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Rana B, Chandola R, Sanwal P, Joshi GK. Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing. Sci Rep 2024; 14:4031. [PMID: 38369518 PMCID: PMC10874962 DOI: 10.1038/s41598-024-53350-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the keem sample could be categorized into 3347, 57, and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem, and KEGG Orthology (KO) annotations. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research.
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Affiliation(s)
- Babita Rana
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India
| | - Renu Chandola
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India
| | - Pankaj Sanwal
- Department of Biochemical Engineering, BTKIT, Dwarahat, Uttarakhand, India
| | - Gopal Krishna Joshi
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India.
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2
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Feng Y, Qiu M, Shao L, Jiang Y, Zhang W, Jiang W, Xin F, Jiang M. Strategies for the biological production of ectoine by using different chassis strains. Biotechnol Adv 2024; 70:108306. [PMID: 38157997 DOI: 10.1016/j.biotechadv.2023.108306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/27/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
As an amino acid derivative and a typical compatible solute, ectoine can assist microorganisms in resisting high osmotic pressure. Own to its long-term moisturizing effects, ectoine shows extensive applications in cosmetics, medicine and other fields. With the rapid development of synthetic biology and fermentation engineering, many biological strategies have been developed to improve the ectoine production and simplify the production process. Currently, the microbial fermentation has been widely used for large scaling ectoine production. Accordingly, this review will introduce the metabolic pathway for ectoine synthesis and also comprehensively evaluate both wild-type and genetically modified strains for ectoine production. Furthermore, process parameters affecting the ectoine production efficiency and adoption of low cost substrates will be evaluated. Lastly, future prospects on the improvement of ectoine production will be proposed.
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Affiliation(s)
- Yifan Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Lei Shao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
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3
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Murakami A, Toyomoto K, Namai F, Sato T, Fujii T, Tochio T, Shimosato T. Oral administration of Brevibacterium linens from washed cheese increases the proportions of short-chain fatty acid-producing bacteria and lactobacilli in the gut microbiota of mice. Anim Sci J 2023; 94:e13905. [PMID: 38102883 DOI: 10.1111/asj.13905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023]
Abstract
Brevibacterium linens (B. linens) is a dairy microorganism used in the production of washed cheese. However, there has been little research on B. linens, especially regarding its effects in vivo. Herein, we report the morphological characteristics of B. linens, such as its two-phase growth and V- and Y-shaped bodies. We also report that oral administration of B. linens increased the diversity of the gut microbiota and promoted the growth of lactobacilli and short-chain fatty acid-producing bacteria, such as Lachnospiraceae and Muribaculaceae. These findings suggest that the ingestion of B. linens may have beneficial effects in humans and animals.
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Affiliation(s)
- Aito Murakami
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Koharu Toyomoto
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Fu Namai
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Takashi Sato
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Tadashi Fujii
- Department of Medical Research on Prebiotics and Probiotics, Fujita Health University, Toyoake, Aichi, Japan
| | - Takumi Tochio
- Department of Medical Research on Prebiotics and Probiotics, Fujita Health University, Toyoake, Aichi, Japan
| | - Takeshi Shimosato
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
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4
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Wufuer R, Li W, Wang S, Duo J. Isolation and Degradation Characteristics of PBAT Film Degrading Bacteria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:17087. [PMID: 36554967 PMCID: PMC9779299 DOI: 10.3390/ijerph192417087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
In recent years, PBAT (polybutylene adipate-co-terephthalate) mulch has become one of the most commonly used biodegradable mulching films. In this paper, five potential strains of PBAT film degrading bacteria were screened from the soil sample using PBAT film as the sole carbon source. A highly efficient PBAT degrading strain JZ1 was isolated by comparing the degradation performance of PBAT mulching film identified as Peribacillus frigoritolerans S2313 by 16S rDNA sequence analysis. The capacity of the strain to degrade PBAT film was optimized by adjusting the cultivation conditions such as nitrogen source, pH, and inoculum volume. After 8 weeks of cultivation, the actual degradation rate of the strain to PBAT mulch film reached 12.45%. SEM (scanning electron microscopy) coupled with EDX (energy dispersive spectroscopy) analysis showed that microbial degradation is an oxidation process and is mainly due to the amorphous regions of the PBAT film. The biodegradation of PBAT film by Peribacillus frigoritolerans may provide a promising method for regulating the degradation progress of PBAT film in the farmlands.
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Affiliation(s)
- Rehemanjiang Wufuer
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Wenfeng Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Shuzhi Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Jia Duo
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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5
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Huang Y, Dong L, Gong J, Yang J, Lu S, Lai XH, Jin D, Huang Q, Pu J, Liu L, Xu J. Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces. J Microbiol 2022; 60:977-985. [PMID: 35984616 PMCID: PMC9390107 DOI: 10.1007/s12275-022-2134-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022]
Abstract
Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20′54″N, 106°49′20″E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09′10″N, 102°04′39″E, October 2013) of South China, respectively. Optimal growth is obtained at 25–28°C (range, 4–32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0–10.0) in the presence of 0.5–1.0% NaCl (w/v) (range, 0–15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739T (16S rRNA similarity, both 98.5%; dDDH, 46.7–46.8%; ANI, 91.9–92.1%). Strain HY170T contained MK-8(H2), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170T. Anteiso-C15:0 and anteiso-C17:0 were the major fatty acids (> 10%) of strains HY170T and HY001, with anteiso-C17:1A predominant in strain HY170T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170T = CGMCC 1.18600T = JCM 34230T).
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Lingzhi Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
| | - Jian Gong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Qianni Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China.
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China.
- Research Institute of Public Health, Nankai University, Tianjin, 300350, China.
- Peking University School of Public Health, Beijing, 100083, China.
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Wiernasz N, Gigout F, Cardinal M, Cornet J, Rohloff J, Courcoux P, Vigneau E, Skírnisdottír S, Passerini D, Pilet MF, Leroi F. Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products. Foods 2021; 10:foods10112517. [PMID: 34828798 PMCID: PMC8623285 DOI: 10.3390/foods10112517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/02/2023] Open
Abstract
Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This work aimed to compare three products that were obtained from the same batch of fish: cold-smoked salmon (CSS) stored under vacuum packaging (VP) or a modified atmosphere packaging (MAP) and VP salmon dill gravlax (SG). Classical microbiological analyses and 16S rRNA metabarcoding, biochemical analyses (trimethylamine, total volatile basic nitrogen (TVBN), biogenic amines, pH, volatile organic compounds (VOCs)) and sensory analyses (quantitative descriptive analysis) were performed on each product throughout their storage at a chilled temperature. The three products shared the same initial microbiota, which were mainly dominated by Photobacterium, Lactococcus and Lactobacillus genera. On day 28, the VP CSS ecosystem was mainly composed of Photobacterium and, to a lesser extent, Lactococcus and Lactobacillus genera, while Lactobacillus was dominant in the MAP CSS. The diversity was higher in the SG, which was mainly dominated by Enterobacteriaceae, Photobacterium, Lactobacillus and Lactococcus. Although the sensory spoilage was generally weak, gravlax was the most perishable product (slight increase in amine and acidic off-odors and flavors, fatty appearance, slight discoloration and drop in firmness), followed by the VP CSS, while the MAP CSS did not spoil. Spoilage was associated with an increase in the TVBN, biogenic amines and spoilage associated VOCs, such as decanal, nonanal, hexadecanal, benzaldehyde, benzeneacetaldehyde, ethanol, 3-methyl-1-butanol, 2,3-butanediol, 1-octen-3-ol, 2-butanone and 1-octen-3-one. This study showed that the processing and packaging conditions both had an effect on the microbial composition and the quality of the final product.
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Affiliation(s)
- Norman Wiernasz
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
- UMR 1014, Secalim, INRAE, Oniris, 44307 Nantes, France;
| | - Frédérique Gigout
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Mireille Cardinal
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Josiane Cornet
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Jens Rohloff
- NTNU, Department of Biology, 7491 Trondheim, Norway;
| | | | | | - Sigurlaug Skírnisdottír
- Matıs, Research and Innovation, Exploitation and Utilization of Genetic Resources, 101-155 Reykjavik, Iceland;
| | - Delphine Passerini
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | | | - Françoise Leroi
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
- Correspondence:
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Crippen TL, Sheffield CL, Singh B, Byrd JA, Beier RC, Anderson RC. Poultry litter and the environment: Microbial profile of litter during successive flock rotations and after spreading on pastureland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146413. [PMID: 33774310 DOI: 10.1016/j.scitotenv.2021.146413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
With the increasing demand for broiler meat, a thorough evaluation of the microbial community within the broiler houses and sites where litter is deposited is critical to animal and environmental wellbeing. However not much is known in this arena, so our work evaluates the litter bacterial microbial community within a house over a 2.5 year period through 11 flock rotations, a partial and a total cleanout, and the subsequent deposition of the litter as fertilizer on pastureland. The effects of both time and management practices correlated with alterations of the litter microbial community. The cleanout practices and introduction of new bedding had minimal influence on the house microbial community once it was established, which generally showed a consistent increase in the proportion of Actinobacteria and a decrease in Firmicutes over the 11 flock rotations. Analysis of the bacterial profile at the genus level gave increased resolution, revealing changes during the first and second flock rotation and after the total cleanout. The disturbance of the partial cleanout seemed to be buffered by the supporting conditions within the house while the total cleanout showed a small, but significant influence. The pastureland deposition of litter, however, was affected by time and abiotic factors that changed the litter microbial community structure weekly. The stockpiled litter had an increase in the phyla Actinobacteria and the class Bacilli that commonly have microbes utilizing nitrogen and decaying materials, in comparison to Native soil. Further, the soil beneath where the litter was stored for 20 weeks, lost diversity, indicating a possible effect of the litter stockpiling on environmental quality at that site. How management practices affect the composition of the microbial community within the litter of the broiler house is of interest in terms of bird health and environmentally for future utilization of spent litter.
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Affiliation(s)
- Tawni L Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, 2881 F & B Road, College Station, TX 77845, USA.
| | - Cynthia L Sheffield
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, 2881 F & B Road, College Station, TX 77845, USA
| | - Baneshwar Singh
- Department of Forensic Science, 1015 Floyd Avenue, Room 2010, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - J Allen Byrd
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, 2881 F & B Road, College Station, TX 77845, USA
| | - Ross C Beier
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, 2881 F & B Road, College Station, TX 77845, USA
| | - Robin C Anderson
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, 2881 F & B Road, College Station, TX 77845, USA
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8
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Weiland-Bräuer N, Prasse D, Brauer A, Jaspers C, Reusch TBH, Schmitz RA. Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi. Microbiologyopen 2020; 9:e1094. [PMID: 32652897 PMCID: PMC7520997 DOI: 10.1002/mbo3.1094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
The associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health, and homeostasis. Cooperative and competitive interactions between bacteria, due to release of, for example, antibacterial substances and quorum sensing (QS)/quorum quenching (QQ) molecules, ultimately affect the establishment and dynamics of the associated microbial community. Aiming to address interspecies competition of cultivable microbes associated with emerging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi), we performed a classical isolation approach. Overall, 84 bacteria were isolated from A. aurita medusae and polyps, 64 bacteria from M. leidyi, and 83 bacteria from ambient seawater, followed by taxonomically classification by 16S rRNA gene analysis. The results show that A. aurita and M. leidyi harbor a cultivable core microbiome consisting of typical marine ubiquitous bacteria also found in the ambient seawater. However, several bacteria were restricted to one host suggesting host‐specific microbial community patterns. Interbacterial interactions were assessed by (a) a growth inhibition assay and (b) QS interference screening assay. Out of 231 isolates, 4 bacterial isolates inhibited growth of 17 isolates on agar plates. Moreover, 121 of the 231 isolates showed QS‐interfering activities. They interfered with the acyl‐homoserine lactone (AHL)‐based communication, of which 21 showed simultaneous interference with autoinducer 2. Overall, this study provides insights into the cultivable part of the microbiota associated with two environmentally important marine non‐model organisms and into interbacterial interactions, which are most likely considerably involved in shaping a healthy and resilient microbiota.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Molekulare Mikrobiologie, Institut für Allgemeine Mikrobiologie, Kiel University, Kiel, Germany
| | - Daniela Prasse
- Molekulare Mikrobiologie, Institut für Allgemeine Mikrobiologie, Kiel University, Kiel, Germany
| | - Annika Brauer
- Molekulare Mikrobiologie, Institut für Allgemeine Mikrobiologie, Kiel University, Kiel, Germany
| | - Cornelia Jaspers
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Ruth A Schmitz
- Molekulare Mikrobiologie, Institut für Allgemeine Mikrobiologie, Kiel University, Kiel, Germany
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9
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de Melo AG, Rousseau GM, Tremblay DM, Labrie SJ, Moineau S. DNA tandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages. Environ Microbiol 2020; 22:3413-3428. [PMID: 32510858 DOI: 10.1111/1462-2920.15113] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/23/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
This report presents the characterization of the first virulent phages infecting Brevibacterium aurantiacum, a bacterial species used during the manufacture of surface-ripened cheeses. These phages were also responsible for flavour and colour defects in surface-ripened cheeses. Sixteen phages (out of 62 isolates) were selected for genome sequencing and comparative analyses. These cos-type phages with a long non-contractile tail currently belong to the Siphoviridae family (Caudovirales order). Their genome sizes vary from 35,637 to 36,825 bp and, similar to their host, have a high GC content (~61%). Genes encoding for an immunity repressor, an excisionase and a truncated integrase were found, suggesting that these virulent phages may be derived from a prophage. Their genomic organization is highly conserved, with most of the diversity coming from the presence of long (198 bp) DNA tandem repeats (TRs) within an open reading frame coding for a protein of unknown function. We categorized these phages into seven genomic groups according to their number of TR, which ranged from two to eight. Moreover, we showed that TRs are widespread in phage genomes, found in more than 85% of the genomes available in public databases.
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Affiliation(s)
- Alessandra G de Melo
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | - Geneviève M Rousseau
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | - Denise M Tremblay
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | | | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
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10
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Chen WC, Yuan FW, Wang LF, Chien CC, Wei YH. Ectoine production with indigenous Marinococcus sp. MAR2 isolated from the marine environment. Prep Biochem Biotechnol 2019; 50:74-81. [PMID: 31517565 DOI: 10.1080/10826068.2019.1663534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Ectoine has fostered the development of products for skin care and cosmetics. In this study, we employed the marine bacterial strain Marinococcus sp. MAR2 to increase ectoine production by optimizing medium constituents using Response Surface Methodology (RSM) and a fed-batch strategy. The results from the steepest ascent and central composite design indicated that 54 g/L of yeast extract, 14.0 g/L of ammonium acetate, 74.4 g/L of sodium glutamate, and 6.2 g/L of sodium citrate constituted the optimal medium with maximum ectoine production (3.5 g/L). In addition, we performed fed-batch culture in the bioreactor, combining pH and dissolved oxygen to produce ectoine by Marinococcus sp. MAR2. The ectoine production, content, and productivity of 5.6 g/L, 10%, and 3.9 g/L/day were further reached by a fed-batch culture. Thus, the ectoine production by Marinococcus sp. MAR2 using RSM and fed-batch strategy shows its potential for industrial production.
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Affiliation(s)
- Wei-Chuan Chen
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
| | - Fang-Wei Yuan
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
| | - Li-Fen Wang
- Department of Applied Chemistry and Materials Science, Fooyin University, Kaohsiung, Taiwan (R.O.C.)
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
| | - Yu-Hong Wei
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan, Taiwan (R.O.C.)
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11
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12
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Anast JM, Dzieciol M, Schultz DL, Wagner M, Mann E, Schmitz-Esser S. Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment. Sci Rep 2019; 9:6164. [PMID: 30992535 PMCID: PMC6467879 DOI: 10.1038/s41598-019-42525-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/02/2019] [Indexed: 02/01/2023] Open
Abstract
The genus Brevibacterium harbors many members important for cheese ripening. We performed real-time quantitative PCR (qPCR) to determine the abundance of Brevibacterium on rinds of Vorarlberger Bergkäse, an Austrian artisanal washed-rind hard cheese, over 160 days of ripening. Our results show that Brevibacterium are abundant on Vorarlberger Bergkäse rinds throughout the ripening time. To elucidate the impact of Brevibacterium on cheese production, we analysed the genomes of three cheese rind isolates, L261, S111, and S22. L261 belongs to Brevibacterium aurantiacum, whereas S111 and S22 represent novel species within the genus Brevibacterium based on 16S rRNA gene similarity and average nucleotide identity. Our comparative genomic analysis showed that important cheese ripening enzymes are conserved among the genus Brevibacterium. Strain S22 harbors a 22 kb circular plasmid which encodes putative iron and hydroxymethylpyrimidine/thiamine transporters. Histamine formation in fermented foods can cause histamine intoxication. We revealed the presence of a putative metabolic pathway for histamine degradation. Growth experiments showed that the three Brevibacterium strains can utilize histamine as the sole carbon source. The capability to utilize histamine, possibly encoded by the putative histamine degradation pathway, highlights the importance of Brevibacterium as key cheese ripening cultures beyond their contribution to cheese flavor production.
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Affiliation(s)
- Justin M Anast
- Interdepartmental Microbiology Graduate Program Iowa State University, Ames, IA, USA.,Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Monika Dzieciol
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Dylan L Schultz
- Interdepartmetal Microbiology Undergraduate Program, Iowa State University, Ames, IA, USA
| | - Martin Wagner
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria.,Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFoQSI), Technopark C, 3430, Tulln, Austria
| | - Evelyne Mann
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stephan Schmitz-Esser
- Interdepartmental Microbiology Graduate Program Iowa State University, Ames, IA, USA. .,Department of Animal Science, Iowa State University, Ames, IA, USA.
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13
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Pham NP, Layec S, Dugat-Bony E, Vidal M, Irlinger F, Monnet C. Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat. BMC Genomics 2017; 18:955. [PMID: 29216827 PMCID: PMC5719810 DOI: 10.1186/s12864-017-4322-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains. Results The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe3+/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains. Conclusions Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components. Electronic supplementary material The online version of this article (10.1186/s12864-017-4322-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nguyen-Phuong Pham
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Séverine Layec
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Eric Dugat-Bony
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Marie Vidal
- US 1426, GeT-PlaGe, Genotoul, INRA, 31326, Castanet-Tolosan, France
| | - Françoise Irlinger
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Christophe Monnet
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
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14
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Abstract
Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.
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15
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Evans EE, Mitchell MA, Whittington JK, Roy A, Tully TN. Measuring the Level of Agreement Between Cloacal Gram's Stains and Bacterial Cultures in Hispaniolan Amazon Parrots ( Amazona ventralis ). J Avian Med Surg 2015; 28:290-6. [PMID: 25843466 DOI: 10.1647/2012-042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cloacal or fecal Gram's stains and bacterial cultures are routinely performed during avian physical examinations to assess the microbial flora of the gastrointestinal tract. Although cloacal or fecal Gram's stains and bacterial cultures are considered routine diagnostic procedures, the level of agreement between the individual tests has not been determined. To investigate the level of agreement between results from Gram's stain and bacterial culture when used to assess cloacal or fecal samples from psittacine birds, samples were taken from 21 clinically healthy Hispaniolan Amazon parrots ( Amazona ventralis ) and tested by Gram's stain cytology and bacterial culture. Most bacteria (97.2%) identified by Gram's stain were gram positive. However, gram-negative organisms were identified in 7 of 21 (33.3%; 95% confidence interval: 13.3%-53.3%) birds. Escherichia coli was the only gram-negative organism identified on culture. Agreement between results of Gram's stain and culture was fair (weighted κ = 0.27). The results of this study suggest that Gram's stains and bacterial culture may need to be performed with a parallel testing strategy to limit the likelihood of misclassifying the microbial flora of psittacine patients.
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16
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17
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Shabbiri K, Botting CH, Adnan A, Fuszard M. Charting the cellular and extracellular proteome analysis of Brevibacterium linens DSM 20158 with unsequenced genome by mass spectrometry-driven sequence similarity searches. J Proteomics 2013; 83:99-118. [PMID: 23507220 DOI: 10.1016/j.jprot.2013.02.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 02/27/2013] [Indexed: 11/26/2022]
Abstract
UNLABELLED Brevibacterium linens DSM 20158 is an industrially important actinobacterium which is well-known for the production of amino acids and enzymes. However, as this strain has an unsequenced genome, there is no detailed information regarding its proteome although another strain of this microbe, BL2, has a shotgun genome sequence. However, this still does not cover the entire scope of its proteome. The present study is carried out by first identifying proteins by homology matches using the Mascot search algorithm followed by an advanced approach using de novo sequencing and MS BLAST to expand the B. linens proteome. The proteins identified in the secretome and cellular portion appear to be involved in various metabolic and physiological processes of this unsequenced organism. This study will help to enhance the usability of this strain of B. linens in different areas of research in the future rather than mainly in the food industries. BIOLOGICAL SIGNIFICANCE The present study describes the construction of the first detailed proteomic reference map of B. linens DSM 20158 with unsequenced genome by comparative proteome research analysis. This opens new horizons in proteomics to understand the role of proteins involved in the metabolism and physiology of other organisms with unsequenced genomes.
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Affiliation(s)
- Khadija Shabbiri
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland, United Kingdom
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18
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Franciscon E, Grossman MJ, Paschoal JAR, Reyes FGR, Durrant LR. Decolorization and biodegradation of reactive sulfonated azo dyes by a newly isolated Brevibacterium sp. strain VN-15. SPRINGERPLUS 2012; 1:37. [PMID: 23396675 PMCID: PMC3566399 DOI: 10.1186/2193-1801-1-37] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/17/2012] [Indexed: 12/02/2022]
Abstract
Azo dyes constitute the largest and most versatile class of synthetic dyes used in the textile, pharmaceutical, food and cosmetics industries and represent major components in wastewater from these industrial dying processes. Biological decolorization of azo dyes occurs efficiently under low oxygen to anaerobic conditions. However, this process results in the formation of toxic and carcinogenic amines that are resistant to further detoxification under low oxygen conditions. Moreover, the ability to detoxify these amines under aerobic conditions is not a wide spread metabolic activity. In this study we describe the use of Brevibacterium sp. strain VN-15, isolated from an activated sludge process of a textile company, for the sequential decolorization and detoxification of the azo dyes Reactive Yellow 107 (RY107), Reactive Black 5 (RB5), Reactive Red 198 (RR198) and Direct Blue 71 (DB71). Tyrosinase activity was observed during the biotreatment process suggesting the role of this enzyme in the decolorization and degradation process, but no-activity was observed for laccase and peroxidase. Toxicity, measured using Daphnia magna, was completely eliminated.
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Affiliation(s)
- Elisangela Franciscon
- Department of Food Science, Food Engineering School, University of Campinas, (UNICAMP) Rua Monteiro Lobato 80, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
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19
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Rodriguez H, Reveron I, Doria F, Costantini A, De Las Rivas B, Muňoz R, Garcia-Moruno E. Degradation of ochratoxin a by Brevibacterium species. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:10755-10760. [PMID: 21892825 DOI: 10.1021/jf203061p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability to degrade ochratoxin A was studied in different bacteria with a well-known capacity to transform aromatic compounds. Strains belonging to Rhodococcus, Pseudomonas, and Brevibacterium genera were grown in liquid synthetic culture medium containing ochratoxin A. Brevibacterium spp. strains showed 100% degradation of ochratoxin A. Ochratoxin α was detected and identified by high-performance liquid chromatography-mass spectrometry (HPLC-MS) as a degradation product in the cell-free supernatants. The degradation of ochratoxin A is of public concern for food and environmental safety, because it could contribute to the development of new biological ochratoxin A detoxification systems in foodstuffs. In this study, the degradation of ochratoxin A by bacteria belonging to the food chain was demonstrated for the first time.
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Affiliation(s)
- Hector Rodriguez
- Lab. Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN) , CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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20
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Stahl W, Sies H. Photoprotection by dietary carotenoids: concept, mechanisms, evidence and future development. Mol Nutr Food Res 2011; 56:287-95. [PMID: 21953695 DOI: 10.1002/mnfr.201100232] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/12/2011] [Accepted: 06/16/2011] [Indexed: 01/18/2023]
Abstract
Carotenoids are micronutrients present mainly in fruits and vegetables, and they are ingested from these sources with the diet. They exhibit specific antioxidant activity but also influence signaling and gene expression at the cellular level. β-Carotene and lycopene, the colorants of carrots and tomatoes, respectively, are among the most prominent members of this group of lipids, and they are usually the dominating carotenoids in human blood and tissues. Both compounds modulate skin properties when ingested as supplements or as dietary products. There is evidence that they protect the skin against sunburn (solar erythema) by increasing the basal defense against UV light-mediated damage. Their photoprotective efficacy, however, is not comparable to the use of a sunscreen. In vitro data show that also other carotenoids are efficient photoprotectors. Among them are lutein and structurally unusual phenolic polyenes like 3,3'-dihydroxyisorenieratene.
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Affiliation(s)
- Wilhelm Stahl
- Institute of Biochemistry and Molecular Biology I, Faculty of Medicine, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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21
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Dumas MD, Polson SW, Ritter D, Ravel J, Gelb J, Morgan R, Wommack KE. Impacts of poultry house environment on poultry litter bacterial community composition. PLoS One 2011; 6:e24785. [PMID: 21949751 PMCID: PMC3174962 DOI: 10.1371/journal.pone.0024785] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 08/17/2011] [Indexed: 11/25/2022] Open
Abstract
Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.
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Affiliation(s)
- Michael D. Dumas
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Shawn W. Polson
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America
| | - Don Ritter
- Mountaire Farms Inc., Millsboro, Delaware, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jack Gelb
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Robin Morgan
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
| | - K. Eric Wommack
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
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22
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Dib JR, Wagenknecht M, Hill RT, Farías ME, Meinhardt F. Novel linear megaplasmid from Brevibacterium sp. isolated from extreme environment. J Basic Microbiol 2010; 50:280-4. [PMID: 20473959 DOI: 10.1002/jobm.200900332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Brevibacterium sp. Ap13, isolated from flamingo's feces in Laguna Aparejos, a high-altitude lake located at approximately 4,200 m in the northwest of Argentina was previously found to be resistant to multiple antibiotics, and was therefore screened for plasmids that may be implicated in antibiotic resistance. Brevibacterium sp. Ap13 was found to contain two plasmids of approximately 87 and 436 kb, designated pAP13 and pAP13c, respectively. Only pAP13 was stably maintained and was extensively characterized by pulsed-field gel electrophoresis to reveal that this plasmid is linear and likely has covalently linked terminal proteins associated with its 5' ends. This is the first report of a linear plasmid in the genus Brevibacterium and may provide a new tool for genetic manipulation of this commercially important genus.
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Affiliation(s)
- Julián Rafael Dib
- Planta Piloto de Procesos Industriales Microbiológicos-CONICET, Tucumán, Argentina
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23
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Weidhaas J, Macbeth T, Olsen R, Sadowsky M, Norat D, Harwood V. Identification of a
Brevibacterium
marker gene specific to poultry litter and development of a quantitative PCR assay. J Appl Microbiol 2010; 109:334-47. [DOI: 10.1111/j.1365-2672.2010.04666.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | | | - M.J. Sadowsky
- Department of Soil, Water, and Climate and BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - D. Norat
- Department of Soil, Water, and Climate and BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - V.J. Harwood
- Department of Biology, University of South Florida, Tampa, FL, USA
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24
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Properties and antimicrobial activity of the smear surface cheese coryneform bacterium Brevibacterium linens. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0856-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Onraedt A, De Mey M, Walcarius B, Soetaert W, Vandamme EJ. Transport kinetics of ectoine, an osmolyte produced by Brevibacterium epidermis. Biotechnol Lett 2006; 28:1741-7. [PMID: 16900330 DOI: 10.1007/s10529-006-9149-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 06/26/2006] [Indexed: 11/30/2022]
Abstract
Brevibacterium epidermis DSM 20659 is a halotolerant Gram-positive bacterium which can synthesize the osmolyte, ectoine, but prefers to take it up from its environment. The present study revealed that B. epidermis is equipped with at least one transport system for ectoine, with a maximal transport velocity of 15.7 +/- 4.3 nmol/g CDW.min. The transport requires energy (ATP) and is completely inhibited by the proton uncoupler, CCCP. The ectoine uptake system is constitutively expressed at a basal level of activity and its activity is immediately 10-fold increased by hyper-osmotic stress. Initial uptake rates are not influenced by the intensity of the hyper-osmotic shock but the duration of the increased activity of the uptake system could be directly related to the osmotic strength of the assay solution. Competition assays indicate that betaine, but not proline, is also transported by the ectoine uptake system.
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Affiliation(s)
- A Onraedt
- Laboratory of Industrial Microbiology and Biocatalysis, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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