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Zhang Q, Wang Y, Hou Y, Zhao Q, Yang L, Zhang Y, Zhou L. Metabarcode insights into the airborne fungal diversity in the indoor and outdoor environments in archives from Yunnan, Southwestern China. Braz J Microbiol 2024; 55:1601-1618. [PMID: 38587763 PMCID: PMC11153435 DOI: 10.1007/s42770-024-01323-z] [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: 06/09/2023] [Accepted: 03/28/2024] [Indexed: 04/09/2024] Open
Abstract
Monitoring dynamics of airborne fungal species and controlling of harmful ones are of vital importance to conservation of cultural relics. However, the evaluation of air quality and the community structure characteristics of microorganisms, especially fungi, in the atmosphere of archives is in a stage of continuous exploration though more than 4,000 archives were constructed in China. Seventy-two air samples were collected in this study under different spatial and weather conditions from the archives of Kunming Medical University, located in the Kunming metropolitan area, Yunnan province, southwestern China. A total of 22 airborne fungal classes, 160 genera and 699 ASVs were identified, the species diversity is on the rise with the strengthening of air circulation with the outside space, and thus the intensive energy metabolism and activity were found in the spaces with window and sunny weather, except for the higher lipid synthesis of indoor samples than that of outdoor ones. Furthermore, there were significant differences in fungal community composition and abundance between sunny and rainy weathers. A considerable number of species have been identified as indicator in various environmental and weather conditions of the archives, and temperature and humidity were thought to have significant correlations with the abundance of these species. Meanwhile, Cladosporium and Alternaria were the dominant genera here, which may pose a threat to the health of archive professionals. Therefore, monitoring and controlling the growth of these fungal species is crucial for both conservation of paper records and health of archive professionals.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650032, China
| | - Yuan Wang
- Archives of Kunming Medical University, Kunming, 650500, China
| | - Yutong Hou
- The School of Health, Fujian Medical University, Fuzhou, 350100, China
| | - Qingxue Zhao
- School of Basic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Liu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650032, China
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650032, China.
| | - Lu Zhou
- Archives of Kunming Medical University, Kunming, 650500, China.
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Ahmed O, Boucher C, Langmead B. Cliffy: robust 16S rRNA classification based on a compressed LCA index. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595899. [PMID: 38854039 PMCID: PMC11160684 DOI: 10.1101/2024.05.25.595899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Taxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r -index enable full-text pattern matching against large sequence collections. But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections. Previous work proposed the document array profiles, which use 𝒪 ( rd ) words of space where r is the number of maximal-equal letter runs in the Burrows-Wheeler transform and d is the number of distinct genomes. The linear dependence on d is limiting, since real taxonomies can easily contain 10,000s of leaves or more. We propose a method called cliff compression that reduces this size by a large factor, over 250x when indexing the SILVA 16S rRNA gene database. This method uses Θ( r log d ) words of space in expectation under a random model we propose here. We implemented these ideas in an open source tool called Cliffy that performs efficient taxonomic classification of sequencing reads with respect to a compressed taxonomic index. When applied to simulated 16S rRNA reads, Cliffy's read-level accuracy is higher than Kraken2's by 11-18%. Clade abundances are also more accurately predicted by Cliffy compared to Kraken2 and Bracken. Overall, Cliffy is a fast and space-economical extension to compressed full-text indexes, enabling them to perform fast and accurate taxonomic classification queries. 2012 ACM Subject Classification Applied computing → Computational genomics.
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Ma X, Li Z, Cai L, Xiao M, He F, Liu Z, Chen D, Wang Y, Shen L, Gu Y. Analysis of fungal diversity in the gut feces of wild takin ( Budorcas taxicolor). Front Microbiol 2024; 15:1364486. [PMID: 38699479 PMCID: PMC11063333 DOI: 10.3389/fmicb.2024.1364486] [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: 01/31/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction The composition of the intestinal microbiome correlates significantly with an animal's health status. Hence, this indicator is highly important and sensitive for protecting endangered animals. However, data regarding the fungal diversity of the wild Budorcas taxicolor (takin) gut remain scarce. Therefore, this study analyzes the fungal diversity, community structure, and pathogen composition in the feces of wild B. taxicolor. Methods To ensure comprehensive data analyses, we collected 82 fecal samples from five geographical sites. Amplicon sequencing of the internal transcribed spacer (ITS) rRNA was used to assess fecal core microbiota and potential pathogens to determine whether the microflora composition is related to geographical location or diet. We further validated the ITS rRNA sequencing results via amplicon metagenomic sequencing and culturing of fecal fungi. Results and discussion The fungal diversity in the feces of wild Budorcas taxicolor primarily comprised three phyla (99.69%): Ascomycota (82.19%), Fungi_unclassified (10.37%), and Basidiomycota (7.13%). At the genus level, the predominant fungi included Thelebolus (30.93%), Functional_unclassified (15.35%), and Ascomycota_unclassified (10.37%). Within these genera, certain strains exhibit pathogenic properties, such as Thelebolus, Cryptococcus, Trichosporon, Candida, Zopfiella, and Podospora. Collectively, this study offers valuable information for evaluating the health status of B. taxicolor and formulating protective strategies.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiguo Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lijun Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Mei Xiao
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Fang He
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dong Chen
- Sichuan Provincial Center for Animal Disease Prevention and Control, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Limin Shen
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China
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4
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Inciuraite R, Gedgaudas R, Lukosevicius R, Tilinde D, Ramonaite R, Link A, Kasetiene N, Malakauskas M, Kiudelis G, Jonaitis LV, Kupcinskas J, Juzenas S, Skieceviciene J. Constituents of stable commensal microbiota imply diverse colonic epithelial cell reactivity in patients with ulcerative colitis. Gut Pathog 2024; 16:16. [PMID: 38521943 PMCID: PMC10960424 DOI: 10.1186/s13099-024-00612-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Despite extensive research on microbiome alterations in ulcerative colitis (UC), the role of the constituent stable microbiota remains unclear. RESULTS This study, employing 16S rRNA-gene sequencing, uncovers a persistent microbial imbalance in both active and quiescent UC patients compared to healthy controls. Using co-occurrence and differential abundance analysis, the study highlights microbial constituents, featuring Phocaeicola, Collinsella, Roseburia, Holdemanella, and Bacteroides, that are not affected during the course of UC. Co-cultivation experiments, utilizing commensal Escherichia coli and Phocaeicola vulgatus, were conducted with intestinal epithelial organoids derived from active UC patients and controls. These experiments reveal a tendency for a differential response in tight junction formation and maintenance in colonic epithelial cells, without inducing pathogen recognition and stress responses, offering further insights into the roles of these microorganisms in UC pathogenesis. These experiments also uncover high variation in patients' response to the same bacteria, which indicate the need for more comprehensive, stratified analyses with an expanded sample size. CONCLUSION This study reveals that a substantial part of the gut microbiota remains stable throughout progression of UC. Functional experiments suggest that members of core microbiota - Escherichia coli and Phocaeicola vulgatus - potentially differentially regulate the expression of tight junction gene in the colonic epithelium of UC patients and healthy individuals.
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Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania.
| | - Rolandas Gedgaudas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rima Ramonaite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital Magdeburg, Magdeburg, Germany
| | - Neringa Kasetiene
- Department of Food Safety and Quality, Academy of Veterinary, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mindaugas Malakauskas
- Department of Food Safety and Quality, Academy of Veterinary, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Simonas Juzenas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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Hu ZQ, Hung YM, Chen LH, Lai LC, Pan MH, Chuang EY, Tsai MH. NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:254-264. [PMID: 38568776 DOI: 10.1109/tcbb.2024.3349572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.
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Golob JL. Human Microbiomes and Disease for the Biomedical Data Scientist. Annu Rev Biomed Data Sci 2023; 6:259-273. [PMID: 37159872 DOI: 10.1146/annurev-biodatasci-020722-043017] [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] [Indexed: 05/11/2023]
Abstract
The human microbiome is complex, variable from person to person, essential for health, and related to both the risk for disease and the efficacy of our treatments. There are robust techniques to describe microbiota with high-throughput sequencing, and there are hundreds of thousands of already-sequenced specimens in public archives. The promise remains to use the microbiome both as a prognostic factor and as a target for precision medicine. However, when used as an input in biomedical data science modeling, the microbiome presents unique challenges. Here, we review the most common techniques used to describe microbial communities, explore these unique challenges, and discuss the more successful approaches for biomedical data scientists seeking to use the microbiome as an input in their studies.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA; ,
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Selim MS, Mohamed SS, Asker MS, Ibrahim AY, El-Newary SA, El Awady ME. Characterization and in-vitro Alzheimer's properties of exopolysaccharide from Bacillus maritimus MSM1. Sci Rep 2023; 13:11399. [PMID: 37452077 PMCID: PMC10349148 DOI: 10.1038/s41598-023-38172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Four bacterial isolates were obtained from marine sediments collected from Sahl Hashish, Hurghada Red Sea, Egypt. This study was designed to search for promising anti-Alzheimer natural polysaccharide; therefore, four isolates were screened for exopolysaccharides (EPSs) production and acetylcholinesterase inhibition. The isolate S16 provided the highest EPS yield (7.51 g/L) and acetylcholinesterase inhibition. It was identified morphologically and genetically using 16S rRNA gene sequence analysis as Bacillus maritimus. A Physicochemical analysis of S16 exopolysaccharide (BMEPS) was estimated, which pointed to the presence of uronic acid and sulfate (24.7% and 18.3%, respectively). HPLC analysis indicated that mannuronic acid, glucuronic acid, glucose, and mannose are presented in a molar ratio of 0.8:1.0:2.8:2.3, respectively. Furthermore, FT-IR revealed an abundance of β-configurations. The GPC estimated the average molecular weight (Mw) as 4.31 × 104 g/mol. BMEPS inhibited AChE (IC50; 691.77 ± 8.65 μg/ ml), BChE (IC50; 288.27 ± 10.50 μg/ ml), and tyrosinase (IC50; 3.34 ± 0.09, 14.00 ± 0.14, and 22.96 ± 1.23 μg/ ml during incubation durations of 10, 20, and 40 min). It also demonstrated a selective anti-inflammatory action against COX-2 rather than COX-1. Moreover, BMEPS exhibited antioxidant capabilities as free radical and oxygen reactive species (ROS) scavenger, metal chelator, reductant agent, and lipid peroxidation suppressor. These activities are due to the distinct chemical composition. The findings of this study indicate that BMEPS could be considered as promising anti-disease Alzheimer's (AD) material in an in-vitro model, which qualifies it for advanced in-vivo studies in the discovery of alternative Alzheimer's treatment.
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Affiliation(s)
- Manal S Selim
- Microbial Biotechnology Department, Institute of Biotechnology Research, National Research Centre, Giza, 12622, Egypt
| | - Sahar S Mohamed
- Microbial Biotechnology Department, Institute of Biotechnology Research, National Research Centre, Giza, 12622, Egypt
| | - Mohsen S Asker
- Microbial Biotechnology Department, Institute of Biotechnology Research, National Research Centre, Giza, 12622, Egypt
| | - Abeer Y Ibrahim
- Medicinal and Aromatic Plants Research Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, 12622, Egypt
| | - Samah A El-Newary
- Medicinal and Aromatic Plants Research Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, 12622, Egypt
| | - Mohamed E El Awady
- Microbial Biotechnology Department, Institute of Biotechnology Research, National Research Centre, Giza, 12622, Egypt.
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Lehr K, Nikitina D, Vilchez-Vargas R, Steponaitiene R, Thon C, Skieceviciene J, Schanze D, Zenker M, Malfertheiner P, Kupcinskas J, Link A. Microbial composition of tumorous and adjacent gastric tissue is associated with prognosis of gastric cancer. Sci Rep 2023; 13:4640. [PMID: 36944721 PMCID: PMC10030820 DOI: 10.1038/s41598-023-31740-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection has been considered as the main causal factor in gastric carcinogenesis, but other bacterial species may also play an important role in pathophysiology of gastric cancer. The aim of the study was to explore the link between gastric cancer prognosis and the mucosal microbial community in tumorous and adjacent gastric tissue. The bacterial profile was analysed using 16S sequencing (V1-V2 region). Microbial differences were mostly characterized by lower relative abundances of H. pylori in tumorous gastric tissues. Bacterial community and outcome data analysis revealed the genus Fusobacterium and Prevotella significantly associated with worse overall survival in gastric cancer patients. In particular, Fusobacterium was associated with significant increase in hazard ratio in both univariable and multivariable analysis and independently validated using TCMA data. Phylogenetic biodiversity of Fusobacterium species in the stomach revealed F. periodonticum as the most prevalent in healthy subjects, while F. nucleatum was most abundant in patients with gastric cancer. Bacterial community network analysis in gastric cancer suggests substantial complexity and a strong interplay between F. nucleatum and Prevotella. In summary, mucosal microbial community in the stomach was associated with worse overall survival in gastric cancer patients. Strongest negative impact on prognosis was linked to the abundance of F. nucleatum in tumorous specimens, suggesting its translational relevance in management of gastric cancer patients.
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Affiliation(s)
- Konrad Lehr
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
| | - Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Ruta Steponaitiene
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Cosima Thon
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Denny Schanze
- Institute of Human Genetics, Otto-Von-Guericke University, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, Otto-Von-Guericke University, Magdeburg, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Department of Internal Medicine 2, University Hospital, LMU Munich, Munich, Germany
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
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Xie T, Liu X, Xu Y, Bryson S, Zhao L, Huang K, Huang S, Li X, Yang Q, Dong H, Winkler MKH. Coupling methanotrophic denitrification to anammox in a moving bed biofilm reactor for nitrogen removal under hypoxic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158795. [PMID: 36115405 DOI: 10.1016/j.scitotenv.2022.158795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/11/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N2. The ammonium and nitrate removal rates reached 72.09 ± 5.81 mgNH4+-N/L/d and 62.61 ± 4.17 mgNO3--N/L/d when the MBBR was operated in continuous mode. Nitrate removal by the methane-fed mixed consortia was confirmed in a batch test revealing a CH4/NO3- molar removal ratio of 1.15. The functional populations were unveiled by FISH analysis and 16S rRNA gene sequencing, which showed that the biofilm was dominated by Anammox bacteria (Candidatus Kuenenia) and diverse taxa associated with the capacity for denitrification: aerobic methanotrophs (Methylobacter, Methylomonas, and unclassified Methylococcaceae), methylotrophic denitrifiers (Opitutaceae and Methylophilaceae), and other heterotrophic denitrifiers (Ignavibacteriaceae, Anaerolineaceae, Comamonadaceae, Rhodocyclaceae and Thauera). Neither DAMO archaea nor DAMO bacteria were found in the sequencing analysis, indicating that more unknown community members possess the metabolic capacity of methanotrophic denitrification.
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Affiliation(s)
- Ting Xie
- School of Materials and Environment, Guangxi Colleges and Universities Key Laboratory of Environmental-friendly Materials and New Technology for Carbon Neutralization, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530006, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinyu Liu
- School of Materials and Environment, Guangxi Colleges and Universities Key Laboratory of Environmental-friendly Materials and New Technology for Carbon Neutralization, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530006, China
| | - Yiming Xu
- School of Materials and Environment, Guangxi Colleges and Universities Key Laboratory of Environmental-friendly Materials and New Technology for Carbon Neutralization, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530006, China
| | - Samuel Bryson
- Department of Civil and Environmental Engineering, University of Washington, Seattle 98105, USA
| | - Lu Zhao
- Department of Civil and Environmental Engineering, University of Washington, Seattle 98105, USA
| | - Kai Huang
- School of Materials and Environment, Guangxi Colleges and Universities Key Laboratory of Environmental-friendly Materials and New Technology for Carbon Neutralization, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530006, China
| | - Shiqi Huang
- School of Materials and Environment, Guangxi Colleges and Universities Key Laboratory of Environmental-friendly Materials and New Technology for Carbon Neutralization, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530006, China
| | - Xiaoming Li
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Changsha 410082, China.
| | - Qi Yang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Changsha 410082, China
| | - Huiyu Dong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives. Animals (Basel) 2022; 12:ani12233375. [PMID: 36496896 PMCID: PMC9736591 DOI: 10.3390/ani12233375] [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: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.
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Gelmez E, Lehr K, Kershaw O, Frentzel S, Vilchez-Vargas R, Bank U, Link A, Schüler T, Jeron A, Bruder D. Characterization of Maladaptive Processes in Acute, Chronic and Remission Phases of Experimental Colitis in C57BL/6 Mice. Biomedicines 2022; 10:biomedicines10081903. [PMID: 36009449 PMCID: PMC9405850 DOI: 10.3390/biomedicines10081903] [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: 06/29/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic recurrent inflammatory disease with unknown etiology. Dextran sulfate sodium (DSS) induced colitis is a widely used mouse model in IBD research. DSS colitis involves activation of the submucosal immune system and can be used to study IBD-like disease characteristics in acute, chronic, remission and transition phases. Insight into colon inflammatory parameters is needed to understand potentially irreversible adaptations to the chronification of colitis, determining the baseline and impact of further inflammatory episodes. We performed analyses of non-invasive and invasive colitis parameters in acute, chronic and remission phases of the DSS colitis in C57BL/6 mice. Non-invasive colitis parameters poorly reflected inflammatory aspects of colitis in chronic remission phase. We found invasive inflammatory parameters, positively linked to repeated DSS-episodes, such as specific colon weight, inflamed colon area, spleen weight, absolute cell numbers of CD4+ and CD8+ T cells as well as B cells, blood IFN-γ level, colonic chemokines BLC and MDC as well as the prevalence of Turicibacter species in feces. Moreover, microbial Lactobacillus species decreased with chronification of disease. Our data point out indicative parameters of recurrent gut inflammation in context of DSS colitis.
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Affiliation(s)
- Elif Gelmez
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Konrad Lehr
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-Associated Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Olivia Kershaw
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Sarah Frentzel
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-Associated Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ute Bank
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-Associated Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Andreas Jeron
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dunja Bruder
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Correspondence: ; Tel.: +49-391-67-13374
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Hsieh YP, Hung YM, Tsai MH, Lai LC, Chuang EY. 16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences. FRONTIERS IN BIOINFORMATICS 2022; 2:905489. [PMID: 36304264 PMCID: PMC9580931 DOI: 10.3389/fbinf.2022.905489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Analyzing 16S ribosomal RNA (rRNA) sequences allows researchers to elucidate the prokaryotic composition of an environment. In recent years, third-generation sequencing technology has provided opportunities for researchers to perform full-length sequence analysis of bacterial 16S rRNA. RDP, SILVA, and Greengenes are the most widely used 16S rRNA databases. Many 16S rRNA classifiers have used these databases as a reference for taxonomic assignment tasks. However, some of the prokaryotic taxonomies only exist in one of the three databases. Furthermore, Greengenes and SILVA include a considerable number of taxonomies that do not have the resolution to the species level, which has limited the classifiers’ performance. In order to improve the accuracy of taxonomic assignment at the species level for full-length 16S rRNA sequences, we manually curated the three databases and removed the sequences that did not have a species name. We then established a taxonomy-based integrated database by considering both taxonomies and sequences from all three 16S rRNA databases and validated it by a mock community. Results showed that our taxonomy-based integrated database had improved taxonomic resolution to the species level. The integrated database and the related datasets are available at https://github.com/yphsieh/ItgDB.
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Affiliation(s)
- Yu-Peng Hsieh
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
| | - Yuan-Mao Hung
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- *Correspondence: Eric Y. Chuang, ; Liang-Chuan Lai,
| | - Eric Y. Chuang
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- College of Biomedical Engineering, China Medical University, Taichung, Taiwan
- *Correspondence: Eric Y. Chuang, ; Liang-Chuan Lai,
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13
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Chiriac MC, Bulzu PA, Andrei AS, Okazaki Y, Nakano SI, Haber M, Kavagutti VS, Layoun P, Ghai R, Salcher MM. Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR. MICROBIOME 2022; 10:84. [PMID: 35659305 PMCID: PMC9166423 DOI: 10.1186/s40168-022-01274-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples. RESULTS A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress. CONCLUSIONS A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.
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Affiliation(s)
- Maria-Cecilia Chiriac
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Yusuke Okazaki
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Shin-ichi Nakano
- Center of Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga Japan
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, Czech Republic
| | - Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Michaela M. Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
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14
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Peng M, Wang C, Wang Z, Huang X, Zhou F, Yan S, Liu X. Differences between the effects of plant species and compartments on microbiome composition in two halophyte Suaeda species. Bioengineered 2022; 13:12475-12488. [PMID: 35593105 PMCID: PMC9275862 DOI: 10.1080/21655979.2022.2076009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Root-related or endophytic microbes in halophytes play an important role in adaptation to extreme saline environments. However, there have been few comparisons of microbial distribution patterns in different tissues associated with halophytes. Here, we analyzed the bacterial communities and distribution patterns of the rhizospheres and tissue endosphere in two Suaeda species (S. salsa and S. corniculata Bunge) using the 16S rRNA gene sequencing. The results showed that the bacterial abundance and diversity in the rhizosphere were significantly higher than that of endophytic, but lower than that of bulk soil. Microbial-diversity analysis showed that the dominant phyla of all samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria and Firmicutes, among which Proteobacteria were extremely abundant in all the tissue endosphere. Heatmap and Linear discriminant analysis Effect Size (LEfSe) results showed that there were notable differences in microbial community composition related to plant compartments. Different networks based on plant compartments exhibited distinct topological features. Additionally, the bulk soil and rhizosphere networks were more complex and showed higher centrality and connectedness than the three endosphere networks. These results strongly suggested that plant compartments, and not species, affect microbiome composition.
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Affiliation(s)
- Mu Peng
- College of Biological Science and Technology, Hubei Minzu University, Hubei, China.,College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Chao Wang
- Zibo Academy of Agricultural Sciences, Zibo, China
| | - Zhiyong Wang
- College of Biological Science and Technology, Hubei Minzu University, Hubei, China
| | - Xiufang Huang
- College of Biological Science and Technology, Hubei Minzu University, Hubei, China
| | - Fangzhen Zhou
- College of Biological Science and Technology, Hubei Minzu University, Hubei, China
| | - Shaopeng Yan
- College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Xiaopeng Liu
- College of Biological Science and Technology, Hubei Minzu University, Hubei, China
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15
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Bryson SJ, Hunt KA, Stahl DA, Winkler MKH. Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations. Front Microbiol 2022; 13:825104. [PMID: 35547121 PMCID: PMC9083452 DOI: 10.3389/fmicb.2022.825104] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.
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Affiliation(s)
- Samuel J Bryson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Mari-Karoliina H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
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16
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Zhang FL, Yang YL, Zhang Z, Yao YY, Xia R, Gao CC, Du DD, Hu J, Ran C, Liu Z, Zhou ZG. Surface-Displayed Amuc_1100 From Akkermansia muciniphila on Lactococcus lactis ZHY1 Improves Hepatic Steatosis and Intestinal Health in High-Fat-Fed Zebrafish. Front Nutr 2021; 8:726108. [PMID: 34722607 PMCID: PMC8548614 DOI: 10.3389/fnut.2021.726108] [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: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 01/14/2023] Open
Abstract
Fatty liver and intestinal barrier damage were widespread in most farmed fish, which severely restrict the development of aquaculture. Therefore, there was an urgent need to develop green feed additives to maintain host liver and intestinal health. In this study, a probiotic pili-like protein, Amuc_1100 (AM protein), was anchored to the surface of Lactococcus lactis ZHY1, and the effects of the recombinant bacteria AM-ZHY1 on liver fat accumulation and intestinal health were evaluated. Zebrafish were fed a basal diet, high-fat diet, and high-fat diet with AM-ZHY1 (108 cfu/g) or control bacteria ZHY1 for 4 weeks. Treatment with AM-ZHY1 significantly reduced hepatic steatosis in zebrafish. Quantitative PCR (qPCR) detection showed that the expression of the lipogenesis [peroxisome-proliferator-activated receptors (PPARγ), sterol regulatory element-binding proteins-1c (SREBP-1c), fatty acid synthase (FAS), and acetyl-CoA carboxylase 1 (ACC1)] and lipid transport genes (CD36 and FABP6) in the liver were significantly downregulated (p < 0.05), indicating that AM-ZHY1 could reduce liver fat accumulation by inhibiting lipid synthesis and absorption. Moreover, supplementing AM-ZHY1 to a high-fat diet could significantly reduce serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels, indicating that liver injury caused by high-fat diets was improved. The expression of tumor necrosis factor (TNF)-a and interleukin (IL)-6 in the liver decreased significantly (p < 0.05), while IL-1β and IL-10 did not change significantly in the AM-ZHY1 group. Compared to the high-fat diet-fed group, the AM-ZHY1 group, but not the ZHY1 group, significantly increased the expression of intestinal tight junction (TJ) proteins (TJP1a, claudina, claudin7, claudin7b, claudin11a, claudin12, and claudin15a; p < 0.05). Compared to the high-fat diet group, the Proteobacteria and Fusobacteria were significantly reduced and increased in the AM-ZHY1 group, respectively. In conclusion, the recombinant bacteria AM-ZHY1 has the capacity to maintain intestinal health by protecting intestinal integrity and improving intestinal flora structure and improving fatty liver disease by inhibiting lipid synthesis and absorption. This study will lay a foundation for the application of AM protein in improving abnormal fat deposition and restoring the intestinal barrier in fish.
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Affiliation(s)
- Feng-Li Zhang
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ya-Lin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan-Yuan Yao
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Xia
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chen-Chen Gao
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong-Dong Du
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Hu
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Zhi-Gang Zhou
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Ma L, Wang WQ, Shi R, Zhang XM, Li X, Yang YS, Mo MH. Effects of organic acids on the chemotaxis profiles and biocontrol traits of antagonistic bacterial endophytes against root-rot disease in Panax notoginseng. Antonie van Leeuwenhoek 2021; 114:1771-1789. [PMID: 34510303 DOI: 10.1007/s10482-021-01636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Understanding the role of chemotaxis in ecological interactions between plants and microbes in the rhizosphere is necessary to optimize biocontrol strategies targeting plant soil-borne diseases. Therefore, we examined and profiled the antagonistic endophytic bacteria (AEB) population with chemotaxis potential in the medicinal plant Panax notoginseng using a cheA gene-based approach coupled with 16S rRNA sequencing. Phylogenetic analysis of the chemotactic AEB (CAEB) community in P. notoginseng enabled the identification of 56 CAEB strains affiliated with 30 species of Actinobacteria, Firmicutes, and Proteobacteria; Firmicutes, especially Bacillus, were predominant. We then systematically quantified the chemotactic response profiles of CAEB toward five organic acid (OA) attractants: citric acid, fumaric acid (FA), malic acid, oxalic acid, and succinic acid. Further hierarchical cluster analysis revealed that the chemotaxis of CAEB to the same attractant exhibited different patterns among not only genera but also species and even strains of the same species. Following chemotaxis and hierarchical analysis, we selected the strongest chemoattractant, fumaric acid (FA), as the target for evaluating the effects of OAs on the representative CAEB strain Bacillus amyloliquefaciens subsp. plantarum YP1. Application of FA significantly stimulated the chemotaxis ability and growth of YP1, and increased the transcript levels of cheA and biocontrol-related genes in YP1. This is the first study to characterise the diversity of chemotaxis profiles toward OAs in natural bacterial assemblages of P. notoginseng and to highlight how FA promotes the biocontrol-related traits of P. notoginseng-associated CAEB.
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Affiliation(s)
- Li Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Wu-Qin Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Rui Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Xue-Mei Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Xin Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Yu-Sen Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Ming He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China. .,Ministry of Education Key Laboratory for Microbial Resources, Yunnan University, Kunming, 650091, China.
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18
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Cappello S, Caruso G, Bergami E, Macrì A, Venuti V, Majolino D, Corsi I. New insights into the structure and function of the prokaryotic communities colonizing plastic debris collected in King George Island (Antarctica): Preliminary observations from two plastic fragments. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125586. [PMID: 34030422 DOI: 10.1016/j.jhazmat.2021.125586] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
In Antarctic regions, the composition and metabolic activity of microbial assemblages associated with plastic debris ("plastisphere") are almost unknown. A macroplastic item from land (MaL, 30 cm) and a mesoplastic from the sea (MeS, 4 mm) were collected in Maxwell Bay (King George Island, South Shetland) and analyzed by Fourier transform infrared spectroscopy in attenuated total reflectance geometry (FTIR-ATR), which confirmed a polystyrene foam and a composite high-density polyethylene composition for MaL and MeS, respectively. The structure and function of the two plastic-associated prokaryotic communities were studied by complementary 16S ribosomal RNA gene clone libraries, total bacterioplankton and culturable heterotrophic bacterial counts, enzymatic activities of the whole community and enzymatic profiles of bacterial isolates. Results showed that Gamma- and Betaproteobacteria (31% and 28%, respectively) dominated in MeS, while Beta- and Alphaproteobacteria (21% and 13%, respectively) in MaL. Sequences related to oil degrading bacteria (Alcanivorax,Marinobacter) confirmed the known anthropogenic pressure in King George Island. This investigation on plastic-associated prokaryotic structure and function represents the first attempt to characterize the ecological role of plastisphere in this Antarctic region and provides the necessary background for future research on the significance of polymer type, surface characteristics and environmental conditions in shaping the plastisphere.
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Affiliation(s)
- Simone Cappello
- Institute for Biological Resources and Marine Biotechnologies (IRBIM), National Research Council (CNR), Spianata San Raineri 86, Messina 98122, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences (ISP), National Research Council (CNR), Spianata San Raineri 86, Messina 98122, Italy.
| | - Elisa Bergami
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli 4, Siena 53100, Italy
| | - Angela Macrì
- Institute for Biological Resources and Marine Biotechnologies (IRBIM), National Research Council (CNR), Spianata San Raineri 86, Messina 98122, Italy; Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, Messina 98166, Italy
| | - Valentina Venuti
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, Messina 98166, Italy
| | - Domenico Majolino
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, Messina 98166, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli 4, Siena 53100, Italy
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Production, structural and biochemical characterization relevant to antitumor property of acidic exopolysaccharide produced from Bacillus sp. NRC5. Arch Microbiol 2021; 203:4337-4350. [PMID: 34110482 DOI: 10.1007/s00203-021-02422-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
This study targeted the production of exopolysaccharide from Bacillus sp. NRC5 grown in Egyptian seawater to use it as natural antitumor therapy. The biological activities of selected exopolysaccharide (BEPS) as an antioxidant, anti-inflammatory and anticancer have been studied. BEPS was evaluated as an anti-inflammatory in vitro against cyclooxygenase (COX-1 and COX-2) and evaluated as an anticancer on human breast and prostate cancer cell lines (MCF-7 and PC3). In addition, BEPS antitumor activity was tested against the Ehrlich Ascites Carcinoma (EAC) model. The BEPS presented potent antioxidant activities, consisted of glucose, mannose, and mannuronic acid in a molar ratio of 1.0:1.7:0.8 with a molecular weight of 3.59 × 105 g/mol. BEPS showed a promising COX-2 inhibitory effect in comparison with the reference drug celecoxib. BEPS appeared efficient anticancer property, where it killed 64.20 and 70.20% of MCF-7 and PC3 cells at 100 µg/ml, respectively (IC50, 76.70, and 70.40 µg/ml, respectively). BEPS exhibited antitumor ability as it prolonged the lifespan of mice to reach 75 days instead of 20 days in the tumor control, reduced viable cancer cells count, tumor volume and weight, modulated blood components, and white blood cells differentiation. BEPS produced from Bacillus sp. NRC5 showed its antioxidant and anti-inflammatory abilities and antitumor abilities, which may all be attributed to its unique composition containing sulfated moieties and uronic acids.
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Ding Q, Zhang Z, Li Y, Liu H, Hao Q, Yang Y, Ringø E, Olsen RE, Clarke JL, Ran C, Zhou Z. Propionate induces intestinal oxidative stress via Sod2 propionylation in zebrafish. iScience 2021; 24:102515. [PMID: 34142031 PMCID: PMC8188496 DOI: 10.1016/j.isci.2021.102515] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/17/2021] [Accepted: 05/03/2021] [Indexed: 12/21/2022] Open
Abstract
Propionate and propionyl-CoA accumulation have been associated with the development of mitochondrial dysfunction. In this study, we show that propionate induces intestinal damage in zebrafish when fed a high-fat diet (HFD). The intestinal damage was associated with oxidative stress owing to compromised superoxide dismutase 2 (Sod2) activity. Global lysine propionylation analysis of the intestinal samples showed that Sod2 was propionylated at lysine 132 (K132), and further biochemical assays demonstrated that K132 propionylation suppressed Sod2 activity. In addition, sirtuin 3 (Sirt3) played an important role in regulating Sod2 activity via modulating de-propionylation. Finally, we revealed that intestinal oxidative stress resulting from Sod2 propionylation contributed to compositional change of gut microbiota. Collectively, our results in this study show that there is a link between Sod2 propionylation and oxidative stress in zebrafish intestines and highlight the potential mechanism of intestinal problems associated with high propionate levels. Propionate supplementation in high-fat diet induces intestinal damage Propionate induces oxidative stress via Sod2 propionylation at 132 lysine site Increased Sod2 propionylation is associated with reduced expression of Sirt3 Intestinal oxidative stress alters gut microbiota composition
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Affiliation(s)
- Qianwen Ding
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Li
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongliang Liu
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang Hao
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Einar Ringø
- Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Rolf Erik Olsen
- Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | | | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhou
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Ye L, Liu G, Yao T, Lu J. Monitoring of antimicrobial resistance genes in the spotted sea bass (Lateolabrax maculatus): Association with the microbiome and its environment in aquaculture ponds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 276:116714. [PMID: 33592436 DOI: 10.1016/j.envpol.2021.116714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/18/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance genes (ARGs) pose a serious threat to environment and human health. However, few studies address the abundance and distribution of ARGs associated with farmed fish and their aquaculture environment. Here we conducted an analysis of the abundance and distribution of gut and gill ARGs by quantitative PCR techniques associated with the spotted sea bass (Lateolabrax maculatus) as well as the bacterial communities in the surrounding environment (water and sediment). For this purpose, we sampled six aquaculture ponds in Zhuhai, Guangdong Province, the largest spotted sea bass cultivation site in China. Predominant ARGs were floR, sul2, and tetM-01 in the gut and tetQ, sul1, and floR in the gills. The copy numbers of sul1, sul2, and cmlA1-01 were significantly higher in the environment. Moreover, significant differences were found among the microbiota of the gut, gills, and environment. The former was more similar to those of the environmental microbial communities compared with other sources. The fish gut and gill microbiota were predominantly populated by Fusobacteria and Actinobacteria, respectively. In contrast, Proteobacteria were dominant in water and sediment. Correlation analysis showed that Fusobacteria and Actinobacteria positively correlated with floR and tetQ, respectively, indicating that these microbes were potential hosts for ARGs. Our results showed that ARGs in farmed fish showed marked difference with their aquaculture environment, thus providing a valuable reference for identifying deleterious ARGs in aquatic fish.
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Affiliation(s)
- Lingtong Ye
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Guangfeng Liu
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Tuo Yao
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Jie Lu
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
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Guo Y, Chen J, Tsolmon B, He A, Guo J, Yang J, Bao Y. Effects of subsidence and transplanted trees on soil arbuscular mycorrhizal fungal diversity in a coal mining area of the Loess Plateau. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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23
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Jones RB, Berger PK, Plows JF, Alderete TL, Millstein J, Fogel J, Iablokov SN, Rodionov DA, Osterman AL, Bode L, Goran MI. Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants. Gut Microbes 2020; 12:1813534. [PMID: 32887539 PMCID: PMC7524300 DOI: 10.1080/19490976.2020.1813534] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 02/03/2023] Open
Abstract
Infant formula feeding, compared with human milk, has been associated with development of a distinct infant gut microbiome, but no previous study has examined effects of formula with added sugars. This work examined differences in gut microbiota among 91 Hispanic infants who consumed human milk [at breast (BB) vs. pumped in bottle (BP)] and 2 kinds of infant formula [(traditional lactose-based (TF) vs. lactose-reduced with added sugar (ASF)]. At 1 and 6 months, infant stool was collected to characterize gut microbiota. At 6 months, mothers completed 24-hour dietary recalls and questionnaires to determine infant consumption of human milk (BB vs. BP) or formula (TF vs. ASF). Linear regression models were used to determine associations of milk consumption type and microbial features at 6 months. Infants in the formula groups exhibited a significantly more 'mature' microbiome than infants in the human milk groups with the most pronounced differences observed between the ASF vs. BB groups. In the ASF group, we observed reduced log-normalized abundance of Bifidobacteriaceae (TF-BB Mean Difference = -0.71, ASF-BB Mean Difference = -1.10), and increased abundance of Lachnospiraceae (TF-BB Mean Difference = +0.89, ASF-BB Mean Difference = +1.20). We also observed a higher Community Phenotype Index of propionate, most likely produced by Lachnospiraceae, in the ASF group (TF-BB Mean Difference = +0.27, ASF-BB Mean Difference = +0.36). This study provides the first evidence that consumption of infant formula with added sugar may have a stronger association than birth delivery mode, infant caloric intake, and maternal BMI on the infant's microbiome at 6 months of age.
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Affiliation(s)
- Roshonda B. Jones
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Paige K. Berger
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Jasmine F. Plows
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Joshua Millstein
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jennifer Fogel
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Stanislav N. Iablokov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Dmitry A. Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California, San Diego, CA, USA
| | - Michael I. Goran
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
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24
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Performance of Anaerobic Digestion of Acidified Palm Oil Mill Effluent under Various Organic Loading Rates and Temperatures. WATER 2020. [DOI: 10.3390/w12092432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This study compared the performance of thermophilic and mesophilic digesters of an anaerobic digestion system from palm oil mill effluent (POME), in which temperature is a key parameter that can greatly affect the performance of anaerobic digestion. The digesters were incubated at two distinct temperatures of 55 and 37 °C, and operated with varying organic loading rates (OLRs) of 2.4, 3.2, and 4.0 g COD/L.d by altering the chemical oxygen demand (COD) of acidified POME during feeding. The results indicated that the performance of anaerobic digestion increased as the OLR increased from 2.4 to 4.0 g COD/L.d. At the OLR of 4.0 g COD/L.d, the thermophilic condition showed the highest methane yield of 0.31 ± 0.01 L/g COD, accompanied by the highest COD removal and volatile solid reduction, which were found to be higher than the mesophilic condition. Microbial community analysis via denaturing gradient gel electrophoresis (DGGE) revealed that Methanothermobacter sp. emerges as the dominant microbe, which is known to utilize the carbon dioxide pathway with hydrogen acting as an electron donor for methane formation
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25
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Fan D, Subramanian S, Smith DL. Plant endophytes promote growth and alleviate salt stress in Arabidopsis thaliana. Sci Rep 2020; 10:12740. [PMID: 32728116 PMCID: PMC7391687 DOI: 10.1038/s41598-020-69713-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) are a functionally diverse group of microbes having immense potential as biostimulants and stress alleviators. Their exploitation in agro-ecosystems as an eco-friendly and cost-effective alternative to traditional chemical inputs may positively affect agricultural productivity and environmental sustainability. The present study describes selected rhizobacteria, from a range of origins, having plant growth promoting potential under controlled conditions. A total of 98 isolates (ectophytic or endophytic) from various crop and uncultivated plants were screened, out of which four endophytes (n, L, K and Y) from Phalaris arundinacea, Solanum dulcamara, Scorzoneroides autumnalis, and Glycine max, respectively, were selected in vitro for their vegetative growth stimulating effects on Arabidopsis thaliana Col-0 seedlings with regard to leaf surface area and shoot fresh weight. A 16S rRNA gene sequencing analysis of the strains indicated that these isolates belong to the genera Pseudomonas, Bacillus, Mucilaginibacter and Rhizobium. Strains were then further tested for their effects on abiotic stress alleviation under both Petri-plate and pot conditions. Results from Petri-dish assay indicated strains L, K and Y alleviated salt stress in Arabidopsis seedlings, while strains K and Y conferred increases in fresh weight and leaf area under osmotic stress. Results from subsequent in vivo trials indicated all the isolates, especially strains L, K and Y, distinctly increased A. thaliana growth under both normal and high salinity conditions, as compared to control plants. The activity of antioxidant enzymes (ascorbate peroxidase, catalase and peroxidase), proline content and total antioxidative capacity also differed in the inoculated A. thaliana plants. Furthermore, a study on spatial distribution of the four strains, using either conventional Petri-plate counts or GFP-tagged bacteria, indicated that all four strains were able to colonize the endosphere of A. thaliana root tissue. Thus, the study revealed that the four selected rhizobacteria are good candidates to be explored as plant growth stimulators, which also possess salt stress mitigating property, partially by regulating osmolytes and antioxidant enzymes. Moreover, the study is the first report of Scorzoneroides autumnalis (fall dandelion) and Solanum dulcamara (bittersweet) associated endophytes with PGP effects.
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Affiliation(s)
- Di Fan
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| | - Sowmyalakshmi Subramanian
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| | - Donald L Smith
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada.
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26
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Fan D, Subramanian S, Smith DL. Plant endophytes promote growth and alleviate salt stress in Arabidopsis thaliana. Sci Rep 2020. [PMID: 32728116 DOI: 10.1038/s41598-020-69713-] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) are a functionally diverse group of microbes having immense potential as biostimulants and stress alleviators. Their exploitation in agro-ecosystems as an eco-friendly and cost-effective alternative to traditional chemical inputs may positively affect agricultural productivity and environmental sustainability. The present study describes selected rhizobacteria, from a range of origins, having plant growth promoting potential under controlled conditions. A total of 98 isolates (ectophytic or endophytic) from various crop and uncultivated plants were screened, out of which four endophytes (n, L, K and Y) from Phalaris arundinacea, Solanum dulcamara, Scorzoneroides autumnalis, and Glycine max, respectively, were selected in vitro for their vegetative growth stimulating effects on Arabidopsis thaliana Col-0 seedlings with regard to leaf surface area and shoot fresh weight. A 16S rRNA gene sequencing analysis of the strains indicated that these isolates belong to the genera Pseudomonas, Bacillus, Mucilaginibacter and Rhizobium. Strains were then further tested for their effects on abiotic stress alleviation under both Petri-plate and pot conditions. Results from Petri-dish assay indicated strains L, K and Y alleviated salt stress in Arabidopsis seedlings, while strains K and Y conferred increases in fresh weight and leaf area under osmotic stress. Results from subsequent in vivo trials indicated all the isolates, especially strains L, K and Y, distinctly increased A. thaliana growth under both normal and high salinity conditions, as compared to control plants. The activity of antioxidant enzymes (ascorbate peroxidase, catalase and peroxidase), proline content and total antioxidative capacity also differed in the inoculated A. thaliana plants. Furthermore, a study on spatial distribution of the four strains, using either conventional Petri-plate counts or GFP-tagged bacteria, indicated that all four strains were able to colonize the endosphere of A. thaliana root tissue. Thus, the study revealed that the four selected rhizobacteria are good candidates to be explored as plant growth stimulators, which also possess salt stress mitigating property, partially by regulating osmolytes and antioxidant enzymes. Moreover, the study is the first report of Scorzoneroides autumnalis (fall dandelion) and Solanum dulcamara (bittersweet) associated endophytes with PGP effects.
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Affiliation(s)
- Di Fan
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| | - Sowmyalakshmi Subramanian
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| | - Donald L Smith
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada.
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Fan W, Wu J. Short-term effects of returning granulated straw on soil microbial community and organic carbon fractions in dryland farming. J Microbiol 2020; 58:657-667. [PMID: 32583286 DOI: 10.1007/s12275-020-9266-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 11/25/2022]
Abstract
We conducted a 2-year field experiment which was comprised of five treatments, namely no straw returning (CK), straw mulching (SM), straw plowed into the soil (SP), and straw returned in granulated form (SG). The aim of this study was to investigate the effects of different straw returning modes on soil bacterial and fungal community structure and their relationships to soil organic carbon (SOC) fractions at three different soil depths (0-20, 20-40, and 40-60 cm) in a dryland under maize cultivation in Northeast (NE) China. SM, SP, and SG treatments significantly increased SOC content. Compared with SM and SP treatments, SG treatment significantly increased the content of SOC and easily oxidizable carbon (EOC) in the topsoil (0-20 cm depth), and increased dissolved organic carbon (DOC) and SOC content of the light fraction (LFOC) in the 20-40 cm layer. Meanwhile, SG treatment exhibited the highest microbial biomass C (MBC) content in all of the three soil depths. SG treatment also enhanced bacterial richness as well as fungal richness and diversity in the upper 40 cm of soil. In addition, SG treatment increased the relative abundance of Proteobacteria in all depths, and had the highest relative abundance of Basidiomycota in the first 20 cm of soil. SP treatment showed the lowest soil organic carbon content in all fractions and soil microbial community composition. SM treatment exhibited similar results to SG treatment in SOC, DOC, and LFOC contents, and bacterial diversity in the topsoil and subsoil. As a whole, treatment SG improved soil quality and maize yield, hence we recommend returning granulated straw as the most effective practice for enhancing labile SOC fractions as well as maintaining soil diversity and microbial richness of arid farmlands in NE China.
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Affiliation(s)
- Wei Fan
- College of Resources and Environment Sciences, Jilin Agricultural University, Changchun, 130118, P. R. China
| | - Jinggui Wu
- College of Resources and Environment Sciences, Jilin Agricultural University, Changchun, 130118, P. R. China.
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28
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Moss EL, Maghini DG, Bhatt AS. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat Biotechnol 2020; 38:701-707. [PMID: 32042169 PMCID: PMC7283042 DOI: 10.1038/s41587-020-0422-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 12/12/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.
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Affiliation(s)
- Eli L Moss
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Dylan G Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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Partial enteral nutrition has no benefit on bone health but improves growth in paediatric patients with quiescent or mild Crohn's disease. Clin Nutr 2020; 39:3786-3796. [PMID: 32376096 DOI: 10.1016/j.clnu.2020.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/28/2020] [Accepted: 04/14/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND AND AIMS Exclusive enteral nutrition induces remission, improves bone health and growth in paediatric Crohn's disease (CD) patients, but is highly demanding for patients. We investigated efficacy of partial enteral nutrition (PEN) on bone health, growth and course in CD patients and assessed microbial and metabolic changes induced by PEN. METHODS We performed a two centre, non-randomized controlled intervention study in quiescent CD patients aged <19 years. Patients in intervention group received a liquid formula providing ~25% of daily energy for one year. At baseline, after 3, 6, 9 and 12 months, we collected data on bone, muscle (peripheral quantitative computertomography), anthropometry, disease activity (weighted paediatric CD activity index), metabolomic profile (liquid chromatography mass spectrometry), and faecal microbiome (16S rRNA gene sequencing). RESULTS Of 41 CD patients, 22 received the intervention (PEN) (mean age 15.0 ± 1.9 years, 50% male), 19 served as controls (non-PEN) (12.8 ± 3.1 years, 58% male). At baseline, mean bone quality was comparable to reference population with no improvement during the intervention. Relapse rate was low (8/41, PEN 4/22 and non-PEN 4/19, ns). PEN was not associated with microbiota community changes (beta diversity) but significantly reduced species diversity. Metabolome changes with upregulation of phosphatidylcholines in PEN patients are likely related to lipid and fatty acid composition of the formula. PEN significantly improved growth in a subgroup with Tanner stage 1-3. CONCLUSION In our cohort of paediatric CD patients, PEN did not affect bone health but improved growth in patients with a potential to grow.
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Paul T, Mukherjee SK. Induction of inflammatory response in human cell lines by arsenic-contaminated soil-isolated bacterium Micrococcus sp. KUMAs15. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Gu Z, Wu Y, Wang Y, Sun H, You Y, Piao C, Liu J, Wang Y. Lactobacillus rhamnosus Granules Dose-Dependently Balance Intestinal Microbiome Disorders and Ameliorate Chronic Alcohol-Induced Liver Injury. J Med Food 2019; 23:114-124. [PMID: 31747353 DOI: 10.1089/jmf.2018.4357] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
As the functions of Lactobacilli become better understood, there are increasing numbers of applications for Lactobacillus products. Previously, we have demonstrated that Lactobacillus rhamnosus GG (LGG) can prevent alcoholic liver injury. LGG granules were produced by fluid bed granulation with a media composed of starch, skimmed milk powder, whey powder, microcrystalline cellulose and maltose, and LGG fermented liquid that comprised 30-50% of the total weight. We found LGG granules dose-dependently protected against chronic alcoholic liver disease. When alcohol was consumed for 8 weeks with LGG treatment during the last 2 weeks, we demonstrated that the dose dependence of LGG granules can improve alcohol-induced liver injury through decreasing the levels of lipopolysaccharide and tumor necrosis factor-α in serum and prevent liver steatosis by suppressing triglyceride, free fatty acid, and malondialdehyde production in liver. Alcohol feeding caused a decline in the number of both Lactobacillus and Bifidobacterium, with a proportional increase in the number of Clostridium perfringens in ileum, and expansion of the Gram-negative bacteria Proteobacteria, Campylobacterales, and Helicobacter in cecum. However, LGG granule treatment restored the content of these microorganisms. In conclusion, LGG granule supplementation can improve the intestinal microbiota, reduce the number of gram-negative bacteria, and ameliorate alcoholic liver injury.
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Affiliation(s)
- Zelin Gu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Yanfeng Wu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Yu Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Haiyue Sun
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Ying You
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Chunhong Piao
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Jilin Agricultural University, Changchun, China
| | - Junmei Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Jilin Agricultural University, Changchun, China
| | - Yuhua Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun, China
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32
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Enrichment and characterization of a highly efficient tetrahydrofuran-degrading bacterial culture. Biodegradation 2019; 30:467-479. [DOI: 10.1007/s10532-019-09888-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 08/14/2019] [Indexed: 01/26/2023]
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33
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Tehler A, Farris JS, Lipscomb DL, Källersjö M. Phylogenetic analyses of the fungi based on large rDNA data sets. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Anders Tehler
- Naturhistoriska riksmuseet, Sektionen för kryptogambotanik, Box 50007, S-104 05 Stockholm, Sweden
| | - James S. Farris
- Naturhistoriska riksmuseet, Molekylärsystematiska laboratoriet, Box 50007, S-104 05 Stockholm, Sweden
| | - Diana L. Lipscomb
- Department of Biological Sciences, George Washington University, Washington D. C. 20052
| | - Mari Källersjö
- Naturhistoriska riksmuseet, Molekylärsystematiska laboratoriet, Box 50007, S-104 05 Stockholm, Sweden
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Sheth BP, Punia S, Dheer M, Rakhashiya PM, Patel PP, Thaker VS. Phylogenetic implications and secondary structure analyses of Vigna mungo (L.) Hepper genotypes based on nrDNA ITS2 sequences. Comput Biol Chem 2019; 78:389-397. [PMID: 30606693 DOI: 10.1016/j.compbiolchem.2018.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/25/2018] [Indexed: 01/07/2023]
Abstract
The internal transcribed spacers are highly preferred nuclear markers for the phylogenetic assessment of most eukaryotes, including plants. More recently, ITS2 has shown to possess equivalent phylogenetic significance as the entire ITS region. Vigna mungo L. Hepper is comparatively less explored from the molecular aspects as compared to the other species of the Vigna genus. The study presents the intra-individual characterization of 24 distinct genotypes Vigna mungo L. Hepper, using morphological as well as nrDNA ITS2 sequences and secondary structural data. The morphological characterization has been carried out using nine important agro-morphological traits. The molecular phylogeny of the sequence data, using the maximum parsimony and neighbor joining methods, shows the significant distinction based on the haplotypic variations amongst blackgram genotypes. The ITS2 secondary structures predicted using the homology modeling approach were compatible with the eukaryote-universal ITS2 secondary structure. The sequence-structure phylogeny reconstructed using the profile neighbour joining approach, also showed the presence of haplotypic variations in form of clusters on the phylogenetic tree. Further, the high GC content in the sequence data and highly negative ΔG values of the folded secondary structures ruled out the possibilities of the presence of any pseudogenes in the data set. Our analysis recommends the use of ITS2 sequence and secondary structure data at the intraspecific levels of plant taxonomical classification. Moreover, this study for the very first time reports the combined use morphological, and molecular data (using ITS2 sequence and secondary structural information) for the characterization of plants at the varietal level of taxonomical classification.
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Affiliation(s)
- Bhavisha P Sheth
- DST-Centre for Policy Research, Entrepreneurship Development Institute of India, P.O. Bhat 382428. Gandhinagar, Gujarat, India.
| | - Sumer Punia
- College of Agriculture, Sri Karan Narendra Agriculture University, Jobner, Jaipur, Rajasthan, India
| | - Meenakshi Dheer
- Agricultural Research Station, Ummedganj, Kota 324001. Rajasthan, India
| | - Purvi M Rakhashiya
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Pooja P Patel
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Vrinda S Thaker
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India.
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Peng C, Wang H, Jiang Y, Yang J, Lai H, Wei X. Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China. MICROBIAL ECOLOGY 2018; 76:1053-1062. [PMID: 29744532 DOI: 10.1007/s00248-018-1197-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.
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Affiliation(s)
- Chu Peng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - He Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Yingying Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Jinhua Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
| | - Xiaomin Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
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Apopa PL, Alley L, Penney RB, Arnaoutakis K, Steliga MA, Jeffus S, Bircan E, Gopalan B, Jin J, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Shah N, Boysen G, Ussery D, Nookaew I, Fagan P, Bebek G, Orloff MS. PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin. Front Microbiol 2018; 9:1757. [PMID: 30127774 PMCID: PMC6087756 DOI: 10.3389/fmicb.2018.01757] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the major form of lung cancer, with adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being its major subtypes. Smoking alone cannot completely explain the lung cancer etiology. We hypothesize that altered lung microbiome and chronic inflammatory insults in lung tissues contribute to carcinogenesis. Here we explore the microbiome composition of LUAD samples, compared to LUSC and normal samples. Extraction of microbiome DNA in formalin-fixed, paraffin-embedded (FFPE) lung tumor and normal adjacent tissues was meticulously performed. The 16S rRNA product from extracted microbiota was subjected to microbiome amplicon sequencing. To assess the contribution of the host genome, CD36 expression levels were analyzed then integrated with altered NSCLC subtype-specific microbe sequence data. Surprisingly phylum Cyanobacteria was consistently observed in LUAD samples. Across the NSCLC subtypes, differential abundance across four phyla (Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes) was identified based on the univariate analysis (p-value < 6.4e-4 to 3.2e-2). In silico metagenomic and pathway analyses show that presence of microcystin correlates with reduced CD36 and increased PARP1 levels. This was confirmed in microcystin challenged NSCLC (A427) cell lines and Cyanobacteria positive LUAD tissues. Controlling the influx of Cyanobacteria-like particles or microcystin and the inhibition of PARP1 can provide a potential targeted therapy and prevention of inflammation-associated lung carcinogenesis.
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Affiliation(s)
- Patrick L Apopa
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Lisa Alley
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Rosalind B Penney
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Konstantinos Arnaoutakis
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mathew A Steliga
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Susan Jeffus
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Emine Bircan
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Jing Jin
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Preecha Patumcharoenpol
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Nishi Shah
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - David Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Pebbles Fagan
- Department of Health Behavior and Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Gurkan Bebek
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, United States.,Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, United States.,Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States
| | - Mohammed S Orloff
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Ding Q, Zhang Z, Ran C, He S, Yang Y, Du Z, Zhang J, Zhou Z. The Hepatotoxicity of Palmitic Acid in Zebrafish Involves the Intestinal Microbiota. J Nutr 2018; 148:1217-1228. [PMID: 29982798 DOI: 10.1093/jn/nxy084] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/09/2018] [Indexed: 12/13/2022] Open
Abstract
Background Palmitic acid (PA) is the main saturated fatty acid naturally occurring in animal fats and vegetable oils. In recent decades, palm oil, an alternative lipid source containing high amounts of PA, has been widely used to replace fish oil in aquafeed. Objective We investigated the hepatotoxicity of PA in zebrafish and the underlying mechanism. Methods One-month-old zebrafish fed a high-fat diet (HFD) containing 16% soybean oil and 3 PA-incorporated HFDs [4%, 8%, and 12% PA (12PA)] for 2 wk (experiment 1) and 4 wk (experiment 2) were used to evaluate PA-induced liver damage and endoplasmic reticulum (ER) stress. Germ-free (GF) zebrafish fed low-fat, high-fat, or 12PA diets for 5 d were used to study the direct effects of PA on liver damage (experiment 3). GF zebrafish colonized with HFD or 12PA microbiota for 48 h were used to elucidate the indirect effects of PA-altered microbiota on liver damage (experiment 4). Last, GF zebrafish colonized with HFD or 12PA microbiota were used to evaluate the effects of different microbiotas on PA absorption (experiment 5). Results In experiment 1, the proportion of PA in the liver linearly increased as its percentage in dietary lipid increased (r2 = 0.83, P < 0.05). In experiment 2, the expression of glucose-regulated protein 78 (Grp78) and C/EBP-homologous protein (Chop) was higher in the 12PA group than in the HFD group (2.2- and 2.7-fold, respectively; P < 0.05). The activity of caspase-12 was increased by 61.1% in the 12PA group compared with the HFD group (P < 0.05). In experiment 3, caspase-12 activity was higher in the 12PA group than in the HFD group (P < 0.05). In experiment 4, GF zebrafish colonized with PA-altered microbiota had higher caspase-12 activity (P < 0.05) than those colonized by HFD microbiota. In experiment 5, PA-altered microbiota promoted PA absorption (P < 0.05) and aggravated ER stress and liver damage in the context of high-PA feeding. Conclusions The PA-altered microbiota indirectly induced ER stress and liver damage in zebrafish. Moreover, the PA microbiota promoted the absorption of PA, leading to enhanced PA overflow into the liver and aggravated hepatotoxicity of PA in zebrafish.
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Affiliation(s)
- Qianwen Ding
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Suxu He
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Zhenyu Du
- School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Jinxiong Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Zhigang Zhou
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Tuo X, Gu J, Wang X, Sun Y, Duan M, Sun W, Yin Y, Guo A, Zhang L. Prevalence of quinolone resistance genes, copper resistance genes, and the bacterial communities in a soil-ryegrass system co-polluted with copper and ciprofloxacin. CHEMOSPHERE 2018; 197:643-650. [PMID: 29407828 DOI: 10.1016/j.chemosphere.2018.01.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
The presence of high concentrations of residual antibiotics and antibiotic resistance genes (ARGs) in soil may pose potential health and environmental risks. This study investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) genes, copper resistance genes (CRGs), and the bacterial communities in a soil-ryegrass pot system co-polluted with copper and ciprofloxacin (CIP; 0, 20, or 80 mg kg-1 dry soil). Compared with the samples on day 0, the total relative abundances of the PMQR genes and mobile genetic elements (MGEs) were reduced significantly by 80-89% in the ryegrass and soil by the cutting stage (after 75 days). The abundances of PMQR genes and MGEs were reduced by 63-81% in soil treated with 20 mg kg-1 CIP compared with the other treatments, but the abundances of CRGs increased by 18-42%. The presence of 80 mg kg-1 CIP affected the microbial community structure in the soil by increasing the abundances of Acidobacteria and Thaumarchaeota, but decreasing those of Firmicutes. Redundancy analysis indicated that the pH and microbial composition were the main factors that affected the variations in PMQR genes, MGEs, and CRGs, where they could explain 42.2% and 33.3% of the variation, respectively. Furthermore, intI2 may play an important role in the transfer of ARGs. We found that 80 mg kg-1 CIP could increase the abundances of ARGs and CRGs in a soil-ryegrass pot system.
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Affiliation(s)
- Xiaxia Tuo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - YiXin Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Manli Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanan Yin
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Aiyun Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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Huang L, Chen Z, Wen Q, Zhao L, Lee DJ, Yang L, Wang Y. Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces. WATER RESEARCH 2018; 131:167-176. [PMID: 29281810 DOI: 10.1016/j.watres.2017.12.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
The Feast-Famine (FF) process has been frequently used to select polyhydroxyalkanoate (PHA)-accumulating mixed cultures (MCs), but there has been little insight into the ecophysiology of the microbial community during the selection process. In three FF systems with well-defined conditions, synchronized variations in higher-order properties of MCs and complicate microbial community succession mainly including enrichment and elimination of non-top competitors and unexpected turnover of top competitors, were observed. Quantification of PHA-accumulating function genes (phaC) revealed that the top competitors maintained the PHA synthesis by playing consecutive roles when the highly dynamic turnover occurred. Due to its specific physiological characteristics during the PHA-accumulating process, Thauera strain OTU 7 was found to be responsible for the fluctuating SVI, which threatened the robustness of the FF system. This trait was also responsible for its later competitive exclusion by the other PHA-producer, Paracoccus strain OTU 1. Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase. However, neutral processes, likely caused by predation from bacterial phages, also occurred, which led to the unpredictable temporal dynamics of the top competitors.
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Affiliation(s)
- Long Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Lizhi Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Lian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yao Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Zhao B, Hu Q, Guo X, Liao Z, Sarmiento F, Mesbah NM, Yan Y, Li J, Wiegel J. Natronolimnobius aegyptiacus sp. nov., an extremely halophilic alkalithermophilic archaeon isolated from the athalassohaline Wadi An Natrun, Egypt. Int J Syst Evol Microbiol 2018; 68:498-506. [DOI: 10.1099/ijsem.0.002524] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Qingping Hu
- College of Life science, Shanxi Normal University, Linfen, Shanxi 041000, PR China
| | - Xiaomeng Guo
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Life science, Shanxi Normal University, Linfen, Shanxi 041000, PR China
| | - Ziya Liao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Felipe Sarmiento
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Noha M. Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismaili 41522, Egypt
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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41
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Affiliation(s)
- William Wade
- Molecular Microbial Ecology Programme, Guy's, King's and St Thomas' Dental Institute, King's College London, Floor 28, Guy's Tower, Guy's Hospital, London SE1 9RT, UK.
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Wübbeler JH, Oppermann-Sanio FB, Ockenfels A, Röttig A, Osthaar-Ebker A, Verbarg S, Poehlein A, Madkour MH, Al-Ansari AM, Almakishah NH, Daniel R, Steinbüchel A. Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil. Int J Syst Evol Microbiol 2017; 67:4057-4063. [PMID: 28905699 DOI: 10.1099/ijsem.0.002249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Sphingomonas strain was isolated from a sample of desert soil collected near Jeddah in Saudi Arabia. A polyphasic approach was performed to characterize this strain, initially designated as G39T. Cells of strain G39T are motile, Gram-negative, catalase- and oxidase-positive. The strain is able to grow aerobically at 20-35 °C, pH 6.5-8 and tolerates up to 4 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the closest relative type strains of G39T are Sphingomonas mucosissima DSM 17494T (98.6 %), S. dokdonensis DSM 21029T (98.4 %) and S. hankookensis DSM 23329T (97.4 %). Furthermore, the average nucleotide identities between the draft genome sequence of strain G39T and the genome sequences of all other available and related Sphingomonas species are significantly below the threshold of 94 %. The G+C content of the draft genome (3.12 Mbp) is 65.84 %. The prevalent (>5 %) cellular fatty acids of G39T were C18 : 1ω7c, C16 : 1ω7c and/or C16 : 1ω6c, C14 : 0 2-OH and C16 : 0. The only detectable respiratory quinone was ubiquinone-10 and the polar lipids profile is composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, as well as unidentified lipids, phospholipids and glycolipids. The results of the conducted polyphasic approach confirmed that this isolate represents a novel species of the genus Sphingomonas, for which the name Sphingomonas jeddahensis sp. nov. is proposed. The type strain of this species is G39T (=DSM 103790T=LMG 29955T).
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Fred Bernd Oppermann-Sanio
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Andrea Ockenfels
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Annika Röttig
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Alena Osthaar-Ebker
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Susanne Verbarg
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Mohamed H Madkour
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Ahmed M Al-Ansari
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Naief H Almakishah
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany.,Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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Du C, Geng Z, Wang Q, Zhang T, He W, Hou L, Wang Y. Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest. J Microbiol 2017; 55:684-693. [PMID: 28865070 DOI: 10.1007/s12275-017-6466-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/13/2017] [Accepted: 07/05/2017] [Indexed: 01/16/2023]
Abstract
Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0-10, 10-20, 20-40, and 40-60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40-60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40-60 cm (62.88%). In particular, the 40-60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.
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Affiliation(s)
- Can Du
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Zengchao Geng
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China.
| | - Qiang Wang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Tongtong Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Wenxiang He
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Lin Hou
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yueling Wang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
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El-Newary SA, Ibrahim AY, Asker MS, Mahmoud MG, El Awady ME. Production, characterization and biological activities of acidic exopolysaccharide from marine Bacillus amyloliquefaciens 3MS 2017. ASIAN PAC J TROP MED 2017; 10:652-662. [PMID: 28870341 DOI: 10.1016/j.apjtm.2017.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/22/2017] [Accepted: 06/17/2017] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To evaluate in-vitro antioxidant, anti-inflammatory and antitumor abilities against human breast adenocarcinoma (MCF7) and human prostate cancer (PC3) as well as the suppressor effect of bacterial exopolysaccharide (BAEPS) on Ehrlich ascites carcinoma (EAC). METHODS In-vitro antioxidants characters of BAEPS were determined using various methods, while anti-inflammatory activity was estimated against cyclooxygenase (COX-1 and COX-2). In-vitro study, anticancer against MCF7 and PC3 were assessed by the mitochondrial dependent reduction of yellow MTT. In in-vivo study against EAC progression, mice were inoculated with EAC cells and then were orally administered BAEPS at 200 mg/kg after 24 h (equals to 0.10 of determined LD50)/10 d. RESULTS BAEPS was acidic exopolysaccharide contained uronic acid (12.3%) and sulfate (22.8%) with constitution of glucose, galactose and glucuronic acid in a molar ratio 1.6:1.0:0.9, respectively, with a molecular mass of 3.76 × 104 g/mol. BAEPS appeared potent antioxidant characters as free radical scavenging, oxygen reactive species scavenging and metal chelation, while its reducing power was low. BAEPS showed selective anti-inflammatory activity against COX-2 than COX-1, COX-2 selective. BAEPS exhibited potent and selective effect to breast cell cancer MCF7, the death percentage was 65.20% with IC50 = 70 μg/mL and IC90 = 127.40 μg/mL. BAEPS decreased counted viable EAC cells and induced non-viable cells. BAEPS improved all assessed hematological parameters. These improvements were reflected in the increasing median survival time and significant increment (P < 0.05) in life span. CONCLUSIONS BAEPS has anti-tumor activity with a good margin of safety. The anti-tumor activity of BAEPS may be due to its content from sulfated groups and uronic acids and they have antioxidant and anti-inflammatory properties.
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Affiliation(s)
- Samah A El-Newary
- Department of Medicinal and Aromatic Plants Research, National Research Centre, Dokki, Cairo, Egypt.
| | - Abeer Y Ibrahim
- Department of Medicinal and Aromatic Plants Research, National Research Centre, Dokki, Cairo, Egypt
| | - Mohsen S Asker
- Microbial Biotechnology Department, National Research Centre, Dokki, Cairo, Egypt
| | - Manal G Mahmoud
- Microbial Biotechnology Department, National Research Centre, Dokki, Cairo, Egypt
| | - Mohamed E El Awady
- Microbial Biotechnology Department, National Research Centre, Dokki, Cairo, Egypt
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Golob JL, Margolis E, Hoffman NG, Fredricks DN. Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities. BMC Bioinformatics 2017; 18:283. [PMID: 28558684 PMCID: PMC5450146 DOI: 10.1186/s12859-017-1690-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/16/2017] [Indexed: 02/01/2023] Open
Abstract
Background Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we evaluate the accuracy of operational taxonomic unit (OTU) generation, taxonomic classification, alpha- and beta-diversity measures for different settings in QIIME, MOTHUR and a pplacer-based classification pipeline, using a novel software package: DECARD. Results In-silico we generated 100 synthetic bacterial communities approximating human stool microbiomes to be used as a gold-standard for evaluating the colligative performance of microbiome analysis software. Our synthetic data closely matched the composition and complexity of actual healthy human stool microbiomes. Genus-level taxonomic classification was correctly done for only 50.4–74.8% of the source organisms. Miscall rates varied from 11.9 to 23.5%. Species-level classification was less successful, (6.9–18.9% correct); miscall rates were comparable to those of genus-level targets (12.5–26.2%). The degree of miscall varied by clade of organism, pipeline and specific settings used. OTU generation accuracy varied by strategy (closed, de novo or subsampling), reference database, algorithm and software implementation. Shannon diversity estimation accuracy correlated generally with OTU-generation accuracy. Beta-diversity estimates with Double Principle Coordinate Analysis (DPCoA) were more robust against errors introduced in processing than Weighted UniFrac. The settings suggested in the tutorials were among the worst performing in all outcomes tested. Conclusions Even when using the same classification pipeline, the specific OTU-generation strategy, reference database and downstream analysis methods selection can have a dramatic effect on the accuracy of taxonomic classification, and alpha- and beta-diversity estimation. Even minor changes in settings adversely affected the accuracy of the results, bringing them far from the best-observed result. Thus, specific details of how a pipeline is used (including OTU generation strategy, reference sets, clustering algorithm and specific software implementation) should be specified in the methods section of all microbiome studies. Researchers should evaluate their chosen pipeline and settings to confirm it can adequately answer the research question rather than assuming the tutorial or standard-operating-procedure settings will be adequate or optimal. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1690-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan L Golob
- Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA. .,Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
| | - Elisa Margolis
- Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA.,Seattle Childrens Hospital, Seattle, WA, USA
| | - Noah G Hoffman
- Department Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutch, 1100 Eastlake Ave E, E4-100, Seattle, WA, 98109, USA.,Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
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Zhao B, Lu W, Zhang S, Liu K, Yan Y, Li J. Reclassification of Bacillus saliphilus as Alkalicoccus saliphilus gen. nov., comb. nov., and description of Alkalicoccus halolimnae sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2017; 67:1557-1563. [DOI: 10.1099/ijsem.0.001759] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Baisuo Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Weidong Lu
- School of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, PR China
| | - Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Kang Liu
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
- School of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, PR China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
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Ersahin ME, Tao Y, Ozgun H, Gimenez JB, Spanjers H, van Lier JB. Impact of anaerobic dynamic membrane bioreactor configuration on treatment and filterability performance. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2016.12.057] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jumpponen A, Newsham KK, Neises DJ. Filamentous ascomycetes inhabiting the rhizoid environment of the liverwortCephaloziella variansin Antarctica are assessed by direct PCR and cloning. Mycologia 2017. [DOI: 10.1080/15572536.2004.11833090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Kevin K. Newsham
- Biosciences Division, British Antarctic Survey, Cambridge CB3 0ET, United Kingdom
| | - Daniel J. Neises
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
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The Effect of Land Use on Bacterial Communities in Saline–Alkali Soil. Curr Microbiol 2017; 74:325-333. [DOI: 10.1007/s00284-017-1195-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
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Beligala DH, Michaels HJ, Devries M, Phuntumart V. Multilocus Sequence Analysis of Root Nodule Bacteria Associated with <i>Lupinus</i> spp. and <i>Glycine max</i>. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/aim.2017.711063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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