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Mustafa A, Azim MK, Laraib Q, Rehman QMU. Hybrid constructed wetlands and filamentous fungi for treatment of mixed sewage and industrial effluents. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:44230-44243. [PMID: 38941051 DOI: 10.1007/s11356-024-34037-8] [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: 07/08/2023] [Accepted: 06/15/2024] [Indexed: 06/29/2024]
Abstract
Developing countries face multifaceted problems of water pollution and futile measures to combat water pollution. This study was conducted to explore the potential application of sustainable nature-based solutions, hybrid constructed wetlands, and the application of filamentous fungi to treat polluted river water that receives sewage and industrial wastewater. A pilot-scale hybrid constructed wetland design comprising two types of floating plants in distinct tanks along with a floating wetland and a free-water surface wetland connected in series was commissioned and tested. The system successfully removed organic pollution (BOD 94% and COD 90%), nutrients (NH4-N and NO3-N 67% and PO4-P 81%), and heavy metals (Cr 75%, Ni 56%, and Fe 79%) in 40 h and showed a high buffering capacity to cope with the varying pollutant loads. Metagenomics analysis of treated and untreated samples of river water revealed a diversified spatial bacterial community with ~ 25% sequences related to sulfur-metabolizing bacteria, genus Sulfuricurvum. The application of an immobilized strain of A. niger as a mycoremediation technique was also tested. It successfully removed pollutants in the combined sewage and industrial wastewater present in river water: COD (96%), TSS (97%), NH4-N (65%), NO3-N (67%), and PO4-P (78%). This study demonstrated that hybrid constructed wetlands and mycoremediation can be used as sustainable wastewater treatment options in the local context and also in developing countries where most of the conventional wastewater treatment plants do not operate.
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Affiliation(s)
- Atif Mustafa
- Department of Environmental Engineering, NED University of Engineering and Technology, Karachi, 75270, Pakistan.
| | - Muhammad Kamran Azim
- Department of Biosciences, Mohammad Ali Jinnah University, Karachi, 75400, Pakistan
| | - Qandeel Laraib
- Department of Biosciences, Mohammad Ali Jinnah University, Karachi, 75400, Pakistan
| | - Qazi Muneeb Ur Rehman
- Department of Environmental Engineering, NED University of Engineering and Technology, Karachi, 75270, Pakistan
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Narasimman V, Ramachandran S. Purification, structural characterization, and neuroprotective effect of 3,6-diisobutyl-2,5-piperazinedione from Halomonas pacifica CARE-V15 against okadaic acid-induced neurotoxicity in zebrafish model. J Biochem Mol Toxicol 2024; 38:e23708. [PMID: 38597299 DOI: 10.1002/jbt.23708] [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: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Halomonas pacifica CARE-V15 was isolated from the southeastern coast of India to determine its genome sequence. Secondary metabolite gene clusters were identified using an anti-SMASH server. The concentrated crude ethyl acetate extract was evaluated by GC-MS. The bioactive compound from the crude ethyl acetate extract was fractionated by gel column chromatography. HPLC was used to purify the 3,6-diisobutyl-2,5-piperazinedione (DIP), and the structure was determined using FTIR and NMR spectroscopy. Purified DIP was used in an in silico molecular docking analysis. Purified DIP exhibits a stronger affinity for antioxidant genes like glutathione peroxidase (GPx), glutathione-S-transferase (GST), and glutathione reductase (GSR). Using in silco molecular docking analysis, the protein-ligand binding affinities of GSR (-4.70 kcal/mol), GST (-5.27 kcal/mol), and GPx (-5.37 kcal/mol) were measured. The expression of antioxidant genes were investigated by qRT-PCR. The in vivo reactive oxygen species production, lipid peroxidation, and cell death levels were significantly (p ≤ 0.05) increased in OA-induced group, but all these levels were significantly (p ≤ 0.05) decreased in the purified DIP pretreated group. Purified DIP from halophilic bacteria could thus be a useful treatment for neurological disorders associated with oxidative stress.
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Affiliation(s)
- Vignesh Narasimman
- Native Medicine and Marine Pharmacology Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education (Deemed to be University), Chettinad Health City, Kelambakkam, Tamil Nadu, India
| | - Saravanan Ramachandran
- Native Medicine and Marine Pharmacology Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education (Deemed to be University), Chettinad Health City, Kelambakkam, Tamil Nadu, India
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Hotopp AM, Olsen BJ, Ishaq SL, Frey SD, Kovach AI, Kinnison MT, Gigliotti FN, Roeder MR, Cammen KM. Plumage microorganism communities of tidal marsh sparrows. iScience 2024; 27:108668. [PMID: 38230264 PMCID: PMC10790016 DOI: 10.1016/j.isci.2023.108668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024] Open
Abstract
Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America's Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution.
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Affiliation(s)
- Alice M. Hotopp
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Brian J. Olsen
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Suzanne L. Ishaq
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Serita D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael T. Kinnison
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Franco N. Gigliotti
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Kristina M. Cammen
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
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4
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Wang P, Xie C. Identification and analysis of a clinically isolated strain of Halomonas based on whole-genome sequencing and comparative genomics. Lab Med 2024; 55:80-87. [PMID: 37210212 DOI: 10.1093/labmed/lmad040] [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] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVE The aim of this study was to identify the species of a Halomonas strain isolated from a neonatal blood sample and to understand the potential pathogenicity and characteristic genes of the strain. METHODS The genomic DNA of strain 18071143 (identified as Halomonas by matrix-assisted laser desorption-ionization time of flight-mass spectrometry and the 16S ribosomal RNA (rRNA) gene sequence) was sequenced using Nanopore PromethION platforms. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated using the complete genome sequences of the strain. Comparative genomic analyses were performed on strain 18071143 and 3 strains of Halomonas (Halomonas stevensii S18214, Halomonas hamiltonii KCTC 22154, and Halomonas johnsoniae KCTC 22157) that were associated with human infections and had high genomic similarity to strain 18071143. RESULTS Phylogenetic, ANI, and dDDH similarity analyses based on genome sequence indicated that strain 18071143 belonged to the species H stevensii. Similarities exist between strain 18071143 and the other 3 Halomonas strains in terms of gene structure and protein function. Nonetheless, strain 18071143 has greater potential for DNA replication, recombination, repair, and horizontal transfer. CONCLUSION Whole-genome sequencing holds great promise for accurate strain identification in clinical microbiology. In addition, the results of this study provide data for understanding Halomonas from the perspective of pathogenic bacteria.
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Affiliation(s)
- Pinjia Wang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Chengbin Xie
- Department of Laboratory Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, China
- Department of Laboratory Medicine, Women's and Children's Hospital Affiliated to Chengdu Medical College, Chengdu, China
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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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Tichy J, Waldherr M, Ortbauer M, Graf A, Sipek B, Jembrih-Simbuerger D, Sterflinger K, Piñar G. Pretty in pink? Complementary strategies for analysing pink biofilms on historical buildings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166737. [PMID: 37659529 DOI: 10.1016/j.scitotenv.2023.166737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Salt-weathering is a deterioration mechanism affecting building materials that results from repetitive cycles of salt crystallisation-dissolution in the porous mineral network under changing environmental conditions, causing damage to surfaces. However, an additional biodeterioration phenomenon frequently associated with salt efflorescence is the appearance of coloured biofilms, comprising halotolerant/halophilic microorganisms, containing carotenoid pigments that cause pinkish patinas. In this work, two Austrian historical salt-weathered buildings showing pink biofilms, the St. Virgil's Chapel and the Charterhouse Mauerbach, were investigated. Substrate chemistry (salt concentration/composition) was analysed by ion chromatography and X-ray diffraction to correlate these parameters with the associated microorganisms. Microbiomes were analysed by sequencing full-length 16S rRNA amplicons using Nanopore technology. Data demonstrates that microbiomes are not only influenced by salt concentration, but also by its chemical composition. The chapel showed a high overall halite (NaCl) concentration, but the factor influencing the microbiome was the presence/absence of K+. The K+ areas showed a dominance of Aliifodinibius and Salinisphaera species, capable of tolerating high salt concentrations through the "salt-in" strategy by transporting K+ into cells. Conversely, areas without K+ showed a community shift towards Halomonas species, which favour the synthesis of compatible solutes for salt tolerance. In the charterhouse, the main salts were sulphates. In areas with low concentrations, Rubrobacter species dominated, while in areas with high concentrations, Haloechinothrix species did. Among archaea, Haloccoccus species were dominant in all samples, except at high sulphate concentrations, where Halalkalicoccus prevailed. Finally, the biological pigments visible in both buildings were analysed by Raman spectroscopy, showing the same spectra in all areas investigated, regardless of the building and the microbiomes, demonstrating the presence of carotenoids in the pink biofilms. Comprehensive information on the factors affecting the microbiome associated with salt-weathered buildings should provide the basis for selecting the most appropriate desalination treatment to remove both salt efflorescence and associated biofilms.
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Affiliation(s)
- Johannes Tichy
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria.
| | - Monika Waldherr
- Department of Applied Life Sciences/Bioengineering/Bioinformatics, FH Campus Wien, Favoritenstrasse 226, A-1100 Vienna, Austria
| | - Martin Ortbauer
- Institute for Conservation - Restoration, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Alexandra Graf
- Department of Applied Life Sciences/Bioengineering/Bioinformatics, FH Campus Wien, Favoritenstrasse 226, A-1100 Vienna, Austria
| | - Beate Sipek
- Institute for Conservation - Restoration, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Dubravka Jembrih-Simbuerger
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Katja Sterflinger
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Guadalupe Piñar
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
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Zhou L, Yang X, Wang X, Feng L, Wang Z, Dai J, Zhang H, Xie Y. Effects of bacterial inoculation on lignocellulose degradation and microbial properties during cow dung composting. Bioengineered 2023; 14:213-228. [PMID: 37471462 PMCID: PMC10599258 DOI: 10.1080/21655979.2023.2185945] [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: 05/30/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 07/22/2023] Open
Abstract
Inoculation with exogenous microbial agents is a common method to promote organic waste degradation and improve the quality of compost. However, the biotic effects of different microbial agents are often quite different. To evaluate the potential effects of a complex bacterial agent comprised of three strains (belonging to Bacillus and Geobacillus) on lignocellulose degradation and the underlying microbial mechanisms during cow dung composting, two lab-scale composting experiments, a control and a bacterial inoculation treatment, were established. The results suggest that bacterial inoculation accelerated the rate of temperature increase and extended the thermophilic phase. Compared to those in the negative control group, cellulose, hemicellulose, and lignin degradation rates in the inoculated group increased from 53.3% to 70.0%, 50.2% to 61.3%, and 46.4% to 60.0%, respectively. The microbial community structure and diversity in the compost were clearly changed by the bacterial inoculation. Moreover, stamp analysis showed that inoculation modulated the key compost microbial functional populations linked to the degradation of lignocellulose. Correlation matrix analysis indicated that the expression of bacterial lignocellulolytic enzymes is closely related to key microbial functional populations. Overall, the results confirm the importance of bacterial inoculation, and have important implications for promoting the efficiency and quality of cow dung compost.
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Affiliation(s)
- Liuyan Zhou
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Xinping Yang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Xiaowu Wang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Lei Feng
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Zhifang Wang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Jinping Dai
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Huitao Zhang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
| | - Yuqing Xie
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, XinjiangPR China
- Xinjiang Key Laboratory of Special Environmental Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, PR China
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Hernández-Soto LM, Martínez-Abarca F, Ramírez-Saad H, López-Pérez M, Aguirre-Garrido JF. Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas. BMC Genomics 2023; 24:696. [PMID: 37986038 PMCID: PMC10662389 DOI: 10.1186/s12864-023-09800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.
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Affiliation(s)
- Luis Mario Hernández-Soto
- Doctorado en Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Francisco Martínez-Abarca
- Estructura, Dinámica y Función de Genomas de Rizobacterias, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - Hugo Ramírez-Saad
- Departamento Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de Mexico, México
| | - Marcos López-Pérez
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México.
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Veloso M, Waldisperg A, Arros P, Berríos-Pastén C, Acosta J, Colque H, Varas MA, Allende ML, Orellana LH, Marcoleta AE. Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes. Microorganisms 2023; 11:2819. [PMID: 38004830 PMCID: PMC10673233 DOI: 10.3390/microorganisms11112819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.
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Affiliation(s)
- Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Angie Waldisperg
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Joaquín Acosta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Hazajem Colque
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Macarena A. Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Miguel L. Allende
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany;
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
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Xu W, Lv Z, Guo Q, Deng Z, Yang C, Cao Z, Li Y, Huang C, Wu Z, Chen S, He Y, Sun J, Liu Y, Gan L. Selective Antagonism of Lactiplantibacillus plantarum and Pediococcus acidilactici against Vibrio and Aeromonas in the Bacterial Community of Artemia nauplii. Microbiol Spectr 2023; 11:e0053323. [PMID: 37428079 PMCID: PMC10434253 DOI: 10.1128/spectrum.00533-23] [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: 02/09/2023] [Accepted: 06/16/2023] [Indexed: 07/11/2023] Open
Abstract
Empiric probiotics are commonly consumed by healthy individuals as a means of disease prevention, pathogen control, etc. However, controversy has existed for a long time regarding the safety and benefits of probiotics. Here, two candidate probiotics, Lactiplantibacillus plantarum and Pediococcus acidilactici, which are antagonistic to Vibrio and Aeromonas species in vitro, were tested on Artemia under in vivo conditions. In the bacterial community of Artemia nauplii, L. plantarum reduced the abundance of the genera Vibrio and Aeromonas and P. acidilactici significantly increased the abundance of Vibrio species in a positive dosage-dependent manner, while higher and lower dosages of P. acidilactici increased and decreased the abundance of the genus Aeromonas, respectively. Based on the liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) analyses of the metabolite of L. plantarum and P. acidilactici, pyruvic acid was used in an in vitro test to explain such selective antagonism; the results showed that pyruvic acid was conducive or suppressive to V. parahaemolyticus and beneficial to A. hydrophila. Collectively, the results of this study demonstrate the selective antagonism of probiotics on the bacterial community composition of aquatic organisms and the associated pathogens. IMPORTANCE Over the last decade, the common preventive method for controlling potential pathogens in aquaculture has been the use of probiotics. However, the mechanisms of probiotics are complicated and mostly undefined. At present, less attention has been paid to the potential risks of probiotic use in aquaculture. Here, we investigated the effects of two candidate probiotics, L. plantarum and P. acidilactici, on the bacterial community of Artemia nauplii and the in vitro interactions between these two candidate probiotics and two pathogens, Vibrio and Aeromonas species. The results demonstrated the selective antagonism of probiotics on the bacterial community composition of an aquatic organism and its associated pathogens. This research contributes to providing a basis and reference for the long-term rational use of probiotics and to reducing the inappropriate use of probiotics in aquaculture.
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Affiliation(s)
- Weihua Xu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Zhaolin Lv
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Qingqi Guo
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Zhaojie Deng
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Canmin Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Zhaozhao Cao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Yi Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Cuifen Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Zizhan Wu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Shijun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Yuhui He
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Jijia Sun
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Yiying Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangzhou, China
| | - Lian Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
- Guangdong Laboratory for Linnan Modern Agriculture, Guangzhou, China
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11
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Bitalac JMS, Lantican NB, Gomez NCF, Onda DFL. Attachment of potential cultivable primo-colonizing bacteria and its implications on the fate of low-density polyethylene (LDPE) plastics in the marine environment. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131124. [PMID: 36871466 DOI: 10.1016/j.jhazmat.2023.131124] [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: 09/16/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Plastics released in the environment become suitable matrices for microbial attachment and colonization. Plastics-associated microbial communities interact with each other and are metabolically distinct from the surrounding environment. However, pioneer colonizing species and their interaction with the plastic during initial colonization are less described. Marine sediment bacteria from sites in Manila Bay were isolated via a double selective enrichment method using sterilized low-density polyethylene (LDPE) sheets as the sole carbon source. Ten isolates were identified to belong to the genera Halomonas, Bacillus, Alteromonas, Photobacterium, and Aliishimia based on 16S rRNA gene phylogeny, and majority of the taxa found exhibit a surface-associated lifestyle. Isolates were then tested for their ability to colonize polyethylene (PE) through co-incubation with LDPE sheets for 60 days. Growth of colonies in crevices, formation of cell-shaped pits, and increased roughness of the surface indicate physical deterioration. Fourier-transform infrared (FT-IR) spectroscopy revealed significant changes in the functional groups and bond indices on LDPE sheets separately co-incubated with the isolates, demonstrating that different species potentially target different substrates of the photo-oxidized polymer backbone. Understanding the activity of primo-colonizing bacteria on the plastic surface can provide insights on the possible mechanisms used to make plastic more bioavailable for other species, and their implications on the fate of plastics in the marine environment.
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Affiliation(s)
- Justine Marey S Bitalac
- The Marine Science Institute, University of the Philippines Diliman, 1101 Quezon City, Philippines; Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Nacita B Lantican
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Norchel Corcia F Gomez
- The Marine Science Institute, University of the Philippines Diliman, 1101 Quezon City, Philippines; Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Deo Florence L Onda
- The Marine Science Institute, University of the Philippines Diliman, 1101 Quezon City, Philippines.
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12
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Bao Y, Chen Y, Wang F, Xu Z, Zhou S, Sun R, Wu X, Yan K. East Asian monsoon manipulates the richness and taxonomic composition of airborne bacteria over China coastal area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162581. [PMID: 36889406 DOI: 10.1016/j.scitotenv.2023.162581] [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: 11/19/2022] [Revised: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Airborne bacteria may have significant impacts on aerosol properties, public health and ecosystem depending on their taxonomic composition and transport. This study investigated the seasonal and spatial variations of bacterial composition and richness over the east coast of China and the roles of East Asian monsoon played through synchronous sampling and 16S rRNA sequencing analysis of airborne bacteria at Huaniao island of the East China Sea (ECS) and the urban and rural sites of Shanghai. Airborne bacteria showed higher richness over the land sites than Huaniao island with the highest values found in the urban and rural springs associated with the growing plants. For the island, the maximal richness occurred in winter as the result of prevailing terrestrial winds controlled by East Asian winter monsoon. Proteobacteria, Actinobacteria and Cyanobacteria were found to be top three phyla, together accounting for 75 % of total airborne bacteria. Radiation-resistant Deinococcus, Methylobacterium belonging to Rhizobiales (related to vegetation) and Mastigocladopsis_PCC_10914 originating from marine ecosystem were indicator genera for urban, rural and island sites, respectively. The Bray-Curits dissimilarity of taxonomic composition between the island and two land sites was the lowest in winter with the representative genera over island also typically from the soil. Our results reveal that seasonal change of monsoon wind directions evidently affects the richness and taxonomic composition of airborne bacteria in China coastal area. Particularly, prevailing terrestrial winds lead to the dominance of land-derived bacteria over the coastal ECS which may have a potential impact on marine ecosystem.
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Affiliation(s)
- Yang Bao
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Ying Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China; Institute of Eco-Chongming (IEC), National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Shanghai 202162, China.
| | - Fanghui Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Zongjun Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Shengqian Zhou
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Ruihua Sun
- Pudong New District Environmental Monitoring Station, Shanghai 200135, China
| | - Xiaowei Wu
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Ke Yan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
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He L, Yang BZ, Ma YJ, Wen L, Liu F, Zhang XJ, Liu TQ. Differences in clinical features and gut microbiota between individuals with methamphetamine casual use and methamphetamine use disorder. Front Cell Infect Microbiol 2023; 13:1103919. [PMID: 36909722 PMCID: PMC9996337 DOI: 10.3389/fcimb.2023.1103919] [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: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Background The transition from methamphetamine (MA) casual use (MCU) to compulsive use is enigmatic as some MA users can remain in casual use, but some cannot. There is a knowledge gap if gut microbiota (GM) play a role in differing MCU from MA use disorder (MUD). We aimed to investigate the clinical features and GM differences between individuals with MCU and MUD. Method We recruited two groups of MA users -MCU and MUD - and matched them according to age and body mass index (n=21 in each group). Participants were accessed using the Semi-Structured Assessment for Drug Dependence and Alcoholism, and their fecal samples were undergone 16S ribosomal DNA sequencing. We compared the hosts' clinical features and GM diversity, composition, and structure (represented by enterotypes) between the two groups. We have identified differential microbes between the two groups and performed network analyses connecting GM and the clinical traits. Result Compared with the casual users, individuals with MUD had higher incidences of MA-induced neuropsychiatric symptoms (e.g., paranoia, depression) and withdrawal symptoms (e.g., fatigue, drowsiness, and increased appetite), as well as stronger cravings for and intentions to use MA, and increased MA tolerance. The GM diversity showed no significant differences between the two groups, but four genera (Halomonas, Clostridium, Devosia, and Dorea) were enriched in the individuals with MUD (p<0.05). Three distinct enterotypes were identified in all MA users, and Ruminococcus-driven enterotype 2 was dominant in individuals with MUD compared to the MCU (61.90% vs. 28.60%, p=0.03). Network analysis shows that Devosia is the hub genus (hub index = 0.75), which is not only related to the counts of the MUD diagnostic criteria (ρ=0.40; p=0.01) but also to the clinical features of MA users such as reduced social activities (ρ=0.54; p<0.01). Devosia is also associated with the increased intention to use MA (ρ=0.48; p<0.01), increased MA tolerance (ρ=0.38; p=0.01), craving for MA (ρ=0.37; p=0.01), and MA-induced withdrawal symptoms (p<0.05). Conclusion Our findings suggest that Ruminococcus-driven enterotype 2 and the genera Devosia might be two influential factors that differentiate MA casual use from MUD, but further studies are warranted.
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Affiliation(s)
- Li He
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - Yue-Jiao Ma
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Wen
- Department of Internal Medicine, Section of Endocrinology & Core Laboratory of Yale Center for Clinical Investigation, Yale University School of Medicine, New Haven, CT, United States
| | - Feng Liu
- Compulsory Detoxification Center of Changsha Public Security Bureau, Changsha, Hunan, China
| | - Xiao-Jie Zhang
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Tie-Qiao Liu
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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14
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Ma Y, You F, Parry D, Urban A, Huang L. Adaptive growth and acidogenic fermentation performance of haloalkaliphilic bacterial communities enriched from biofilms colonising strongly alkaline and saline bauxite residue. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159131. [PMID: 36183768 DOI: 10.1016/j.scitotenv.2022.159131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The present study aimed to characterise the adaptive growth and acidogenic fermentation performance of haloalkaliphilic bacteria sourced from field biofilms colonising seawater-treated bauxite residue, under moderate and extremely alkaline pH conditions (8.5 to 10.8) and coupled saline (EC ≈ 50 mS/cm) conditions. The haloalkaliphilic bacterial communities demonstrated strong adaptiveness to the increasing pH from 8.5 to 10.8. The dominant groups were Exiguobacterales and Bacillales at pH 8.5 and 10, but Lactobacillales and Bacillales at pH 10.8. The exposure to pH 10.8 initially delayed bacterial growth in the first 24 h, but which rapidly recovered to a peak rate at 48 h similar to that in the pH 10 treatment. Correspondingly, lactic acid concentration at pH 10.8 rapidly rose to as high as >2000 mg/L at 48 h. Bacterial growth and organic acid production were positively related to carbohydrate supply. Overall, these bacterial groups fermented glucose to produce mainly lactic acid (>80 %) and other acids (such as acetic acid, formic acid, and succinic acid), leading to 0.5-2.0 units of pH reduction, despite the strong buffering capacity in the culture solution. The bacteria could up-regulate their phosphatase activity to mineralise the organic P in the basal nutrient broth, but increasing soluble phosphate-P at a 1:10 of glucose-C was beneficial. The biofilm-sourced bacteria communities contained redundant fermentative haloalkaliphilic groups which were adaptive to strongly alkaline pH and saline conditions.
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Affiliation(s)
- Yuanying Ma
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - David Parry
- Rio Tinto, Brisbane, Queensland 4000, Australia
| | - Anja Urban
- Queensland Alumina Limited, Gladstone, Queensland 4680, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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Song X, Zhai Y, Song J, Zhang J, Li X. The structural discrepancy between the small and large gut microbiota of Asiatic toad (Bufo gargarizans) during hibernation. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01031-5. [PMID: 36637770 DOI: 10.1007/s12223-023-01031-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/01/2023] [Indexed: 01/14/2023]
Abstract
Hibernating amphibians are suitable for the research on the adaptation of gut microbiota to long-term fasting and cold stresses. However, the previous studies mainly focus on the large or whole gut microbiota but not the small gut microbiota. To test the structural discrepancy between the small and large gut microbiota during hibernation, we performed two independent batches of 16S rRNA gene amplicon sequencing to profile the small and large gut microbiota of hibernating Asiatic toad (Bufo gargarizans) from two wild populations. Both batches of data revealed that Proteobacteria, Bacteroidetes, and Firmicutes were the three most dominant phyla in the small and large gut microbiota. Three core OTUs with 100% occurrence in all gut microbiotas were annotated as Pseudomonas. A significant structural discrepancy was detected between the small and large gut microbiota. For instance, Proteobacteria assembled in the small intestine with a higher proportion than it did in the large intestine, but Bacteroidetes and Firmicutes assembled in the large intestine with a higher proportion than they did in the small intestine. The large gut microbiota exhibited higher diversity than the small gut microbiota. Nevertheless, a severe batch effect existed in the structural analysis of the gut microbiotas. The large gut microbiota showed a better resistance to the batch effect than the small gut microbiota did. This study provides preliminary evidence that microbes assemble in the small and large intestines of amphibians with discrepant patterns during hibernation.
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Affiliation(s)
- Xiaowei Song
- College of Software Engineering, Chengdu University of Information and Technology, Chengdu, Sichuan, China. .,College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, Henan, China. .,CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.
| | - Yuanyuan Zhai
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, Henan, China
| | - Jinghan Song
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, Henan, China
| | - Jingwei Zhang
- Hospital of Xinyang Normal University, Xinyang Normal University, Henan, Xinyang, China
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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16
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Wang L, Cui YW, Jian L, Yao JL. Spontaneous granulation of moderately halophilic sludge inoculated with saltern sediments from single granule into multi-granule aggregation. ENVIRONMENTAL RESEARCH 2023; 216:114813. [PMID: 36395863 DOI: 10.1016/j.envres.2022.114813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
There is very limited research on the application of moderate halophiles for biotreatment of hypersaline wastewater widely generated from some industries. This study demonstrated the development of moderate halophiles inoculated from saltern sediments into aerobic granule sludge (AGS) to treat hypersaline wastewater with a salinity of 100 g/L. The granulation of moderate halophiles can occur without applying the settling velocity selective pressure. The saltern sediment initially aggregated into single small granules and finally developed into 1200 ± 50 μm multiparticle granules. The halophiles affiliated in Halomonas was dominant in the granular bacterial community, with a relative abundance of 94.52%. Halomonas ventosae secreted sulfated polysaccharides. The sulfated polysaccharides content accounted for 63.95 ± 2.10% in the polysaccharides (PS), having an adhesive role in connecting single granules. Multiparticle granules showed the clear stratified structure, with α-D-glucopyranose polysaccharides in the inner bounders and β-D-glucopyranose polysaccharides in the outer. The moderately granular sludge showed the stable chemical oxygen demand (COD) removal efficiency of >90% and the aerobic total inorganic nitrogen (TIN) removal efficiency (equal to ammonia removal) of 70 ± 5.00%. This paper contributes new insight into the formation of moderately halophilic granular sludge and accelerates the application of moderately halophilic granular sludge to treat hypersaline wastewater.
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Affiliation(s)
- Ling Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - You-Wei Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Li Jian
- China Academy of Transportation Sciences, Huixinli Chaoyang District, P.R.C, Beijing, 100029, China
| | - Jia-Lin Yao
- China Academy of Transportation Sciences, Huixinli Chaoyang District, P.R.C, Beijing, 100029, China
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Ni J, Yang Z, Zhang Y, Ma Y, Xiong H, Jian W. Aaqueous exposure to silver nanoparticles synthesized by abalone viscera hydrolysates promotes the growth, immunity and gut health of zebrafish ( Danio rerio). Front Microbiol 2022; 13:1048216. [PMID: 36569079 PMCID: PMC9772453 DOI: 10.3389/fmicb.2022.1048216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Silver nanoparticles (AgNPs) have the potential to be used in aquaculture, but their influence on the growth and health of aquatic organisms has not been extensively investigated. In this study, the abalone viscera hydrolysates decorated AgNPs (AVH-AgNPs) were dispersed into aquaculture water at different concentrations (0, 6, 9, and 18 μg/l) to evaluate the biological effects on zebrafish (Danio rerio). The results showed that the AVH-AgNPs treatments of 6 and 9 μg/l promoted the growth and did not cause obvious damage to the gills, intestines, and livers of zebrafish. All the treatments induced catalase (CAT) and superoxide dismutase (SOD) activities and increased glutathione (GSH) content in the livers and upregulated the expression of immune related genes. The effects of 9 and 18 μg/l AVH-AgNPs treatments were more obvious. After AVH-AgNPs treatment, the abundances of some potential pathogens, such as species Plesimonas shigelloides and Pseudomonas alcaligenes and genus Flavobacterium decreased significantly. In contrast, the abundance of some beneficial bacteria that can degrade pollutants and toxins (e.g., Rhodococcus erythropolis) increased significantly. Thus, the application of low concentrations (6 ~ 18 μg/l) of AVH-AgNPs in aquaculture water is relatively safe and has a positive effect on zebrafish farming.
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Affiliation(s)
- Jing Ni
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Zhuan Yang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Yue Zhang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Ying Ma
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China,*Correspondence: Ying Ma,
| | - Hejian Xiong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China,Hejian Xiong,
| | - Wenjie Jian
- Xiamen Medical College, Institute of Respiratory Diseases, Xiamen, China,Wenjie Jian,
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Kokoulin MS, Sigida EN, Kuzmich AS, Ibrahim IM, Fedonenko YP, Konnova SA. Structure and antiproliferative activity of the polysaccharide from Halomonas aquamarina related to Cobetia pacifica. Carbohydr Polym 2022; 298:120125. [DOI: 10.1016/j.carbpol.2022.120125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/02/2022]
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Xiong J, Liao XS, Yin T, Liu XC, Bao L, Li LQ. Alterations of the gut microbiota and short chain fatty acids in necrotizing enterocolitis and food protein-induced allergic protocolitis infants: A prospective cohort study. Front Cell Infect Microbiol 2022; 12:1030588. [PMID: 36478672 PMCID: PMC9720398 DOI: 10.3389/fcimb.2022.1030588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Background Even though presenting with similar clinical manifestations, necrotizing enterocolitis (NEC) and food protein-induced allergic protocolitis (FPIAP) have completely different treatments and prognosis. Our study aimed to quantify and evaluate differences in gut microbiota and short chain fatty acids (SCFAs) between infants with NEC and FPIAP to better identify these two diseases in clinical settings. Methods A total of 43 infants with NEC or FPIAP in Children's Hospital of Chongqing Medical University, China between December 2020 and December 2021 were enrolled. Stool samples were prospectively collected and froze. Infants defined as NEC were those who presented with clinical courses consistent with NEC and whose radiographs fulfilled criteria for Bell's stage 2 or 3 NEC, while those who were healthy in appearance and had blood in the stool (visible or may be microscopic), had normal bowel sounds in physical examination, were resolved after eliminating the causative food, and/or had recurrence of symptoms after oral food challenge (OFC) were defined as FPIAP. Primers specific for bacterial 16S rRNA genes were used to amplify and pyrosequence fecal DNA from stool samples. Gas chromatography-mass spectrometry (GC-MS) technology was used to determine the concentrations of SCFAs. Results Among the 43 infants, 22 were diagnosed with NEC and 21 were diagnosed with FPIAP. The microbial community structure in NEC infant stools differed significantly from those in FPIAP infant stools. NEC infants had significantly higher proportion of Actinobacteria and reduced proportion of Bacteroidetes compared with FPIAP infants, and the proportions of Halomonas, Acinetobacter, Bifidobacterium, and Stenotrophomonas in NEC infants were significantly higher than that of FPIAP infants. In addition, infants with NEC had significantly lower levels of acetic acid, propionic acid, butyric acid, isovaleric acid, and total SCFAs, and higher level of hexanoic acid as compared to the infants of the FPIAP group. Conclusions The differences of gut microbiota composition and concentrations of SCFAs might represent suitable biomarker targets for early identification of NEC and FPIAP.
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Affiliation(s)
- Jing Xiong
- Neonatal Diagnosis and Treatment Center of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatric, Chongqing, China
| | - Xing-Sheng Liao
- Department of Neonatology, The first People’s Hospital of Jiulongpo District, Chongqing, China
| | - Tong Yin
- Neonatal Diagnosis and Treatment Center of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatric, Chongqing, China
| | - Xiao-Chen Liu
- Neonatal Diagnosis and Treatment Center of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatric, Chongqing, China
| | - Lei Bao
- Neonatal Diagnosis and Treatment Center of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatric, Chongqing, China,*Correspondence: Lei Bao, ; Lu-Quan Li,
| | - Lu-Quan Li
- Neonatal Diagnosis and Treatment Center of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatric, Chongqing, China,*Correspondence: Lei Bao, ; Lu-Quan Li,
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Williamson JR, Callaway TR, Lourenco JM, Ryman VE. Characterization of rumen, fecal, and milk microbiota in lactating dairy cows. Front Microbiol 2022; 13:984119. [PMID: 36225385 PMCID: PMC9549371 DOI: 10.3389/fmicb.2022.984119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p < 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p < 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p < 0.001). While diversity indices were not linked (p > 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.
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21
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Dong H, Zhang F, Xu T, Liu Y, Du Y, Wang C, Liu T, Gao J, He Y, Wang X, Sun S, She Y. Culture-dependent and culture-independent methods reveal microbe-clay mineral interactions by dissimilatory iron-reducing bacteria in an integral oilfield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156577. [PMID: 35688243 DOI: 10.1016/j.scitotenv.2022.156577] [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: 04/05/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Fe(III) may be reasonably considered as one of the most important electron acceptors in petroleum reservoir ecosystems. The microbial mineralization of clay minerals, especially montmorillonite, is also of great significance to the exploration of petroleum and gas reservoirs. The bioreduction mechanisms of iron-poor minerals in petroleum reservoirs have been poorly investigated. This study investigated the bioreduction of montmorillonite by dissimilatory iron-reducing bacteria (DIRB) in petroleum reservoirs based on culture-independent and culture-dependent methods. Microbial diversity analysis revealed that Halolactibacillus, Bacillus, Alkaliphilus, Shewanella, Clostridium, and Pseudomonas were the key genera involved in the bioreduction of Fe(III). Through the traditional culture-dependent method, most of the key genera were isolated from the samples collected from petroleum reservoirs. Traditional culture-dependent methods can be used to reveal the metabolic characteristics of microorganisms (such as iron-reduction efficiency) to further elucidate the roles of different species (B. subtilis and B. alkalitelluris) in the environment. Moreover, many species with high iron-reduction efficiencies and relatively low abundances in the samples, such as Tessaracoccus and Flaviflexus, were isolated from petroleum reservoirs for the first time. The combination of culture-dependent and culture-independent methods can be used to further the understanding of the microbial communities and the metabolic characteristics of DIRB in petroleum reservoirs. Structural alterations that occurred during the interactions of microorganisms and montmorillonite were revealed through scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRD). The physical and chemical analysis results demonstrated that microorganisms from petroleum reservoirs can dissolve iron-poor montmorillonite and promote the release of interlayer water. The secondary minerals illite and clinoptilolite were observed in bioreduced smectite. The formation of secondary minerals was closely related to the dissolution degrees of minerals based on iron reduction.
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Affiliation(s)
- Hao Dong
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China.
| | - Fan Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, College of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China
| | - Ting Xu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Yulong Liu
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Ying Du
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Chen Wang
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Tiansheng Liu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Ji Gao
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Yanlong He
- College of Petroleum Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Xiaotong Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Sun
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Yuehui She
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China.
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Huang G, Wang S, Wang J, Tian L, Yu Y, Zuo X, Li Y. Bile reflux alters the profile of the gastric mucosa microbiota. Front Cell Infect Microbiol 2022; 12:940687. [PMID: 36159635 PMCID: PMC9500345 DOI: 10.3389/fcimb.2022.940687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
Background Bile reflux can cause inflammation, gastric mucosa atrophy, and diseases such as stomach cancer. Alkaline bile flowing back into the stomach affects the intragastric environment and can alter the gastric bacterial community. We sought to identify the characteristics of the stomach mucosal microbiota in patients with bile reflux. Methods Gastric mucosal samples were collected from 52 and 40 chronic gastritis patients with and without bile reflux, respectively. The bacterial profile was determined using 16S rRNA gene analysis. Results In the absence of H. pylori infection, the richness (based on the Sobs and Chao1 indices; P <0.05) and diversity (based on Shannon indices; P <0.05) of gastric mucosa microbiota were higher in patients with bile reflux patients than in those without. There was a marked difference in the microbiota structure between patients with and without bile reflux (ANOSIM, R=0.058, P=0.011). While the genera, Comamonas, Halomonas, Bradymonas, Pseudomonas, Marinobacter, Arthrobacter, and Shewanella were enriched in patients with bile reflux, the genera, Haemophilus, Porphyromonas, and Subdoligranulum, were enriched in those without bile reflux. Conclusion Our results demonstrate that bile reflux significantly alters the composition of the gastric microbiota.
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Huang Z, Zhan M, Cheng G, Lin R, Zhai X, Zheng H, Wang Q, Yu Y, Xu Z. IHNV Infection Induces Strong Mucosal Immunity and Changes of Microbiota in Trout Intestine. Viruses 2022; 14:v14081838. [PMID: 36016461 PMCID: PMC9415333 DOI: 10.3390/v14081838] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The fish intestinal mucosa is among the main sites through which environmental microorganisms interact with the host. Therefore, this tissue not only constitutes the first line of defense against pathogenic microorganisms but also plays a crucial role in commensal colonization. The interaction between the mucosal immune system, commensal microbiota, and viral pathogens has been extensively described in the mammalian intestine. However, very few studies have characterized these interactions in early vertebrates such as teleosts. In this study, rainbow trout (Oncorhynchus mykiss) was infected with infectious hematopoietic necrosis virus (IHNV) via a recently developed immersion method to explore the effects of viral infection on gut immunity and microbial community structure. IHNV successfully invaded the gut mucosa of trout, resulting in severe tissue damage, inflammation, and an increase in gut mucus. Moreover, viral infection triggered a strong innate and adaptive immune response in the gut, and RNA−seq analysis indicated that both antiviral and antibacterial immune pathways were induced, suggesting that the viral infection was accompanied by secondary bacterial infection. Furthermore, 16S rRNA sequencing also revealed that IHNV infection induced severe dysbiosis, which was characterized by large increases in the abundance of Bacteroidetes and pathobiont proliferation. Moreover, the fish that survived viral infection exhibited a reversal of tissue damage and inflammation, and their microbiome was restored to its pre−infection state. Our findings thus demonstrated that the relationships between the microbiota and gut immune system are highly sensitive to the physiological changes triggered by viral infection. Therefore, opportunistic bacterial infection must also be considered when developing strategies to control viral infection.
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Affiliation(s)
- Zhenyu Huang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengting Zhan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaofeng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqi Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiou Zheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchao Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhen Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence:
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Mocé ML, Esteve IC, Pérez-Fuentes S, Gómez EA, Mocé E. Microbiota in Goat Buck Ejaculates Differs Between Breeding and Non-breeding Seasons. Front Vet Sci 2022; 9:867671. [PMID: 35647092 PMCID: PMC9136232 DOI: 10.3389/fvets.2022.867671] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/21/2022] [Indexed: 01/04/2023] Open
Abstract
Changes in semen microbiota are associated with alterations to sperm quality and fertility. However, the microbiota from most livestock species has not yet been studied. Goats are seasonal breeders, but semen microbiota has never been described in this species, and it is unknown how seasonality affects it. Our study objective is 2-fold: to describe the microbiota in goat buck ejaculates and to determine if it differs between breeding and non-breeding seasons. Semen from six males of the Murciano-Granadina breed was collected during both seasons. Two replicates were performed per male and season on different days. The microbiota was characterized by genomic sequencing technology. Sperm quality was also evaluated. Repetition was not significant for the studied variables. Sperm velocities were higher for the breeding than for the non-breeding season. The ejaculates from both seasons also differed in the proportion of apoptotic spermatozoa. The five dominant phyla were Firmicutes, Proteobacteria, Fusobacteria, Actinobacteria, and Bacteroidetes during the breeding season and Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria during the non-breeding season. The dominant genus during both seasons was Ureaplasma. Differences in microbial community structure (the beta diversity) were found. A decrease in the relative abundance of the genus Faecalibacterium and an increase in the genera Sphingomonas and Halomonas were observed in the ejaculates collected during the breeding season. Sphingomonas and Faecalibacterium abundance favorably and unfavorably correlated with sperm quality, respectively. In conclusion, the semen microbiota from goat bucks varies between breeding and non-breeding seasons, and the microbiota remains stable for 7 days within a season. In addition, the genera Sphingomonas and Faecalibacterium could be possible biomarkers of semen quality in goat bucks. These results contribute to an in-depth understanding of the effects of reproductive seasonality on goat buck ejaculates.
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Affiliation(s)
- María Lorena Mocé
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology (PASAPTA), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
| | - Inés Carolina Esteve
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Sara Pérez-Fuentes
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Ernesto A. Gómez
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Eva Mocé
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- *Correspondence: Eva Mocé
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Abosamaha A, Williamson MP, Gilmour DJ. Utilization and accumulation of compatible solutes in Halomonas pacifica: a species of moderately halophilic bacteria isolated from a saline lake in South Libya. Access Microbiol 2022; 4:acmi000359. [PMID: 36003353 PMCID: PMC9394535 DOI: 10.1099/acmi.0.000359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
When grown in high salt concentrations, halophilic bacteria often accumulate compatible solutes, which have major applications in biotechnology because they stabilize cells and proteins. Four Gram-negative bacterial strains, belonging to the family Halomonadaceae, were isolated from Qaberoun and Um-Alma lakes in South Libya using high-salinity medium. The strains were identified using 16S rRNA gene sequencing as belonging to Halomonas pacifica (strain ABQ1), Halomonas venusta (ABQ2), Halomonas elongata (ABU1) and Halomonas salifodinae (ABU2). H. pacifica ABQ1 is a moderate halophile (salinity range 0.05 to 2.5 M NaCl), with a broad tolerance to pH (7 to 9) and temperature (25–37 °C). Addition of the compatible solutes glycine betaine (betaine) and ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) to the medium had a positive effect on growth of H. pacifica at 2 M NaCl. In rich LB medium, betaine was the major compatible solute accumulated, with ectoine only being accumulated at salinities in excess of 1 M NaCl. In minimal M9 medium, betaine was not produced, but increasing amounts of ectoine were synthesized with increasing salinity, and hydroxyectoine [(4S,5S)−5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid] was also synthesized when the cells were grown in very high salt. We have thus identified H. pacifica as a producer of ectoine and hydroxyectoine, with more being produced at higher salinities. As industrial demand for these compatible solutes continues to increase, this system has biotechnological potential.
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Affiliation(s)
- Abdolkader Abosamaha
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - D. James Gilmour
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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Kalaitzidou MP, Alvanou MV, Papageorgiou KV, Lattos A, Sofia M, Kritas SK, Petridou E, Giantsis IA. Pollution Indicators and HAB-Associated Halophilic Bacteria Alongside Harmful Cyanobacteria in the Largest Mussel Cultivation Area in Greece. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095285. [PMID: 35564680 PMCID: PMC9104808 DOI: 10.3390/ijerph19095285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022]
Abstract
Taking into consideration the essential contribution of Mytilus galloprovincialis farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six Mytilus galloprovincialis aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera (Halomonas sp., Planococcus sp., Sulfitobacter sp., and Synechocystis sp.). Members of the Halomonas and Sulfitobacter genera have been isolated from highly polluted sites, Planococcus bacteria have been identified in samples derived directly from plastic debris, and Synechocystis bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.
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Affiliation(s)
- Maria P. Kalaitzidou
- National Reference Laboratory for Marine Biotoxins, Department of Food Microbiology, Biochemical Control, Residues, Marine Biotoxins and Other Water Toxins, Directorate of Veterinary Center of Thessaloniki, Ministry of Rural Development and Food, 54627 Thessaloniki, Greece;
| | - Maria V. Alvanou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Konstantinos V. Papageorgiou
- 3rd Military Veterinary Hospital, General Staff, Hellenic Ministry of Defense, 15th Km Thessaloniki-Vasilika, 57001 Thessaloniki, Greece;
| | - Athanasios Lattos
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
| | - Spyridon K. Kritas
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Evanthia Petridou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
- Correspondence:
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Basili M, Techtmann SM, Zaggia L, Luna GM, Quero GM. Partitioning and sources of microbial pollution in the Venice Lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151755. [PMID: 34848267 DOI: 10.1016/j.scitotenv.2021.151755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/25/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Microbial pollutants are a serious threat to human and environmental health in coastal areas. Based on the hypothesis that pollution from multiple sources may produce a distinct microbial signature and that microbial pollutants seem to distribute between a free-living and a particle-attached fraction, we investigated the occurrence, partitioning and sources of microbial pollutants in water samples collected in the Venice Lagoon (Italy). The area was taken as a case study of an environment characterized by a long history of industrial pollution and by growing human pressure. We found a variety of pollutants from several sources, with sewage-associated and faecal bacteria accounting for up to 5.98% of microbial communities. Sewage-associated pollutants were most abundant close to the city centre. Faecal pollution was highest in the area of the industrial port and was dominated by human inputs, whereas contamination from animal faeces was mainly detected at the interface with the mainland. Microbial pollutants were almost exclusively associated with the particle-attached fraction. The samples also contained other potential pathogens. Our findings stress the need for monitoring and managing microbial pollution in highly urbanized lagoon and semi-enclosed systems and suggest that management plans to reduce microbial inputs to the waterways should include measures to reduce particulate matter inputs to the lagoon. Finally, High-Throughput Sequencing combined with computational approaches proved critical to assess water quality and appears to be a valuable tool to support the monitoring of waterborne diseases.
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Affiliation(s)
- Marco Basili
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, United States
| | - Luca Zaggia
- CNR IGG, National Research Council - Institute of Geosciences and Earth Resources, Via G. Gradenigo 6, 35131 Padova, Italy
| | - Gian Marco Luna
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Grazia Marina Quero
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125 Ancona, Italy.
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Bischofberger AM, Hall AR. Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment. Mol Ecol 2022; 32:2619-2632. [PMID: 35377495 DOI: 10.1111/mec.16456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 03/28/2022] [Indexed: 11/30/2022]
Abstract
Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.
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Affiliation(s)
| | - Alex R Hall
- Institute of Integrative Biology, ETH Zurich, Switzerland
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Dong L, Ge Z, Qu W, Fan Y, Dai Q, Wang J. Characteristics and mechanism of heterotrophic nitrification/aerobic denitrification in a novel Halomonas piezotolerans strain. J Basic Microbiol 2021; 62:124-134. [PMID: 34796543 DOI: 10.1002/jobm.202100446] [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: 08/19/2021] [Revised: 10/10/2021] [Accepted: 11/06/2021] [Indexed: 11/06/2022]
Abstract
A strain was isolated from an activated sludge system and identified as Halomonas piezotolerans HN2 in this study, which is the first strain in H. piezotolerans with the capability of heterotrophic nitrification and aerobic denitrification. Strain HN2 showed the maximum nitrogen removal rate of 9.10 mg/L/h by utilizing ammonium at the salinity of 3.0%. Under saline environment, HN2 could remove nitrogen efficiently in neutral and slightly alkaline environments, with the carbon sources of sodium succinate and sodium citrate and the C/N ratio of 15-20, and the maximum removal efficiencies of ammonium, nitrite, and nitrate were 100%, 96.35%, and 99.7%, respectively. The genomic information revealed the presence of amoA, napA, and nosZ genes in strain HN2, and the target bands of nirS were obtained via a polymerase chain reaction. Therefore, we inferred that ammonium was mainly utilized for the growth of strain HN2 through assimilation, and another part of the initial ammonium was converted into nitrate through nitrification, and then into gaseous nitrogen through denitrification. This report indicated the potential application of strain HN2 and other nitrifying and denitrifying Halomonas strains in the removal of nitrogen pollution in marine-related environments and also implies the important role of Halomonas in the nitrogen cycle process of the ocean.
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Affiliation(s)
- Lingxi Dong
- School of Fishery, Zhejiang Ocean University, Zhoushan, China
| | - Zhewen Ge
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yingping Fan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Qiuping Dai
- Zhejiang Marine Fisheries Research Institute, Zhoushan, China.,Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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30
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Hsu HC, Chen JS, Nagarajan V, Hussain B, Huang SW, Rathod J, Hsu BM. Assessment of Temporal Effects of a Mud Volcanic Eruption on the Bacterial Community and Their Predicted Metabolic Functions in the Mud Volcanic Sites of Niaosong, Southern Taiwan. Microorganisms 2021; 9:microorganisms9112315. [PMID: 34835440 PMCID: PMC8622063 DOI: 10.3390/microorganisms9112315] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial communities inhabiting mud volcanoes have received more attention due to their noteworthy impact on the global methane cycle. However, the impact of temporal effects of volcanic eruptions on the microbial community’s diversity and functions remain poorly characterized. This study aimed to underpin the temporal variations in the bacterial community’s diversity and PICRUSt-predicted functional profile changes of mud volcanic sites located in southern Taiwan using 16S rRNA gene sequencing. The physicochemical analysis showed that the samples were slightly alkaline and had elevated levels of Na+, Cl−, and SO42−. Comparatively, the major and trace element contents were distinctly higher, and tended to be increased in the long-period samples. Alpha diversity metrics revealed that the bacterial diversity and abundance were lesser in the initial period, but increased over time. Instead, day 96 and 418 samples showed reduced bacterial abundance, which may have been due to the dry spell that occurred before each sampling. The initial-period samples were significantly abundant in haloalkaliphilic marine-inhabiting, hydrocarbon-degrading bacterial genera such as Marinobacter, Halomonas, Marinobacterium, and Oceanimonas. Sulfur-reducing bacteria such as Desulfurispirillum and Desulfofarcimen were found dominant in the mid-period samples, whereas the methanogenic archaeon Methanosarcina was abundant in the long-period samples. Unfortunately, heavy precipitation encountered during the mid and long periods may have polluted the volcanic site with animal pathogens such as Desulfofarcimen and Erysipelothrix. The functional prediction results showed that lipid biosynthesis and ubiquinol pathways were significantly abundant in the initial days, and the super pathway of glucose and xylose degradation was rich in the long-period samples. The findings of this study highlighted that the temporal effects of a mud volcanic eruption highly influenced the bacterial diversity, abundance, and functional profiles in our study site.
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Affiliation(s)
- Ho-Chuan Hsu
- Department of Medical Imaging, Cheng Hsin General Hospital, Taipei City 112, Taiwan;
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung City 824, Taiwan;
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; (V.N.); (B.H.)
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; (V.N.); (B.H.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Shih-Wei Huang
- Center for environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung City 824, Taiwan;
- Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung City 824, Taiwan
| | - Jagat Rathod
- Department of Earth Sciences, National Cheng Kung University, Tainan 701, Taiwan;
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; (V.N.); (B.H.)
- Correspondence: ; Tel.: +886-52720411 (ext. 66218)
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31
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Bovine Colostrum for Human Consumption—Improving Microbial Quality and Maintaining Bioactive Characteristics through Processing. DAIRY 2021. [DOI: 10.3390/dairy2040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The main purpose of bovine colostrum, being the milk secreted by a cow after giving birth, is to transfer passive immunity to the calf. The calves have an immature immune system as they lack immunoglobulins (Igs). Subsequently, the supply of good quality bovine colostrum is required. The quality of colostrum is classified by low bacterial counts and adequate Ig concentrations. Bacterial contamination can contain a variety of human pathogens or high counts of spoilage bacteria, which has become more challenging with the emerging use of bovine colostrum as food and food supplements. There is also a growing risk for the spread of zoonotic diseases originating from bovines. For this reason, processing based on heat treatment or other feasible techniques is required. This review provides an overview of literature on the microbial quality of bovine colostrum and processing methods to improve its microbial quality and keep its nutritional values as food. The highlights of this review are as follows: high quality colostrum is a valuable raw material in food products and supplements; the microbial safety of bovine colostrum is increased using an appropriate processing-suitable effective heat treatment which does not destroy the high nutrition value of colostrum; the heat treatment processes are cost-effective compared to other methods; and heat treatment can be performed in both small- and large-scale production.
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32
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Pal D, Mukhopadhyay B. Chemical Synthesis of β-l-Rhamnose Containing the Pentasaccharide Repeating Unit of the O-Specific Polysaccharide from a Halophilic Bacterium Halomonas ventosae RU5S2EL in the Form of Its 2-Aminoethyl Glycoside. J Org Chem 2021; 86:8683-8694. [PMID: 34138579 DOI: 10.1021/acs.joc.1c00467] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Total synthesis of the pentasaccharide repeating unit of the OPS from Halomonas ventosae RU5S2EL is accomplished through a [3+2] block strategy. Picoloyl-induced hydrogen-bond-assisted aglycon delivery (HAD) is used for two consecutive 1,2-cis-l-rhamnosylations, and remote participation is used for α-selective glucosylation. The choice of 2-aminoethyl glycoside at the reducing end is opted for, leaving the scope for further glycoconjugate formation without hampering the reducing-end stereochemistry.
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Affiliation(s)
- Debasish Pal
- Sweet Lab, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia 741246, India
| | - Balaram Mukhopadhyay
- Sweet Lab, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia 741246, India
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33
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Wang L, Liu X, Lai Q, Gu L, Shao Z. Halomonas diversa sp. nov., isolated from deep-sea sediment of the Pacific Ocean. Int J Syst Evol Microbiol 2021; 71. [PMID: 33906704 DOI: 10.1099/ijsem.0.004790] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated as D167-6-1T, was isolated from deep-sea sediment collected from the Pacific Ocean. The cells were catalase- and oxidase-positive, and motile by means of peritrichous flagella. Growth occurred at NaCl concentrations ranging from 0 to 19 % (optimum, 2-8 %, w/v), from pH 6 to 11 (optimum, 7-8) and at temperatures between 4 and 45 °C (optimum, 33 °C). Phylogenetic analysis based on 16S rRNA, gyrB and rpoD gene sequences and its genome sequence revealed that strain D167-6-1T formed a monophyletic branch within the genus Halomonas and was most closely related to Halomonas saliphila, Halomonas pellis, Halomonas kenyensis, Halomonas daqingensis, Halomonas desiderata and Halomonas lactosivorans (with 98.5, 98.5, 98.4, 98.1, 97.5 and 97.8 % 16S rRNA sequence similarity, respectively). The complete genome size of strain D167-6-1T was 4.49 Mb, with a DNA G+C content of 62.8 mol%. The estimated averagenucleotide identity and DNA-DNA hybridization values between strain D167-6-1T and other closely related species were 77.59-85.35 % and 22.0-30.6 %, respectively. The principal cellular fatty acids (>5 %) were C18 : 1 ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C17 : 0 cyclo. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, aminophospholipid and two unidentified phospholipids. The predominant respiratory quinones were Q-9 and Q-8. The combined genotypic and phenotypic data show that strain D167-6-1T represents a novel species of the genus Halomonas, for which the name Halomonas diversa sp. nov. is proposed, with the type strain D167-6-1T (=MCCC 1A13316T=KCTC 72441T).
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Affiliation(s)
- Liping Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,School of Environment, Harbin Institute of Technology, Harbin, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Li Gu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
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34
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Wang L, Shao Z. Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis. Front Microbiol 2021; 12:652766. [PMID: 33815342 PMCID: PMC8014003 DOI: 10.3389/fmicb.2021.652766] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.
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Affiliation(s)
- Liping Wang
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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35
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Wang L, Shao Z. Complete genome sequence of a denitrifying bacterium Halomonas sp. SS10-MC5 isolated from hydrothermal vent of Indian Ocean. Mar Genomics 2021; 58:100849. [PMID: 34217482 DOI: 10.1016/j.margen.2021.100849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 11/19/2022]
Abstract
A denitrifying bacterium Halomonas sp. SS10-MC5, was isolated from a deep-sea hydrothermal vent chimney sample of the Indian Ocean. Here we described the complete genome of strain SS10-MC5 which has one circular chromosome of 4,441,120 bp with a mean G + C content of 66.12 mol%. The complete genome harbors 4094 predicted protein-encoding genes, 65 tRNA genes as well as four 16S-23S-5S rRNA operons. Genes involved in denitrification, assimilation, PHA synthesis, stress response, and so on, were identified in this genome. These metabolic features and related genes revealed genetic basis for the adaptation to the marine environment, which help to further understand its adaptive evolution and ecological role in submarine hydrothermal environments.
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Affiliation(s)
- Liping Wang
- School of Environment, Harbin Institute of Technology, Harbin, China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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36
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Sawada K, Koyano H, Yamamoto N, Yamada T. The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds. Sci Rep 2021; 11:1791. [PMID: 33469050 PMCID: PMC7815776 DOI: 10.1038/s41598-021-81105-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/04/2021] [Indexed: 01/02/2023] Open
Abstract
The microbial community during fermented vegetable production has a large impact on the quality of the final products. Lactic acid bacteria have been well-studied in such processes, but knowledge about the roles of non-lactic acid bacteria is limited. This study aimed to provide useful knowledge about the relationships between the microbiota, including non-lactic acid bacteria, and metabolites in commercial pickle production by investigating Japanese pickles fermented in rice-bran. The samples were provided by six manufacturers, divided into two groups depending on the production conditions. The microbiological content of these samples was investigated by high-throughput sequencing, and metabolites were assessed by liquid chromatography-mass spectrometry and enzymatic assay. The data suggest that Halomonas, halophilic Gram-negative bacteria, can increase glutamic acid content during the pickling process under selective conditions for bacterial growth. In contrast, in less selective conditions, the microbiota consumed glutamic acid. Our results indicate that the glutamic acid content in fermented pickle is influenced by the microbiota, rather than by externally added glutamic acid. Our data suggest that both lactic acid bacteria and non-lactic acid bacteria are positive key factors in the mechanism of commercial vegetable fermentation and affect the quality of pickles.
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Affiliation(s)
- Kazunori Sawada
- Corporate Strategy Office, Gurunavi, Inc., Toho Hibiya Building, 1-2-2 Yurakucho, Chiyoda-ku, Tokyo, 100-0006, Japan
| | - Hitoshi Koyano
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Nozomi Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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37
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Athmika, Ghate SD, Arun AB, Rao SS, Kumar STA, Kandiyil MK, Saptami K, Rekha PD. Genome analysis of a halophilic bacterium Halomonas malpeensis YU-PRIM-29 T reveals its exopolysaccharide and pigment producing capabilities. Sci Rep 2021; 11:1749. [PMID: 33462335 PMCID: PMC7814019 DOI: 10.1038/s41598-021-81395-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/04/2021] [Indexed: 11/08/2022] Open
Abstract
Halomonas malpeensis strain YU-PRIM-29T is a yellow pigmented, exopolysaccharide (EPS) producing halophilic bacterium isolated from the coastal region. To understand the biosynthesis pathways involved in the EPS and pigment production, whole genome analysis was performed. The complete genome sequencing and the de novo assembly were carried out using Illumina sequencing and SPAdes genome assembler (ver 3.11.1) respectively followed by detailed genome annotation. The genome consists of 3,607,821 bp distributed in 18 contigs with 3337 protein coding genes and 53% of the annotated CDS are having putative functions. Gene annotation disclosed the presence of genes involved in ABC transporter-dependent pathway of EPS biosynthesis. As the ABC transporter-dependent pathway is also implicated in the capsular polysaccharide (CPS) biosynthesis, we employed extraction protocols for both EPS (from the culture supernatants) and CPS (from the cells) and found that the secreted polysaccharide i.e., EPS was predominant. The EPS showed good emulsifying activities against the petroleum hydrocarbons and its production was dependent on the carbon source supplied. The genome analysis also revealed genes involved in industrially important metabolites such as zeaxanthin pigment, ectoine and polyhydroxyalkanoate (PHA) biosynthesis. To confirm the genome data, we extracted these metabolites from the cultures and successfully identified them. The pigment extracted from the cells showed the distinct UV-Vis spectra having characteristic absorption peak of zeaxanthin (λmax 448 nm) with potent antioxidant activities. The ability of H. malpeensis strain YU-PRIM-29T to produce important biomolecules makes it an industrially important bacterium.
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Affiliation(s)
- Athmika
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Sudeep D Ghate
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - A B Arun
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Sneha S Rao
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - S T Arun Kumar
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Mrudula Kinarulla Kandiyil
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Kanekar Saptami
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - P D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
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38
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Xiao Z, Shen J, Wang Z, Dong F, Zhao JY. Halomonas bachuensis sp. nov., Isolated from Gobi Soil. Curr Microbiol 2021; 78:397-402. [PMID: 33136204 DOI: 10.1007/s00284-020-02268-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/21/2020] [Indexed: 11/26/2022]
Abstract
A novel aerobic bacterium designated DX6T was isolated from a Gobi soil sample collected in Bachu County, China. Cells are Gram-stain-negative and rod-shaped and colonies are creamy, circular and smooth. The growth range of NaCl concentration was 1-15% (optimum 2-10%, w/v). Growth occurs at 10-45 °C (optimum 37 °C) and pH 5.0-10.0 (optimum pH 7.0-9.0). Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain DX6T formed a distinct lineage in the clade of genus Halomonas and is related to Halomonas desiderata DSM 9502T (98.3%), Halomonas kenyensis AIR-2T (97.7%), Halomonas daqingensis DQD2-30T (97.6%), Halomonas saliphila LCB169T (97.4%) and Halomonas endophytica MC28T (96.2%). Analysis of the housekeeping genes gryB and rpoD and calculation of the average nucleotide identities and the digital DNA-DNA hybridization values between strain DX6T and the related type Halomonas strains further revealed that strain DX6T represented a distinct species. The main respiratory quinones of strain DX6T were ubiquinone 9 (Q-9) and ubiquinone 8 (Q-8). The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified phosphatidylglycolipid, and four unidentified lipids. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic features, strain DX6T represents a novel species of the genus Halomonas. The name Halomonas bachuensis sp. nov. is proposed with strain DX6T (= CCTCC AB 2020094T = KCTC 82196T) designated as the type strain.
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Affiliation(s)
- Zijun Xiao
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Jie Shen
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Zhuo Wang
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Fanghui Dong
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jing-Yi Zhao
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
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39
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Li W, Lu H, He Z, Sang Y, Sun J. Quality characteristics and bacterial community of a Chinese salt-fermented shrimp paste. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Yoo W, Kim B, Jeon S, Kim KK, Kim TD. Identification, characterization, and immobilization of a novel YbfF esterase from Halomonas elongata. Int J Biol Macromol 2020; 165:1139-1148. [PMID: 33031847 DOI: 10.1016/j.ijbiomac.2020.09.247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022]
Abstract
The YbfF esterase family, which has a bifurcated binding pocket for diverse ligands, could serve as excellent biocatalysts in industrial and biotechnological applications. Here, the identification, characterization, and immobilization of a novel YbfF esterase (YbfFHalomonas elongata) from Halomonas elongata DSM 2581 is reported. Biochemical characterization of YbfF was carried out using activity staining, chromatographic analysis, kinetic analysis, activity assay, acetic acid release, and pH-indicator-based hydrolysis. YbfFH.elongata displayed broad substrate specificity, including that for p-nitrophenyl esters, glucose pentaacetate, tert-butyl acetate, and β-lactam-containing compounds, with high efficiency. Based on a homology model of YbfFH.elongata, Trp237 in the substrate-binding pocket, a critical residue for catalytic activity and substrate specificity was identified and characterized. Furthermore, crosslinked enzyme aggregates and nanoflower formation were explored to enhance the chemical stability and recyclability of YbfFH.elongata. The present study is the first report of a YbfF esterase from extremophiles, and explains its protein stability, catalytic activity, substrate specificities and diversities, kinetics, functional residues, amyloid formation, and immobilization.
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Affiliation(s)
- Wanki Yoo
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Precision Medicine, School of Medicine, SungKyunKwan University, Suwon 16419, Republic of Korea
| | - Booyoung Kim
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sangeun Jeon
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, School of Medicine, SungKyunKwan University, Suwon 16419, Republic of Korea
| | - T Doohun Kim
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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41
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Mardanov AV, Kadnikov VV, Beletsky AV, Ravin NV. Sulfur and Methane-Oxidizing Microbial Community in a Terrestrial Mud Volcano Revealed by Metagenomics. Microorganisms 2020; 8:microorganisms8091333. [PMID: 32878336 PMCID: PMC7565565 DOI: 10.3390/microorganisms8091333] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using a metagenomics approach, we analyzed the microbial community of bubbling fluids retrieved from an active mud volcano in eastern Crimea. The microbial community was dominated by chemolithoautotrophic Campylobacterota and Gammaproteobacteria, which are capable of sulfur oxidation coupled to aerobic and anaerobic respiration. Methane oxidation could be enabled by aerobic Methylococcales bacteria and anaerobic methanotrophic archaea (ANME), while methanogens were nearly absent. The ANME community was dominated by a novel species of Ca. Methanoperedenaceae that lacked nitrate reductase and probably couple methane oxidation to the reduction of metal oxides. Analysis of two Ca. Bathyarchaeota genomes revealed the lack of mcr genes and predicted that they could grow on fatty acids, sugars, and proteinaceous substrates performing fermentation. Thermophilic sulfate reducers indigenous to the deep subsurface, Thermodesulfovibrionales (Nitrospirae) and Ca. Desulforudis (Firmicutes), were found in minor amounts. Overall, the results obtained suggest that reduced compounds delivered from the deep subsurface support the development of autotrophic microorganisms using various electron acceptors for respiration.
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42
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Gao P, Lu H, Xing P, Wu QL. Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:5217-5225. [PMID: 32816656 DOI: 10.1099/ijsem.0.004395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, aerobic and non-motile rods bacteria, designated TQ8ST and ZH2ST, were isolated from salt marsh sediment collected from the Tibetan Plateau. Strain TQ8ST was found to grow at 10-40 °C (optimum, 30 °C), pH 6.0-11.0 (optimum, pH 8.0-9.0) and in the presence of 2-12 % (w/v) NaCl (optimum, 6-8 %). Strain ZH2ST was found to grow at 15-40 °C (optimum, 30 °C), pH 7.0-10.0 (optimum pH 9.0) and in the presence of 2-10 % (w/v) NaCl (optimum, 4-6 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains TQ8ST and ZH2ST shared 99.07 % sequence similarity between each other and were affiliated with the genus Halomonas, sharing 97.48 % and 97.41 % of sequence similarity to their closest neighbour Halomonas sulfidaeris Esulfide1T, respectively. DNA-DNA hybridization analyses showed 61.0 % relatedness between strains TQ8ST and ZH2ST. The average nucleotide identity and the average amino acid identity values between the two genomes were 92.33 and 92.84 %, respectively. The values between the two strains and their close phylogenetic relatives were all below 95 %. The major respiratory quinones of strain TQ8ST were Q-9 and Q-8, while that of ZH2ST was Q-9. The main fatty acids shared by the two strains were C18 : 1 ω6c and/or C18 : 1 ω7c, C16 : 1 ω6c and/or C16 : 1 ω7c, C16 : 0 and C12 : 0 3-OH. Strain ZH2ST can be distinguished from TQ8ST by a higher proportion of C19 : 0 cyclo ω8c. The G+C content of the genomic DNA of strains TQ8ST and ZH2ST were 57.20 and 57.14 mol%, respectively. On the basis of phenotypic distinctiveness and phylogenetic divergence, the two isolates are considered to represent two novel species of the genus Halomonas, for which the names Halomonas rituensis sp. nov (type strain TQ8ST=KCTC 62530T=CICC 24572T) and Halomonas zhuhanensis sp. nov (type strain ZH2ST=KCTC 62531T=CICC 24505T) are proposed.
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Affiliation(s)
- Peixin Gao
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Huibin Lu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qinglong L Wu
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
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43
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Dias MF, da Rocha Fernandes G, Cristina de Paiva M, Christina de Matos Salim A, Santos AB, Amaral Nascimento AM. Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings. WATER RESEARCH 2020; 174:115630. [PMID: 32105997 DOI: 10.1016/j.watres.2020.115630] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 05/09/2023]
Abstract
Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. blaKPC, blaGES, blaIMP, blaVIM, blaSPM and blaNDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.
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Affiliation(s)
- Marcela França Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | | | | | | | - Alexandre Bueno Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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44
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Hammad DBM, Hider SL, Liyanapathirana VC, Tonge DP. Molecular Characterization of Circulating Microbiome Signatures in Rheumatoid Arthritis. Front Cell Infect Microbiol 2020; 9:440. [PMID: 32039040 PMCID: PMC6987042 DOI: 10.3389/fcimb.2019.00440] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid Arthritis (RA) has been increasingly associated with perturbations to the microbial communities that reside in and on the body (the microbiome), in both human and animal studies. To date, such studies have mainly focused on the microbial communities that inhabit the gut and oral cavity. Mounting evidence suggests that microbial DNA can be detected in the blood circulation using a range of molecular methods. This DNA may represent an untapped pool of biomarkers that have the potential to report on changes to the microbiome of distant sites (e.g., example, the gut and oral cavity). To this end, through amplification and sequencing of the bacterial 16S rRNA variable region four, we evaluated the presence and identity of microbial DNA in blood samples obtained from RA patients (both prior to and 3 months following the instigation of treatment) in comparison to a small number of healthy control subjects and samples obtained from patients with ankylosing spondylitis (AS) and psoriatic arthritis (PA). Bacterial-derived DNA was identified in the majority of our patient samples. Taxonomic classification revealed that the microbiome community in RA was distinct from AS, PA, and the healthy state. Through analysis of paired patient samples obtained prior to and 3 months following treatment (V0 vs. V3), we found the microbiome to be modulated by treatment, and in many cases, this shift reduced the distance between these samples and the healthy control samples, suggesting a partial normalization following treatment in some patients. This effect was especially evident in seronegative arthritis patients. Herein, we provide further evidence for the existence of a blood microbiome in health and identify specific taxa modulated in disease and following treatment. These blood-derived signatures may have significant utility as disease biomarkers and suggest this area warrants further investigation.
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Affiliation(s)
- Dargham B M Hammad
- Faculty of Natural Sciences, School of Life Sciences, Keele University, Keele, United Kingdom
| | - S L Hider
- Arthritis Research UK Primary Care Centre, Research Institute for Primary Care and Health Sciences, Keele University, Keele, United Kingdom.,Haywood Academic Rheumatology Group, Midlands Partnership Foundation Trust, Staffordshire, United Kingdom
| | | | - Daniel P Tonge
- Faculty of Natural Sciences, School of Life Sciences, Keele University, Keele, United Kingdom
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45
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Fernandes C, Kankonkar H, Meena RM, Menezes G, Shenoy BD, Khandeparker R. Metagenomic analysis of tarball-associated bacteria from Goa, India. MARINE POLLUTION BULLETIN 2019; 141:398-403. [PMID: 30955749 DOI: 10.1016/j.marpolbul.2019.02.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/22/2019] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.
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Affiliation(s)
- Clafy Fernandes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Harshada Kankonkar
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Ram Murti Meena
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Gilda Menezes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Belle Damodara Shenoy
- CSIR-National Institute of Oceanography Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam, 530017, Andhra Pradesh, India
| | - Rakhee Khandeparker
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India.
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46
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Ibrahim IM, Sigida EN, Kokoulin MS, Fedonenko YP, Konnova SA. Structure of the O-specific polysaccharide from a halophilic bacterium Halomonas ventosae RU5S2EL. Carbohydr Res 2019; 473:1-4. [DOI: 10.1016/j.carres.2018.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 11/25/2022]
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47
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Draft Genome Sequence of
Halomonas
sp. Strain SL1, a Putative Polyhydroxyalkanoate-Producing Halophile. Microbiol Resour Announc 2019; 8:MRA00915-18. [PMID: 30637379 PMCID: PMC6318350 DOI: 10.1128/mra.00915-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/26/2018] [Indexed: 11/20/2022] Open
Abstract
Halomonas sp. strain SL1, a halophilic gammaproteobacterium, was isolated from samples from the Great Salt Lake in Utah. We report here the draft genome sequence of SL1, which has an estimated total sequence length of 3.6 Mb. Halomonas sp. strain SL1, a halophilic gammaproteobacterium, was isolated from samples from the Great Salt Lake in Utah. We report here the draft genome sequence of SL1, which has an estimated total sequence length of 3.6 Mb.
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48
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Gu J, Liu T, Hou J, Pan L, Sadiq FA, Yuan L, Yang H, He G. Analysis of bacterial diversity and biogenic amines content during the fermentation processing of stinky tofu. Food Res Int 2018; 111:689-698. [DOI: 10.1016/j.foodres.2018.05.065] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 12/17/2022]
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49
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Seck EH, Dufour JC, Raoult D, Lagier JC. Halophilic & halotolerant prokaryotes in humans. Future Microbiol 2018; 13:799-812. [PMID: 29726267 DOI: 10.2217/fmb-2017-0237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Halophilic prokaryotes are described as microorganisms living in hypersaline environments. Here, we list the halotolerant and halophilic bacteria which have been isolated in humans. Of the 52 halophilic prokaryotes, 32 (61.54%) were moderately halophilic, 17 (32.69%) were slightly halophilic and three (5.76%) were extremely halophilic prokaryotes. At the phylum level, 29 (54.72%) belong to Firmicutes, 15 (28.84%) to Proteobacteria, four (7.69%) to Actinobacteria, three (5.78%) to Euryarchaeota and one (1.92%) belongs to Bacteroidetes. Halophilic prokaryotes are rarely pathogenic: of these 52 halophilic prokaryotes only two (3.92%) species were classified in Risk Group 2 (Vibrio cholerae, Vibrio parahaemolyticus) and one (1.96%), species in Risk Group 3 (Bacillus anthracis).
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Affiliation(s)
- El Hadji Seck
- Aix Marseille University, IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Charles Dufour
- SESSTIM (UMR912), Sciences Economiques et Sociales de la Santé et Traitement de l'Information Médicale, Aix Marseille University, INSERM, IRD, Marseille, France.,Service Biostatistique et Technologies de l'Information et de la Communication (BIOSTIC), Assistance Publique Hôpitaux de Marseille, Hôpital de la Timone, Marseille, France
| | - Didier Raoult
- Aix Marseille University, IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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50
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Investigation on CO2 bio-mitigation using Halomonas stevensii in laboratory scale bioreactor: Design of downstream process and its economic feasibility analysis. J CO2 UTIL 2018. [DOI: 10.1016/j.jcou.2018.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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