- Institute of Bioenergy and College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
| | - Zhaoming Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
| | - Qiwei Qin
- Laboratory of Marine Biology, South China Sea Institute of Oceanology, The Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Fuying Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
| | - Lingwei Ruan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
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Sugahara J, Fujishima K, Nunoura T, Takaki Y, Takami H, Takai K, Tomita M, Kanai A. Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS One 2012; 7:e32504. [PMID: 22403667 PMCID: PMC3293823 DOI: 10.1371/journal.pone.0032504] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/31/2012] [Indexed: 11/27/2022] Open
Abstract
Understanding the mechanistic basis of the disruption of tRNA genes, as manifested in the intron-containing and split tRNAs found in Archaea, will provide considerable insight into the evolution of the tRNA molecule. However, the evolutionary processes underlying these disruptions have not yet been identified. Previously, a composite genome of the deep-branching archaeon Caldiarchaeum subterraneum was reconstructed from a community genomic library prepared from a C. subterraneum–dominated microbial mat. Here, exploration of tRNA genes from the library reveals that there are at least three types of heterogeneity at the tRNAThr(GGU) gene locus in the Caldiarchaeum population. All three involve intronic gain and splitting of the tRNA gene. Of two fosmid clones found that encode tRNAThr(GGU), one (tRNAThr-I) contains a single intron, whereas another (tRNAThr-II) contains two introns. Notably, in the clone possessing tRNAThr-II, a 5′ fragment of the tRNAThr-I (tRNAThr-F) gene was observed 1.8-kb upstream of tRNAThr-II. The composite genome contains both tRNAThr-II and tRNAThr-F, although the loci are >500 kb apart. Given that the 1.8-kb sequence flanked by tRNAThr-F and tRNAThr-II is predicted to encode a DNA recombinase and occurs in six regions of the composite genome, it may be a transposable element. Furthermore, its dinucleotide composition is most similar to that of the pNOB8-type plasmid, which is known to integrate into archaeal tRNA genes. Based on these results, we propose that the gain of the tRNA intron and the scattering of the tRNA fragment occurred within a short time frame via the integration and recombination of a mobile genetic element.
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Affiliation(s)
- Junichi Sugahara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Kosuke Fujishima
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Takuro Nunoura
- Subsurface Geobiology & Advanced Research Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Ken Takai
- Subsurface Geobiology & Advanced Research Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine–Earth Science & Technology, Yokosuka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- * E-mail:
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Hinck S, Mussmann M, Salman V, Neu TR, Lenk S, Beer DD, Jonkers HM. Vacuolated Beggiatoa-like filaments from different hypersaline environments form a novel genus. Environ Microbiol 2011; 13:3194-205. [PMID: 21651683 DOI: 10.1111/j.1462-2920.2011.02513.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this study, members of a specific group of thin (6-14 µm filament diameter), vacuolated Beggiatoa-like filaments from six different hypersaline microbial mats were morphologically and phylogenetically characterized. Therefore, enrichment cultures were established, filaments were stained with fluorochromes to show intracellular structures and 16S rRNA genes were sequenced. Morphological characteristics of Beggiatoa-like filaments, in particular the presence of intracellular vacuoles, and the distribution of nucleic acids were visualized. In the intracellular vacuole nitrate reached concentrations of up to 650 mM. Fifteen of the retrieved 16S rRNA gene sequences formed a monophyletic cluster and were phylogenetically closely related (≥ 94.4% sequence identity). Sequences of known filamentous sulfide-oxidizing genera Beggiatoa and Thioploca that comprise non-vacuolated and vacuolated filaments from diverse habitats clearly delineated from this cluster. The novel monophyletic cluster was furthermore divided into two sub-clusters: one contained sequences originating from Guerrero Negro (Mexico) microbial mats and the other comprised sequences from five distinct Spanish hypersaline microbial mats from Ibiza, Formentera and Lake Chiprana. Our data suggest that Beggiatoa-like filaments from hypersaline environments displaying a thin filament diameter contain nitrate-storing vacuoles and are phylogenetically separate from known Beggiatoa. Therefore, we propose a novel genus for these organisms, which we suggest to name 'Candidatus Allobeggiatoa'.
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Affiliation(s)
- Susanne Hinck
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
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Tao HP, Shen ZY, Zhu F, Xu XF, Tang XD, Xu L. Isolation and Identification of a Pathogen of Silkworm Bombyx mori. Curr Microbiol 2010; 62:876-83. [DOI: 10.1007/s00284-010-9796-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Accepted: 10/04/2010] [Indexed: 10/18/2022]
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Thabet OBD, Wafa T, Eltaief K, Cayol JL, Hamdi M, Fauque G, Fardeau ML. Desulfovibrio legallis sp. nov.: a moderately halophilic, sulfate-reducing bacterium isolated from a wastewater digestor in Tunisia. Curr Microbiol 2010; 62:486-91. [PMID: 20814681 DOI: 10.1007/s00284-010-9733-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
Abstract
A new moderately halophilic sulfate-reducing bacterium (strain H₁(T) ) was enriched and isolated from a wastewater digestor in Tunisia. Cells were curved, motile rods (2-3 x 0.5 μm). Strain H₁(T) grew at temperatures between 22 and 43°C (optimum 35°C), and at pH between 5.0 and 9.2 (optimum 7.3-7.5). Strain H₁(T) required salt for growth (1-45 g of NaCl/l), with an optimum at 20-30 g/l. Sulfate, sulfite, thiosulfate, and elemental sulfur were used as terminal electron acceptors but not nitrate and nitrite. Strain H₁(T) utilized lactate, pyruvate, succinate, fumarate, ethanol, and hydrogen (in the presence of acetate and CO₂) as electron donors in the presence of sulfate as electron acceptor. The main end-products from lactate oxidation were acetate with H₂ and CO₂. The G + C content of the genomic DNA was 55%. The predominant fatty acids of strain H₁(T) were C(15:0) iso (38.8%), C(16:0) (19%), and C(14:0) iso 3OH (12.2%), and menaquinone MK-6 was the major respiratory quinone. Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain H₁(T) was affiliated to the genus Desulfovibrio. On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain H₁(T) is proposed to be assigned to a novel species of sulfate reducers of the genus Desulfovibrio, Desulfovibrio legallis sp. nov. (= DSM 19129(T) = CCUG 54389(T)).
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Affiliation(s)
- Olfa Ben Dhia Thabet
- INSAT, Laboratoire d'Ecologie et de Technologie Microbienne, Centre Urbain Nord, BP 676, 1080, Tunis Cedex, Tunisia
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Voordouw G, Voordouw JK, Jack TR, Foght J, Fedorak PM, Westlake DW. Identification of distinct communities of sulfate-reducing bacteria in oil fields by reverse sample genome probing. Appl Environ Microbiol 2010; 58:3542-52. [PMID: 16348801 PMCID: PMC183142 DOI: 10.1128/aem.58.11.3542-3552.1992] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirty-five different standards of sulfate-reducing bacteria, identified by reverse sample genome probing and defined as bacteria with genomes showing little or no cross-hybridization, were in part characterized by Southern blotting, using 16S rRNA and hydrogenase gene probes. Samples from 56 sites in seven different western Canadian oil field locations were collected and enriched for sulfate-reducing bacteria by using different liquid media containing one of the following carbon sources: lactate, ethanol, benzoate, decanoate, propionate, or acetate. DNA was isolated from the enrichments and probed by reverse sample genome probing using master filters containing denatured chromosomal DNAs from the 35 sulfate-reducing bacterial standards. Statistical analysis of the microbial compositions at 44 of the 56 sites indicated the presence of two distinct communities of sulfate-reducing bacteria. The discriminating factor between the two communities was the salt concentration of the production waters, which were either fresh water or saline. Of 34 standards detected, 10 were unique to the fresh water and 18 were unique to the saline oil field environment, while only 6 organisms were cultured from both communities.
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Affiliation(s)
- G Voordouw
- Division of Biochemistry, Department of Biological Sciences, The University of Calgary, Calgary, Alberta, Canada T2N 1N4; NOVA HUSKY Research Corporation, Calgary, Alberta, Canada T2E 7K7 ; and Department of Microbiology, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
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Voordouw G, Voordouw JK, Karkhoff-Schweizer RR, Fedorak PM, Westlake DW. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl Environ Microbiol 2010; 57:3070-8. [PMID: 16348574 PMCID: PMC183929 DOI: 10.1128/aem.57.11.3070-3078.1991] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a "standard") to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples.
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Affiliation(s)
- G Voordouw
- Division of Biochemistry, Department of Biological Sciences, The University of Calgary, Calgary, Alberta T2N 1N4, and Department of Microbiology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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40
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Boudaud N, Coton M, Coton E, Pineau S, Travert J, Amiel C. Biodiversity analysis by polyphasic study of marine bacteria associated with biocorrosion phenomena. J Appl Microbiol 2009; 109:166-79. [PMID: 20059620 DOI: 10.1111/j.1365-2672.2009.04643.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS A polyphasic approach was used to study the biodiversity bacteria associated with biocorrosion processes, in particular sulfate-reducing bacteria (SRB) and thiosulfate-reducing bacteria (TRB) which are described to be particularly aggressive towards metallic materials, notably via hydrogen sulfide release. METHODS AND RESULTS To study this particular flora, an infrared spectra library of 22 SRB and TRB collection strains were created using a Common Minimum Medium (CMM) developed during this study and standardized culture conditions. The CMM proved its ability to allow for growth of both SRB and TRB strains. These sulfurogen collection strains were clearly discriminated and differentiated at the genus level by fourier transform infrared (FT-IR) spectroscopy. In a second step, infrared spectra of isolates, recovered from biofilms formed on carbon steel coupons immersed for 1 year in three different French harbour areas, were compared to the infrared reference spectra library. In parallel, molecular methods (M13-PCR and 16S rRNA gene sequencing) were used to qualitatively evaluate the intra- and inter-species genetic diversity of biofilm isolates. The biodiversity study indicated that strains belonging to the Vibrio genus were the dominant population; strains belonging to the Desulfovibrio genus (SRB) and Peptostreptococcaceae were also identified. CONCLUSION Overall, the combination of the FT-IR spectroscopy and molecular approaches allowed for the taxonomic and ecological study of a bacterial flora, cultivated on CMM, associated with microbiology-induced corrosion (MIC) processes. SIGNIFICANCE AND IMPACT OF THE STUDY Via the use of the CMM medium, the culture of marine bacteria (including both SRB and TRB bacteria) was allowed, and the implication of nonsulforogen bacteria in MIC was observed. Their involvement in the biocorrosion phenomena will have to be studied and taken into account in the future.
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Affiliation(s)
- N Boudaud
- Equipe de Recherche en Physico-Chimie et Biotechnologies, Université Caen Basse Normandie, Caen Cedex, France
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Desulfovibrio idahonensis sp. nov., sulfate-reducing bacteria isolated from a metal(loid)-contaminated freshwater sediment. Int J Syst Evol Microbiol 2009; 59:2208-14. [DOI: 10.1099/ijs.0.016709-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Isolation and characterization of culturable halophilic microorganisms of salt ponds in Lianyungang, China. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0068-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Community composition of the marine bacterioplankton in Kongsfjorden (Spitsbergen) as revealed by 16S rRNA gene analysis. Polar Biol 2009. [DOI: 10.1007/s00300-009-0641-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Parnell JJ, Crowl TA, Weimer BC, Pfrender ME. Biodiversity in microbial communities: system scale patterns and mechanisms. Mol Ecol 2009; 18:1455-62. [PMID: 19298265 DOI: 10.1111/j.1365-294x.2009.04128.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The relationship between anthropogenic impact and the maintenance of biodiversity is a fundamental question in ecology. The emphasis on the organizational level of biodiversity responsible for ecosystem processes is shifting from a species-centred focus to include genotypic diversity. The relationship between biodiversity measures at these two scales remains largely unknown. By stratifying anthropogenic effects between scales of biodiversity of bacterial communities, we show a statistically significant difference in diversity based on taxonomic scale. Communities with intermediate species richness show high genotypic diversity while speciose and species-poor communities do not. We propose that in species-poor communities, generally comprising stable yet harsh conditions, physiological tolerance and competitive trade-offs limit both the number of species that occur and the loss of genotypes due to decreases in already constrained fitness. In species-rich communities, natural environmental conditions result in well-defined community structure and resource partitioning. Disturbance of these communities disrupts niche space, resulting in lower genotypic diversity despite the maintenance of species diversity. Our work provides a model to inform future research about relationships between species and genotypic biodiversity based on determining the biodiversity consequences of changing environmental context.
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Affiliation(s)
- J Jacob Parnell
- Department of Biology, Utah State University, Logan, UT84322, USA
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Lawsonia intracellularis contains a gene encoding a functional rickettsia-like ATP/ADP translocase for host exploitation. J Bacteriol 2008; 190:5746-52. [PMID: 18606736 DOI: 10.1128/jb.00391-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
ATP/ADP translocases are a hallmark of obligate intracellular pathogens related to chlamydiae and rickettsiae. These proteins catalyze the highly specific exchange of bacterial ADP against host ATP and thus allow bacteria to exploit their hosts' energy pool, a process also referred to as energy parasitism. The genome sequence of the obligate intracellular pathogen Lawsonia intracellularis (Deltaproteobacteria), responsible for one of the most economically important diseases in the swine industry worldwide, revealed the presence of a putative ATP/ADP translocase most similar to known ATP/ADP translocases of chlamydiae and rickettsiae (around 47% amino acid sequence identity). The gene coding for the putative ATP/ADP translocase of L. intracellularis (L. intracellularis nucleotide transporter 1 [NTT1(Li)]) was cloned and expressed in the heterologous host Escherichia coli. The transport properties of NTT1(Li) were determined by measuring the uptake of radioactively labeled substrates by E. coli. NTT1(Li) transported ATP in a counterexchange mode with ADP in a highly specific manner; the substrate affinities determined were 236.3 (+/- 36.5) microM for ATP and 275.2 (+/- 28.1) microM for ADP, identifying this protein as a functional ATP/ADP translocase. NTT1(Li) is the first ATP/ADP translocase from a bacterium not related to Chlamydiae or Rickettsiales, showing that energy parasitism by ATP/ADP translocases is more widespread than previously recognized. The occurrence of an ATP/ADP translocase in L. intracellularis is explained by a relatively recent horizontal gene transfer event with rickettsiae as donors.
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Talbot G, Topp E, Palin MF, Massé DI. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. WATER RESEARCH 2008; 42:513-37. [PMID: 17719078 DOI: 10.1016/j.watres.2007.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 05/16/2023]
Abstract
Molecular techniques have unveiled the complexity of the microbial consortium in anaerobic bioreactors and revealed the presence of several uncultivated species. This paper presents a review of the panoply of classical and recent molecular approaches and multivariate analyses that have been, or might be used to establish the interactions and functions of these anaerobic microorganisms. Most of the molecular approaches used so far are based on the analysis of small subunit ribosomal RNA but recent studies also use quantification of functional gene expressions. There are now several studies that have developed quantitative real-time PCR assays to investigate methanogens. With a view to improving the stability and performance of bioreactors, monitoring with molecular methods is also discussed. Advances in metagenomics and proteomics will lead to the development of promising lab-on chip technologies for cost-effective monitoring.
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Affiliation(s)
- G Talbot
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, Quebec, Canada J1M 0C8.
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Hongxiang X, Min W, Xiaogu W, Junyi Y, Chunsheng W. Bacterial diversity in deep-sea sediment from northeastern Pacific Ocean. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1872-2032(08)60026-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bouity-Voubou MD, Frigon JC, Guiot S, Brousseau R. Comparison of treatment efficacy and stability of microbial populations between raw and anaerobically treated liquid pig manure, using PCR–DGGE and 16S sequencing. Can J Microbiol 2008; 54:83-90. [DOI: 10.1139/w07-120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effects of adding an adapted inoculum to liquid pig manure (LPM) prior to anaerobic digestion were evaluated by standard analytical methods. In parallel, the phylogenetic diversity of the microbial community of raw and anaerobically digested pig manure was studied by both denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA fragments amplified by polymerase chain reaction. Gas production, volative fatty acid production, removal of soluble chemical oxygen demand, and removal of volatile soluble solids were measured on raw and on inoculated liquid pig manure subjected to anaerobic digestion. DGGE profiles of 16S rRNA genes were used to compare the major elements of the bacterial community composition in raw LPM with those present under various incubation conditions. Major bands were excised and sequenced to gain insight into the identities of the bacterial populations from LPM treated under different conditions. The results show that the addition of an adapted inoculum did not have a major impact on the conversion of pig manure into soluble organic matter and did not significantly change the microbial populations present during anaerobic digestion of LPM. Bacterial composition also indicated that Clostridium species are important constituents of the LPM community.
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Affiliation(s)
- Maurice Dieudonné Bouity-Voubou
- Biotechnology Research Institute, National Research Council (NRC), Canada, 6100 Royal Mount Avenue, Montréal, QC H4P 2R2, Canada
| | - Jean Claude Frigon
- Biotechnology Research Institute, National Research Council (NRC), Canada, 6100 Royal Mount Avenue, Montréal, QC H4P 2R2, Canada
| | - Serge Guiot
- Biotechnology Research Institute, National Research Council (NRC), Canada, 6100 Royal Mount Avenue, Montréal, QC H4P 2R2, Canada
| | - Roland Brousseau
- Biotechnology Research Institute, National Research Council (NRC), Canada, 6100 Royal Mount Avenue, Montréal, QC H4P 2R2, Canada
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Mariniello L, Giosafatto CVL, Moschetti G, Aponte M, Masi P, Sorrentino A, Porta R. Fennel waste-based films suitable for protecting cultivations. Biomacromolecules 2007; 8:3008-14. [PMID: 17877395 DOI: 10.1021/bm0702410] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biodegradable, flexible, and moisture-resistant films were obtained by recycling fennel waste and adding to fennel homogenates the bean protein phaseolin that was modified or not modified by the enzyme transglutaminase. All films were analyzed for their morphology, mechanical properties, water vapor permeability, and susceptibility to biodegradation under soil-like conditions. Our experiments showed that transglutaminase treatment of the phaseolin-containing fennel waste homogenates allowed us to obtain films comparable in their mechanical properties and water vapor permeability to the commercial films Ecoflex and Mater-Bi. Furthermore, biodegradability tests demonstrated that the presence of the enzyme in the film-casting sample significantly influences the integrity of such a product that lasts longer than films obtained either with fennel waste alone or with a mixture of fennel waste and phaseolin. These findings indicate the fennel-phaseolin film prepared in the presence of transglutaminase to be a promising candidate for a new environmentally friendly mulching bioplastic.
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Affiliation(s)
- L Mariniello
- Department of Food Science and School of Biotechnological Sciences, University of Naples Federico II, Parco Gussone, 80055 Portici, Naples, Italy.
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Gontang EA, Fenical W, Jensen PR. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 2007; 73:3272-82. [PMID: 17400789 PMCID: PMC1907118 DOI: 10.1128/aem.02811-06] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of >/=98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.
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MESH Headings
- Actinobacteria/classification
- Actinobacteria/genetics
- Actinobacteria/growth & development
- Actinobacteria/isolation & purification
- Bacillaceae/classification
- Bacillaceae/genetics
- Bacillaceae/growth & development
- Bacillaceae/isolation & purification
- Biodiversity
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Geologic Sediments/microbiology
- Gram-Positive Bacteria/classification
- Gram-Positive Bacteria/genetics
- Gram-Positive Bacteria/growth & development
- Gram-Positive Bacteria/isolation & purification
- Molecular Sequence Data
- Palau
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Water Microbiology
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Affiliation(s)
- Erin A Gontang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0204, USA
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