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Thompson C, Silva R, Gibran FZ, Bacha L, de Freitas MAM, Thompson M, Landuci F, Tschoeke D, Zhang XH, Wang X, Zhao W, Gatts PV, de Almeida MG, de Rezende CE, Thompson F. The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes. MICROBIAL ECOLOGY 2024; 87:110. [PMID: 39215820 PMCID: PMC11365853 DOI: 10.1007/s00248-024-02423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ13C and δ15N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.
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Affiliation(s)
- Cristiane Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
| | - Raphael Silva
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Fernando Z Gibran
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), São Bernardo Do Campo, São Paulo, Brazil
| | - Leonardo Bacha
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Mayanne A M de Freitas
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Mateus Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Felipe Landuci
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Diogo Tschoeke
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
- Biomedical Engineer Program, COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Xiao-Hua Zhang
- Microbial Oceanography Lab, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Microbial Oceanography Lab, Ocean University of China, Qingdao, China
| | - Wenbin Zhao
- Microbial Oceanography Lab, Ocean University of China, Qingdao, China
| | - Pedro Vianna Gatts
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, Brazil
| | - Marcelo Gomes de Almeida
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, Brazil
| | - Carlos Eduardo de Rezende
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, Brazil
| | - Fabiano Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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Yoon DS, Kim DH, Kim JH, Sakakura Y, Hagiwara A, Park HG, Lee MC, Lee JS. Interactions between lipid metabolism and the microbiome in aquatic organisms: A review. MARINE POLLUTION BULLETIN 2024; 207:116858. [PMID: 39159571 DOI: 10.1016/j.marpolbul.2024.116858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024]
Abstract
Marine organisms' lipid metabolism contributes to marine ecosystems by producing a variety of lipid molecules. Historically, research focused on the lipid metabolism of the organisms themselves. Recent microbiome studies, however, have revealed that gut microbial communities influence the amount and type of lipids absorbed by organisms, thereby altering the organism's lipid metabolism. This has highlighted the growing importance of research on gut microbiota. This review highlights mechanisms by which gut microbiota facilitate lipid digestion and diversify the lipid pool in aquatic animals through the accelerated degradation of exogenous lipids and the transformation of lipid molecules. We also assess how environmental factors and pollutants, along with the innovative use of probiotics, interact with the gut microbiome to influence lipid metabolism within the host. We aim to elucidate the complex interactions between lipid metabolism and gut microbiota in aquatic animals by synthesizing current research and identifying knowledge gaps, providing a foundation for future explorations.
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Affiliation(s)
- Deok-Seo Yoon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Yoshitaka Sakakura
- Graduate School of Integrated Science and Technology, Nagasaki University, Nagasaki, Nagasaki 852-8521, Japan
| | - Atsushi Hagiwara
- Graduate School of Integrated Science and Technology, Nagasaki University, Nagasaki, Nagasaki 852-8521, Japan; Takuyo Co. Ltd., Kengun 1-35-11, Higashi-ku, Kumamoto 862-0911, Japan
| | - Heum Gi Park
- Department of Marine Ecology and Environment, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Min-Chul Lee
- Department of Food & Nutrition, College of Bio-Nano Technology, Gachon University, Seongnam 13120, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Gao S, Zhang S, Sun J, He X, Xue S, Zhang W, Li P, Lin L, Qu Y, Ward-Fear G, Chen L, Li H. Nanoplastic pollution changes the intestinal microbiome but not the morphology or behavior of a freshwater turtle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173178. [PMID: 38750733 DOI: 10.1016/j.scitotenv.2024.173178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Humans produce 350 million metric tons of plastic waste per year, leading to microplastic pollution and widespread environmental contamination, particularly in aquatic environments. This subsequently impacts aquatic organisms in myriad ways, yet the vast majority of research is conducted in marine, rather than freshwater systems. In this study, we exposed eggs and hatchlings of the Chinese soft-shelled turtle (Pelodiscus sinensis) to 80-nm polystyrene nanoplastics (PS-NPs) and monitored the impacts on development, behavior and the gut microbiome. We demonstrate that 80-nm PS-NPs can penetrate the eggshell and move into developing embryos. This led to metabolic impairments, as evidenced by bradycardia (a decreased heart rate), which persisted until hatching. We found no evidence that nanoplastic exposure affected hatchling morphology, growth rates, or levels of boldness and exploration, yet we discuss some potential caveats here. Exposure to nanoplastics reduced the diversity and homogeneity of gut microbiota in P. sinensis, with the level of disruption correlating to the length of environmental exposure (during incubation only or post-hatching also). Thirteen core genera (with an initial abundance >1 %) shifted after nanoplastic treatment: pathogenic bacteria increased, beneficial probiotic bacteria decreased, and there was an increase in the proportion of negative correlations between bacterial genera. These changes could have profound impacts on the viability of turtles throughout their lives. Our study highlights the toxicity of environmental NPs to the embryonic development and survival of freshwater turtles. We provide insights about population trends of P. sinensis in the wild, and future directions for research.
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Affiliation(s)
- Shuo Gao
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shufang Zhang
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jiahui Sun
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xinni He
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shaoshuai Xue
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wenyi Zhang
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Peng Li
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Longhui Lin
- Herpetological Research Center, Hangzhou Normal University, Hangzhou 311121, China
| | - Yanfu Qu
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Georgia Ward-Fear
- School of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Lian Chen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China.
| | - Hong Li
- Herpetological Research Center, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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D'Hooghe SMTJ, Bosch G, Sun M, Cools A, Hendriks WH, Becker AAMJ, Janssens GPJ. How important is food structure when cats eat mice? Br J Nutr 2024; 131:369-383. [PMID: 37694489 DOI: 10.1017/s0007114523002039] [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: 09/12/2023]
Abstract
Feeding whole prey to felids has shown to benefit their gastrointestinal health. Whether this effect is caused by the chemical or physical nature of whole prey is unknown. Fifteen domestic cats, as a model for strict carnivores, were either fed minced mice (MM) or whole mice (WM), to determine the effect of food structure on digestibility, mean urinary excretion time (MUET) of 15N, intestinal microbial activity and fermentation products. Faeces samples were collected after feeding all cats a commercially available extruded diet (EXT) for 10 d before feeding for 19 d the MM and WM diets with faeces and urine collected from day 11 to 15. Samples for microbiota composition and determination of MUET were obtained from day 16 to 19. The physical structure of the mice diet (minced or not) did not affect large intestinal fermentation as total SCFA and branched-chain fatty acid (BCFA), and most biogenic amine (BA) concentrations were not different (P > 0·10). When changing from EXT to the mice diets, the microbial community composition shifted from a carbolytic (Prevotellaceae) to proteolytic (Fusobacteriaceae) profile and led to a reduced faecal acetic to propionic acid ratio, SCFA, total BCFA (P < 0·001), NH3 (P = 0·04), total BA (P < 0·001) and para-cresol (P = 0·08). The results of this study indicate that food structure within a whole-prey diet is less important than the overall diet type, with major shifts in microbiome and decrease in potentially harmful fermentation products when diet changes from extruded to mice. This urges for careful consideration of the consequences of prey-based diets for gut health in cats.
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Affiliation(s)
- Sylvie M-T J D'Hooghe
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Guido Bosch
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, The Netherlands
| | - Mengmeng Sun
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - An Cools
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Wouter H Hendriks
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, The Netherlands
| | - Anne A M J Becker
- Department of Biomedical sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, Saint Kitts and Nevis
| | - Geert P J Janssens
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
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Alhadainy HA, Abdel-Karim AH, Fouad AF. Prevalence of Fusobacterium Species in Endodontic Infections Detected With Molecular Methods: Systematic Review and Meta-Analysis. J Endod 2023; 49:1249-1261. [PMID: 37611654 DOI: 10.1016/j.joen.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
INTRODUCTION Endodontic infections are polymicrobial; however, investigating the role of bacterial species is critical because they may influence pathogenesis, the development of symptoms, or the persistence of disease. This systematic review aimed to determine the prevalence of Fusobacterium species and its association with different types of endodontic infections. METHODS MEDLINE (Ovid), PubMed, Scopus, Web of Science, and Cochrane Library databases were used as electronic databases to retrieve relevant studies. The studies were evaluated for eligibility criteria, and the certainty in evidence and risk of bias were evaluated using critical appraisal tools for prevalence studies from the Joanna Briggs Institute. Forty studies were selected for meta-analysis and statistically analyzed for the relationship between the prevalence of Fusobacterium species and both the presence of symptoms and the type of infections (primary vs secondary/persistent) using meta-regression analysis. RESULTS The prevalence of Fusobacterium spp. in endodontic infections ranged from 3%-100% (mean = 42.51%) in the 40 included studies. Calculated confidence intervals indicated that the presence of Fusobacterium spp. was not statistically associated with the presence of symptoms or with the type of infections (the set of 2 predictors was not significant; P < .05). CONCLUSIONS The prevalence of Fusobacterium infection, which was identified with molecular methods, was not significant for overall regression using both predictors (ie, symptoms [symptomatic vs asymptomatic] and types of infections [primary vs secondary/persistent]).
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Affiliation(s)
- Hatem A Alhadainy
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Ashraf F Fouad
- Department of Endodontics, University of Alabama at Birmingham, Birmingham, Alabama.
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Bi S, Lai H, Guo D, Yi H, Li H, Liu X, Chen Q, Chen J, Zhang Z, Wei X, Li G, Xin G. The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats. BMC Ecol Evol 2023; 23:16. [PMID: 37158858 PMCID: PMC10165841 DOI: 10.1186/s12862-023-02120-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/28/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments. RESULTS The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines. CONCLUSIONS This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.
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Affiliation(s)
- Sheng Bi
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Guangdong, 518107, China
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Han Lai
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Dingli Guo
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Huadong Yi
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Haiyang Li
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Xuange Liu
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Qiuxian Chen
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Jiahui Chen
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Zhilun Zhang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Xuchong Wei
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Guifeng Li
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China.
| | - Guorong Xin
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Guangdong, 518107, China.
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Shang Y, Zhong H, Liu G, Wang X, Wu X, Wei Q, Shi L, Zhang H. Characteristics of Microbiota in Different Segments of the Digestive Tract of Lycodon rufozonatus. Animals (Basel) 2023; 13:ani13040731. [PMID: 36830518 PMCID: PMC9952230 DOI: 10.3390/ani13040731] [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: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of Lycodon rufozonatus. Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the L. rufozonatus gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.
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Affiliation(s)
- Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Huaming Zhong
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China
| | - Gang Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence:
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Are intratumoral microbiota involved in the progression of intraductal papillary mucinous neoplasms of the pancreas? Surgery 2023; 173:503-510. [PMID: 36404180 DOI: 10.1016/j.surg.2022.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/16/2022] [Accepted: 10/03/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Microbiota have been reported to influence the development of various gastrointestinal neoplasms through the mechanism of sustained inflammation; however, few data are available regarding their influence on intraductal papillary mucinous neoplasms. The aim of this study was to assess the association between specific microbiota and the clinicopathologic characteristics of intraductal papillary mucinous neoplasms of the pancreas. METHODS DNA was extracted from formalin-fixed, paraffin-embedded samples of 30 patients who underwent pancreatectomy for intraductal papillary mucinous neoplasm, and polymerase chain reaction was used to create sequence libraries using the primer set for the V3 and V4 region of 16S recombinant DNA. Filtered sequence reads were then processed into operational taxonomic units with a 97% identity threshold and the relative abundance of bacteria compared between the 2 groups using operational taxonomic units. RESULTS There was a trend toward fewer Firmicutes and more Proteobacteria and Fusobacteria in the relative abundance of main duct operational taxonomic units than in branch duct operational taxonomic units. The relative abundances of Bacteroidetes (P < .01) and Fusobacteria (P = .04) were significantly higher in invasive intraductal papillary mucinous neoplasms than in noninvasive intraductal papillary mucinous neoplasms. The relative abundance of the intestinal type was significantly lower in Firmicutes than the relative abundance of the nonintestinal type (P = .04). Notably, main duct operational taxonomic units with the intestinal subtype were affected by increased proportions of Proteobacteria and Fusobacteria, and Fusobacteria were abundant in the intestinal type of invasive main duct operational taxonomic units. CONCLUSION Intratumoral microbiota may be involved in the progression of operational taxonomic units.
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Bista PK, Pillai D, Roy C, Scaria J, Narayanan SK. Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes. Microbiol Spectr 2022; 10:e0029722. [PMID: 36219094 PMCID: PMC9769765 DOI: 10.1128/spectrum.00297-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/16/2022] [Indexed: 01/05/2023] Open
Abstract
Fusobacterium necrophorum is a Gram-negative, filamentous anaerobe prevalent in the mucosal flora of animals and humans. It causes necrotic infections in cattle, resulting in a substantial economic impact on the cattle industry. Although infection severity and management differ within F. necrophorum species, little is known about F. necrophorum speciation and the genetic virulence determinants between strains. To characterize the clinical isolates, we performed whole-genome sequencing of four bovine isolates (8L1, 212, B17, and SM1216) and one human isolate (MK12). To determine the phylogenetic relationship and evolution pattern and investigate the presence of antimicrobial resistance genes (ARGs) and potential virulence genes of F. necrophorum, we also performed comparative genomics with publicly available Fusobacterium genomes. Using up-to-date bacterial core gene (UBCG) set analysis, we uncovered distinct Fusobacterium species and F. necrophorum subspecies clades. Pangenome analyses revealed a high level of diversity among Fusobacterium strains down to species levels. The output also identified 14 and 26 genes specific to F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme, respectively, which could be essential for bacterial survival under different environmental conditions. ClonalFrameML-based recombination analysis suggested that extensive recombination among accessory genes led to species divergence. Furthermore, the only strain of F. necrophorum with ARGs was F. necrophorum subsp. funduliforme B35, with acquired macrolide and tetracycline resistance genes. Our custom search revealed common virulence genes, including toxins, adhesion proteins, outer membrane proteins, cell envelope, type IV secretion system, ABC (ATP-binding cassette) transporters, and transporter proteins. A focused study on these genes could help identify major virulence genes and inform effective vaccination strategies against fusobacterial infections. IMPORTANCE Fusobacterium necrophorum is an anaerobic bacterium that causes liver abscesses in cattle with an annual incidence rate of 10% to 20%, resulting in a substantial economic impact on the cattle industry. The lack of definite biochemical tests makes it difficult to distinguish F. necrophorum subspecies phenotypically, where genomic characterization plays a significant role. However, due to the lack of a good reference genome for comparison, F. necrophorum subspecies-level identification represents a significant challenge. To overcome this challenge, we used comparative genomics to validate clinical test strains for subspecies-level identification. The findings of our study help predict specific clades of previously uncharacterized strains of F. necrophorum. Our study identifies both general and subspecies-specific virulence genes through a custom search-based analysis. The virulence genes identified in this study can be the focus of future studies aimed at evaluating their potential as vaccine targets to prevent fusobacterial infections in cattle.
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Affiliation(s)
- Prabha K. Bista
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
| | - Deepti Pillai
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
- Indiana Animal Disease and Diagnostic Laboratory, Purdue University, West Lafayette, Indiana, USA
| | - Chayan Roy
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
- Environment Microbial Genomics, Plant and Environmental Microbiology, Copenhagen University, Copenhagen, Denmark
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Sanjeev K. Narayanan
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
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10
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Zhang Z, Fan Z, Yi M, Liu Z, Ke X, Gao F, Cao J, Wang M, Chen G, Lu M. Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition. Arch Microbiol 2022; 204:690. [DOI: 10.1007/s00203-022-03301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
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11
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Fernandes D, Andreyev J. The Role of the Human Gut Microbiome in Inflammatory Bowel Disease and Radiation Enteropathy. Microorganisms 2022; 10:1613. [PMID: 36014031 PMCID: PMC9415405 DOI: 10.3390/microorganisms10081613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
The human gut microbiome plays a key role in regulating host physiology. In a stable state, both the microbiota and the gut work synergistically. The overall homeostasis of the intestinal flora can be affected by multiple factors, including disease states and the treatments given for those diseases. In this review, we examine the relatively well-characterised abnormalities that develop in the microbiome in idiopathic inflammatory bowel disease, and compare and contrast them to those that are found in radiation enteropathy. We discuss how these changes may exert their effects at a molecular level, and the possible role of manipulating the microbiome through the use of a variety of therapies to reduce the severity of the underlying condition.
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Affiliation(s)
- Darren Fernandes
- The Department of Gastroenterology, United Lincolnshire NHS Trust, Lincoln County Hospital, Lincoln LN2 5QY, UK
| | - Jervoise Andreyev
- The Department of Gastroenterology, United Lincolnshire NHS Trust, Lincoln County Hospital, Lincoln LN2 5QY, UK
- The Biomedical Research Centre, Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
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12
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Couch C, Sanders J, Sweitzer D, Deignan K, Cohen L, Broughton H, Steingass S, Beechler B. The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus ( Odobenus rosmarus divergens). Proc Biol Sci 2022; 289:20220079. [PMID: 35382593 PMCID: PMC8984803 DOI: 10.1098/rspb.2022.0079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Arctic species are likely to experience rapid shifts in prey availability under climate change, which may alter their exposure to microbes and parasites. Here, we describe fecal bacterial and macroparasite communities and assess correlations with diet trophic level in Pacific walruses harvested during subsistence hunts by members of the Native Villages of Gambell and Savoonga on St Lawrence Island, Alaska. Fecal bacterial communities were dominated by relatively few taxa, mostly belonging to phyla Fusobacteriota and Firmicutes. Members of parasite-associated phyla Nematoda, Acanthocephala and Platyhelminthes were prevalent in our study population. We hypothesized that high versus low prey trophic level (e.g. fish versus bivalves) would result in different gut bacterial and macroparasite communities. We found that bacterial community structure correlated to diet, with nine clades enriched in walruses consuming higher-trophic-level prey. While no parasite compositional differences were found at the phylum level, the cestode genus Diphyllobothrium was more prevalent and abundant in walruses consuming higher-trophic-level prey, probably because fish are the intermediate hosts for this genus. This study suggests that diet is important for structuring both parasite and microbial communities of this culturally and ecologically important species, with potential implications for population health under climate change.
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Affiliation(s)
- Claire Couch
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA
| | - Justin Sanders
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Danielle Sweitzer
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Kristen Deignan
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Lesley Cohen
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Heather Broughton
- Department of Biology, Oregon State University-Cascades, Bend, OR, USA
| | - Sheanna Steingass
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA.,Oregon State University Marine Mammal Institute, Newport, OR, USA
| | - Brianna Beechler
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
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13
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Gut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strains. Sci Rep 2022; 12:4642. [PMID: 35301363 PMCID: PMC8930983 DOI: 10.1038/s41598-022-08511-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 03/07/2022] [Indexed: 12/29/2022] Open
Abstract
Some marine fishes are algae-feeding, and the microorganisms in their digestive tracts produce carbohydrate hydrolyzing enzymes such as agarose and fucosidase, which are potentially interesting resource for new functional enzymes. The purpose of this study was to establish a method for identifying and utilizing characteristic bacteria from the intestines of two algae-eating fish species: Andamia tetradactylus, which exclusively eats algae on the rock surface, and stellar rockskipper Entomacrodus stellifer, which feeds on both algae and invertebrates. We tested the species composition of the intestinal bacterial flora and found that Proteobacteria were commonly found both in species as in the common gut communities of marine fish, whereas Spirochaetes and Tenericutes occupied the flora of A. tetradactylus. We then performed anaerobic and aerobic cultures and isolated 34 and 44 strains including 48 strains belonged to Vibrio species from A. tetradactylus and E. stellifer. We observed that some Vibrio strains formed a clear boundary to avoid contacting other strains of bacteria. Whole-genome sequencing of such two Vibrio alginolyticus strains revealed two cyclic chromosomes commonly found in the genome of Vibrio species, and some unique genes encoding alginate lyase, chitinases, and type I-F CRISPR-associated endoribonuclease for the first time in Vibrio alginolyticus.
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14
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Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V, Mrazek J. Dysbiosis of skin microbiome and gut microbiome in melanoma progression. BMC Microbiol 2022; 22:63. [PMID: 35216552 PMCID: PMC8881828 DOI: 10.1186/s12866-022-02458-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/29/2022] [Indexed: 12/11/2022] Open
Abstract
Background The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression. Results Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier. Conclusion The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02458-5.
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Affiliation(s)
- Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Helena Kupcova Skalnikova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic
| | - Jana Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic.,Department of Radiobiology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic
| | - Veronika Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 128 00, Prague, Czech Republic
| | - Anna Palanova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic
| | - Vratislav Horak
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic
| | - Jakub Mrazek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
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15
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Li J, Zhou J, Zhao S, Guo R, Zhong C, Xue T, Peng Q, Zhang B, Fan B, Liu C, Ni Y, Ren L, Zhu X, Li B. Pathogenicity, infective dose and altered gut microbiota in piglets infected with porcine deltacoronavirus. Virology 2021; 567:26-33. [PMID: 34952414 DOI: 10.1016/j.virol.2021.12.006] [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: 10/13/2021] [Revised: 12/12/2021] [Accepted: 12/12/2021] [Indexed: 12/16/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that cause severe diarrhea, resulting in high mortality in neonatal piglets. Little is known regarding the pathogenicity of PDCoV in different infective dose and the dynamic changes in the composition of the gut microbiota in PDCoV-induced diarrhea piglets. In this study, 5-day-old piglets were experimentally infected with different dose of PDCoV. The challenged piglets developed typical symptoms, characterized by acute and severe watery diarrhea from 1 to 8 days post-inoculation (DPI), and viral shedding was detected in rectal swab until 11 DPI. Tissues of small intestines displayed significant macroscopic and microscopic lesions with clear viral antigen expression. However, no significant differences among groups were found in challenged piglets. Then alteration in gut microbiota in the jejunum and colon of PDCoV infected-piglets were analyzed using 16S rRNA sequencing. PDCoV infection reduced bacterial diversity and richness, and significantly altered the structure and abundance of the microbiota from the phylum to genus. Fusobacterium, and Proteobacteria was significantly increased (P < 0.05), while the abundance of Bacteroidota was markedly decreased in the infected-piglets. Furthermore, microbial function prediction indicated that the changes in intestinal bacterial also affected the immune system, excretory system, circulatory system, neurodegenerative disease, cardiovascular disease, xenobiotics biodegradation and metabolism, etc. These findings suggest that regulating gut microbiota community may be an effective approach for preventing PDCoV infection.
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Affiliation(s)
- Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; School of Pharmacy, Linyi University, Linyi, 276000, China; Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Shuqing Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; School of Pharmacy, Nanjing Tech University, Nanjing, 21009, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Chunyan Zhong
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; Biological Engineering Department, Southwest Guizhou Vocational and Technical College for Nationalities, Xingyi, 562400, China
| | - Tao Xue
- School of Pharmacy, Linyi University, Linyi, 276000, China
| | - Qi Peng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China
| | - Baotai Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Chuanmin Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; School of Pharmacy, Linyi University, Linyi, 276000, China; Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Yanxiu Ni
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Lili Ren
- School of Pharmacy, Nanjing Tech University, Nanjing, 21009, China
| | - Xing Zhu
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, China; Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
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16
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Fernandes A, Oliveira A, Soares R, Barata P. The Effects of Ionizing Radiation on Gut Microbiota, a Systematic Review. Nutrients 2021; 13:3025. [PMID: 34578902 PMCID: PMC8465723 DOI: 10.3390/nu13093025] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The human gut microbiota is defined as the microorganisms that collectively inhabit the intestinal tract. Its composition is relatively stable; however, an imbalance can be precipitated by various factors and is known to be associated with various diseases. Humans are daily exposed to ionizing radiation from ambient and medical procedures, and gastrointestinal side effects are not rare. METHODS A systematic search of PubMed, EMBASE, and Cochrane Library databases was conducted. Primary outcomes were changes in composition, richness, and diversity of the gut microbiota after ionizing radiation exposure. Standard methodological procedures expected by Cochrane were used. RESULTS A total of 2929 nonduplicated records were identified, and based on the inclusion criteria, 11 studies were considered. Studies were heterogeneous, with differences in population and outcomes. Overall, we found evidence for an association between ionizing radiation exposure and dysbiosis: reduction in microbiota diversity and richness, increase in pathogenic bacteria abundance (Proteobacteria and Fusobacteria), and decrease in beneficial bacteria (Faecalibacterium and Bifidobacterium). CONCLUSIONS This review highlights the importance of considering the influence of ionizing radiation exposure on gut microbiota, especially when considering the side effects of abdominal and pelvic radiotherapy. Better knowledge of these effects, with larger population studies, is needed.
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Affiliation(s)
- Ana Fernandes
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal;
| | - Ana Oliveira
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal;
| | - Raquel Soares
- Department of Biomedicine, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
| | - Pedro Barata
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Department of Pharmaceutical Science, Faculdade de Ciências da Saúde da Universidade Fernando Pessoa, 4249-004 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal
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17
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Lu CH, Liu WD, Huang CF, Liao CH, Lan TY, Kang CM, Lin CC, Yang YH, Hung CC. Primary hypogammaglobulinemia presenting with prostate abscess and Fusobacterium mortiferum bacteremia in a 28-year-old man. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:172-174. [PMID: 34475002 DOI: 10.1016/j.jmii.2021.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Chien-Hung Lu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Wang-Da Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan.
| | - Chun-Fu Huang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Chun-Hua Liao
- Department of Pediatrics, National Taiwan University Hospital Biomedical Park Hospital, Hsinchu, Taiwan.
| | - Ting-Yuan Lan
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Chun-Min Kang
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Chien-Chin Lin
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Yao-Hsu Yang
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan.
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Department of Tropical Medicine and Parasitology, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; China Medical University, Taichung, Taiwan.
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18
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Yang X, He L, Yan S, Chen X, Que G. The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey. BMC Oral Health 2021; 21:319. [PMID: 34172026 PMCID: PMC8229229 DOI: 10.1186/s12903-021-01683-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/19/2021] [Indexed: 12/12/2022] Open
Abstract
Background Supragingival plaque and saliva are commonly used for microbiome analysis. Many epidemiological studies have identified deciduous teeth caries as a risk factor for caries development in first permanent molar (FPM); nevertheless, to the best of our knowledge, there are no reports on the effects of deciduous teeth caries on the microbiome of healthy FPM. Additionally, it remains unclear whether saliva can be used instead of supragingival plaque for caries microbial studies. Therefore, we aimed to elucidate this issue, and to characterize and compare the oral microbiome of healthy FPMs in children with different caries statuses and that from children with and without caries in a similar microhabitat, by PacBio sequencing. Currently, few studies have investigated the oral microbiome of children using this technique. Methods Thirty children (aged 7–9 years) with mixed dentition were enrolled; 15 had dental caries, and 15 did not. Supragingival plaques of deciduous molars and maxillary FPMs, and non-stimulating saliva samples were collected. DNA was extracted and the v1–v9 regions of 16S rRNA were amplified. Subsequently, PacBio sequencing and bioinformatic analyses were performed for microbiome identification. Results The microbial alpha diversity of the saliva samples was lower than that of the supragingival plaque (p < 0.05); however, no differences were detected between deciduous teeth and FPMs (p > 0.05). In addition, the alpha and beta diversity of children with and without caries was also similar (p > 0.05). Nonmetric multidimensional scaling and Adonis analyses indicated that the microbial structure of salivary and supragingival plaque samples differ (p < 0.05). Further analysis of deciduous teeth plaque showed that Streptococcus mutans, Propionibacterium acidifaciens, and Veillonella dispar were more abundant in children with caries than in those without (p < 0.05); while in FPMs plaque, Selenomonas noxia was more abundant in healthy children (p < 0.05). No differences in microorganisms abundance were found in the saliva subgroups (p > 0.05). Conclusion We have determined that supragingival plaque was the best candidate for studying carious microbiome. Furthermore, S. mutans, V. dispar, and P. acidifaciens were highly associated with deciduous teeth caries. S. noxia may be associated with the abiding health of FPM; however, this requires additional studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-021-01683-0.
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Affiliation(s)
- Xiaoxia Yang
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Lidan He
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Siqi Yan
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Xinyi Chen
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Guoying Que
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China.
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19
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Nishi M, Yoshikawa Y, Kaji Y, Okamoto S, Inagaki K. Isolated Septic Arthritis of the Hip Due to Fusobacterium Nucleatum in An Immunocompetent Adult: A Case Report and Review of the Literature. J Orthop Case Rep 2021; 11:37-40. [PMID: 34327162 PMCID: PMC8310635 DOI: 10.13107/jocr.2021.v11.i04.2142] [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: 11/30/2022] Open
Abstract
Introduction: Hip septic arthritis is more common in children than in adults. Staphylococcus aureus and Streptococcus spp. are commonly found in association with septic joints. In contrast, Fusobacterium nucleatum septic arthritis in adults is extremely rare. To the best of our knowledge, only five cases have been reported in the literature in English, and three of them were cases of periprosthetic joint infection. We report a rare case of hip septic arthritis due to F. nucleatum in an immunocompetent adult. Case Presentation: A 56-year-old Asian man with a history of bilateral Perthes’ disease and mild alcoholic liver disease presented to our hospital complaining of worsening right hip pain and difficulty in walking for the previous 3 weeks. On presentation, his temperature was 38.7°C, and laboratory results showed a white blood cell count of 19 200 cells/µL and a C-reactive protein level of 43.56 mg/dL. Hip movements were limited due to pain. Contrast-enhanced computed tomography and magnetic resonance imaging showed fluid retention, suggesting infection. F. nucleatum was detected in the culture test from joint aspirate. Surgical drainage was performed 3 times in combination with antibiotherapy. Finally, we performed two-stage total hip arthroplasty, and the post-operative course was uneventful without implant loosening or infection relapse. Conclusion: The patient had a history of Perthes’ disease and had hip osteoarthritis, which may have contributed to the development of hip septic arthritis. We treated this rare case of hip septic arthritis due to F. nucleatum with two-stage revision surgery and antibiotherapy. Clinicians should be aware that F. nucleatum could be the etiologic agent of hip septic arthritis in an immunocompetent patient.
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Affiliation(s)
- Masanori Nishi
- Department of Orthopaedic Surgery, Showa University School of Medicine, Hatanodai, Shinagawa-ku, Tokyo, Japan
| | - Yasushi Yoshikawa
- Department of Orthopaedic Surgery, Showa University School of Medicine, Hatanodai, Shinagawa-ku, Tokyo, Japan
| | - Yasutaka Kaji
- Department of Orthopaedic Surgery, Showa University School of Medicine, Hatanodai, Shinagawa-ku, Tokyo, Japan
| | - Satoshi Okamoto
- Department of Orthopaedic Surgery, Showa University School of Medicine, Hatanodai, Shinagawa-ku, Tokyo, Japan
| | - Katsunori Inagaki
- Department of Orthopaedic Surgery, Showa University School of Medicine, Hatanodai, Shinagawa-ku, Tokyo, Japan
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20
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Theis KR, Florova V, Romero R, Borisov AB, Winters AD, Galaz J, Gomez-Lopez N. Sneathia: an emerging pathogen in female reproductive disease and adverse perinatal outcomes. Crit Rev Microbiol 2021; 47:517-542. [PMID: 33823747 DOI: 10.1080/1040841x.2021.1905606] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sneathia is an emerging pathogen implicated in adverse reproductive and perinatal outcomes. Although scarce, recent data suggest that vaginally residing Sneathia becomes pathogenic following its ascension into the upper urogenital tract, amniotic fluid, placenta, and foetal membranes. The role of Sneathia in women's health and disease is generally underappreciated because the cultivation of these bacteria is limited by their complex nutritional requirements, slow growth patterns, and anaerobic nature. For this reason, molecular methods are typically required for the detection and differential diagnosis of Sneathia infections. Here, we review the laboratory methods used for the diagnosis of Sneathia infections, the molecular mechanisms underlying its virulence, and its sensitivity to antibiotics. We further review the evidence of Sneathia's contributions to the pathogenesis of bacterial vaginosis, chorioamnionitis, preterm prelabour rupture of membranes, spontaneous preterm labour, stillbirth, maternal and neonatal sepsis, HIV infection, and cervical cancer. Collectively, growing evidence indicates that Sneathia represents an important yet underappreciated pathogen affecting the development and progression of several adverse clinical conditions diagnosed in pregnant women and their neonates, as well as in non-pregnant women.
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Affiliation(s)
- Kevin R Theis
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Violetta Florova
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.,Detroit Medical Center, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - Andrei B Borisov
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Andrew D Winters
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
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21
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Engevik MA, Danhof HA, Ruan W, Engevik AC, Chang-Graham AL, Engevik KA, Shi Z, Zhao Y, Brand CK, Krystofiak ES, Venable S, Liu X, Hirschi KD, Hyser JM, Spinler JK, Britton RA, Versalovic J. Fusobacterium nucleatum Secretes Outer Membrane Vesicles and Promotes Intestinal Inflammation. mBio 2021; 12:e02706-20. [PMID: 33653893 PMCID: PMC8092269 DOI: 10.1128/mbio.02706-20] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/22/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple studies have implicated microbes in the development of inflammation, but the mechanisms remain unknown. Bacteria in the genus Fusobacterium have been identified in the intestinal mucosa of patients with digestive diseases; thus, we hypothesized that Fusobacterium nucleatum promotes intestinal inflammation. The addition of >50 kDa F. nucleatum conditioned media, which contain outer membrane vesicles (OMVs), to colonic epithelial cells stimulated secretion of the proinflammatory cytokines interleukin-8 (IL-8) and tumor necrosis factor (TNF). In addition, purified F. nucleatum OMVs, but not compounds <50 kDa, stimulated IL-8 and TNF production; which was decreased by pharmacological inhibition of Toll-like receptor 4 (TLR4). These effects were linked to downstream effectors p-ERK, p-CREB, and NF-κB. F. nucleatum >50-kDa compounds also stimulated TNF secretion, p-ERK, p-CREB, and NF-κB activation in human colonoid monolayers. In mice harboring a human microbiota, pretreatment with antibiotics and a single oral gavage of F. nucleatum resulted in inflammation. Compared to mice receiving vehicle control, mice treated with F. nucleatum showed disruption of the colonic architecture, with increased immune cell infiltration and depleted mucus layers. Analysis of mucosal gene expression revealed increased levels of proinflammatory cytokines (KC, TNF, IL-6, IFN-γ, and MCP-1) at day 3 and day 5 in F. nucleatum-treated mice compared to controls. These proinflammatory effects were absent in mice who received F. nucleatum without pretreatment with antibiotics, suggesting that an intact microbiome is protective against F. nucleatum-mediated immune responses. These data provide evidence that F. nucleatum promotes proinflammatory signaling cascades in the context of a depleted intestinal microbiome.IMPORTANCE Several studies have identified an increased abundance of Fusobacterium in the intestinal tracts of patients with colon cancer, liver cirrhosis, primary sclerosing cholangitis, gastroesophageal reflux disease, HIV infection, and alcoholism. However, the direct mechanism(s) of action of Fusobacterium on pathophysiological within the gastrointestinal tract is unclear. These studies have identified that F. nucleatum subsp. polymorphum releases outer membrane vesicles which activate TLR4 and NF-κB to stimulate proinflammatory signals in vitro Using mice harboring a human microbiome, we demonstrate that F. nucleatum can promote inflammation, an effect which required antibiotic-mediated alterations in the gut microbiome. Collectively, these results suggest a mechanism by which F. nucleatum may contribute to intestinal inflammation.
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Affiliation(s)
- Melinda A Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Heather A Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wenly Ruan
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Amy C Engevik
- Department of Surgical Sciences, Vanderbilt University Medical Center, Nashville Tennessee, USA
| | - Alexandra L Chang-Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen A Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Zhongcheng Shi
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Yanling Zhao
- Department of Pediatrics, Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Colleen K Brand
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Evan S Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Susan Venable
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Xinli Liu
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, Texas, USA
| | - Kendal D Hirschi
- Department of Pediatrics and Human and Molecular Genetics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph M Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer K Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
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22
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Ares Á, Brisbin MM, Sato KN, Martín JP, Iinuma Y, Mitarai S. Extreme storms cause rapid but short-lived shifts in nearshore subtropical bacterial communities. Environ Microbiol 2021; 22:4571-4588. [PMID: 33448616 DOI: 10.1111/1462-2920.15178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/27/2020] [Accepted: 07/24/2020] [Indexed: 01/04/2023]
Abstract
Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment - locally known as red soil pollution - and caused moderate increases of macronutrients, especially SiO2 and PO4 3-, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Kirk N Sato
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan.,Friday Harbor Laboratories, University of Washington, WA, USA
| | - Juan P Martín
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Yoshiteru Iinuma
- Instrumental Analysis Section, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
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23
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Restivo VE, Kidd KA, Surette MG, Servos MR, Wilson JY. Rainbow darter (Etheostoma caeruleum) from a river impacted by municipal wastewater effluents have altered gut content microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141724. [PMID: 32889463 DOI: 10.1016/j.scitotenv.2020.141724] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Municipal wastewater treatment plant (WWTP) effluent contains pharmaceuticals and personal care products known to affect fish health and reproduction. The microbiome is a community of bacteria integral in maintaining host health and is influenced by species, diet, and environment. This study investigated changes in the diversity and composition of the gut content microbiome of rainbow darter (Etheostoma caeruleum) at ten sites on the Grand River, Ontario, Canada. Gut contents were collected in fall 2018 from these fish at sites upstream and downstream of two municipal wastewater treatment plants (WWTPs; Waterloo and Kitchener). 16S rRNA genes were sequenced to determine the composition and diversity (alpha and beta) of microbial taxa present. Gut content bacterial alpha diversity increased downstream of both WWTP outfalls; dominance of bacterial amplicon sequence variants decreased compared to upstream fish. Fish collected at different sites had distinct bacterial communities, with upstream samples dominant in Proteobacteria and Firmicutes, and downstream samples increasingly abundant in Proteobacteria and Cyanobacteria. In mammals, increased abundance of Proteobacteria is indicative of microbial dysbiosis and has been linked to altered health outcomes, but this is not yet known for fish. This research indicates that the fish gut content microbiome was altered downstream of WWTP effluent outfalls and could lead to negative health outcomes.
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Affiliation(s)
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Joanna Y Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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24
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Effects of Thermal Stress on the Gut Microbiome of Juvenile Milkfish ( Chanos chanos). Microorganisms 2020; 9:microorganisms9010005. [PMID: 33375015 PMCID: PMC7822048 DOI: 10.3390/microorganisms9010005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/04/2023] Open
Abstract
Milkfish, an important aquaculture species in Asian countries, are traditionally cultured in outdoor-based systems. There, they experience potentially stressful fluctuations in environmental conditions, such as temperature, eliciting changes in fish physiology. While the importance of the gut microbiome for the welfare and performance of fish has been recognized, little is known about the effects of thermal stress on the gut microbiome of milkfish and its interactions with the host’s metabolism. We investigated the gut microbiome of juvenile milkfish in a thermal stress experiment, comparing control (26 °C) and elevated temperature (33 °C) treatments over three weeks, analyzing physiological biomarkers, gut microbiome composition, and tank water microbial communities using 16S amplicon sequencing. The gut microbiome was distinct from the tank water and dominated by Cetobacterium, Enterovibrio, and Vibrio. We observed a parallel succession in both temperature treatments, with microbial communities at 33 °C differing more strongly from the control after the initial temperature increase and becoming more similar towards the end of the experiment. As proxy for the fish’s energy status, HSI (hepatosomatic index) was correlated with gut microbiome composition. Our study showed that thermal stress induced changes in the milkfish gut microbiome, which may contribute to the host’s habituation to elevated temperatures over time.
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25
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Rubel IF, Reino FM. Full Femoral Osteomyelitis Caused by Fusobacterium nucleatum in an Immunocompetent Adult: A Case Report. JBJS Case Connect 2020; 10:e20.00320. [PMID: 33449545 DOI: 10.2106/jbjs.cc.20.00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
CASE We present a 46-year-old man who developed a full femoral osteomyelitis caused by Fusobacterium nucleatum. The subtle presentation of the infection and the late onset of appropriate antibiotic treatment caused a devastating bone quality of the full femur. CONCLUSIONS A successful outcome was obtained with surgical debridement, antibiotics, and return to weight bearing guided by a laboratory and radiographic scale specially designed to avoid pathologic fractures toward his full functional recovery.
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Affiliation(s)
- Ivan F Rubel
- Orthopaedics Department, Fleni Institute, Buenos Aires, Argentina
- Internal Medicine Department, Fleni Institute, Buenos Aires, Argentina
| | - Fabricio M Reino
- Internal Medicine Department, Fleni Institute, Buenos Aires, Argentina
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26
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Zhu H, Qiang J, He J, Tao Y, Bao J, Xu P. Physiological parameters and gut microbiome associated with different dietary lipid levels in hybrid yellow catfish (Tachysurus fulvidraco♀× Pseudobagrus vachellii♂). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100777. [PMID: 33296766 DOI: 10.1016/j.cbd.2020.100777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/12/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022]
Abstract
Yellow catfish are intensively farmed in China and are often fed a high-fat diet (HFD) with the aim of using less protein. However, an excess of dietary lipids is likely to affect the gut microflora, which strongly affects immunity and nutrient digestion. To determine the effects of different lipid levels on the growth, physiological parameters and gut microbiome of hybrid yellow catfish, we conducted an 8-week feeding experiment with a low-fat diet (2% lipids, LFD), a normal-fat diet (9% lipids, NFD), and a HFD (15% lipids) (120 fish per group). The HFD group showed higher serum alanine aminotransferase and aspartate transaminase activities, which suggests that excess dietary lipids cause liver damage. A total of 1138 operational taxonomic units, 11 phyla, and 117 genera were identified from fish gut samples. Neither the HFD nor the LFD strongly affected the microbial composition in gut samples. Compared with fish in the NFD, those in the HFD and LFD showed significantly decreased intestinal microbial diversity. The composition of macronutrients in the different diets affected the composition of intestinal microflora, mainly the phyla Fusobacteria, Proteobacteria, and Firmicutes. The HFD and the LFD favored the growth of Fusobacteria, while the HFD and LFD resulted in decreased abundance of Firmicutes and Proteobacteria, respectively. These findings shed light on the complex relationships among diet, intestinal microorganisms, and host metabolism. When using an HFD for farmed fish, its effects on the gut microbiome should be considered to avoid illness and poor growth.
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Affiliation(s)
- Haojun Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Jun Qiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Yifan Tao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Jingwen Bao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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27
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Llama‐Palacios A, Potupa O, Sánchez MC, Figuero E, Herrera D, Sanz M. Proteomic analysis ofFusobacterium nucleatumgrowth in biofilm versus planktonic state. Mol Oral Microbiol 2020; 35:168-180. [DOI: 10.1111/omi.12303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/01/2020] [Accepted: 06/11/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Arancha Llama‐Palacios
- Oral Microbiology Laboratory at the Faculty of Odontology University Complutense Madrid Spain
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - Oksana Potupa
- Oral Microbiology Laboratory at the Faculty of Odontology University Complutense Madrid Spain
| | - María C. Sánchez
- Oral Microbiology Laboratory at the Faculty of Odontology University Complutense Madrid Spain
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - Elena Figuero
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - David Herrera
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - Mariano Sanz
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
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28
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Lai KP, Lin X, Tam N, Ho JCH, Wong MKS, Gu J, Chan TF, Tse WKF. Osmotic stress induces gut microbiota community shift in fish. Environ Microbiol 2020; 22:3784-3802. [PMID: 32618094 DOI: 10.1111/1462-2920.15150] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.
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Affiliation(s)
- Keng Po Lai
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, 541004, China.,Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Jeff Cheuk Hin Ho
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Marty Kwok-Shing Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8564, Japan
| | - Jie Gu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
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29
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Soni K, Fricker Z, Long MT. Pyogenic liver abscesses from Fusobacterium nucleatum in an immunocompetent host. Clin Res Hepatol Gastroenterol 2020; 44:e59-e60. [PMID: 31607642 PMCID: PMC7145721 DOI: 10.1016/j.clinre.2019.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/26/2019] [Accepted: 09/02/2019] [Indexed: 02/04/2023]
Affiliation(s)
| | - Zachary Fricker
- Section of Gastroenterology, Boston University School of Medicine, Boston, MA, United States
| | - Michelle Theresa Long
- Section of Gastroenterology, Boston University School of Medicine, Boston, MA, United States,Corresponding author: Section of Gastroenterology, Boston University School of Medicine, Boston, MA, United States. (M.T. Long)
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30
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Robles-Malagamba MJ, Walsh MT, Ahasan MS, Thompson P, Wells RS, Jobin C, Fodor AA, Winglee K, Waltzek TB. Characterization of the bacterial microbiome among free-ranging bottlenose dolphins ( Tursiops truncatus). Heliyon 2020; 6:e03944. [PMID: 32577542 PMCID: PMC7305398 DOI: 10.1016/j.heliyon.2020.e03944] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/07/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
Marine animals represent a dynamic and complex habitat for diverse microbial communities. The microbiota associated with bottlenose dolphins (Tursiops truncatus) are believed to influence their health status, but it remains poorly understood. We therefore characterized and compared the bacterial microbiome of bottlenose dolphins from six different anatomical sites that represent four different body systems (respiratory, digestive, reproductive, and integumentary). In this study, a total of 14 free-ranging bottlenose dolphins were sampled during the 2015 Sarasota Bay Dolphin Health Assessment. Bacterial diversity and abundance were assessed by PCR amplification of the hypervariable V3-V4 regions of the bacterial 16S rRNA gene for each sample, followed by sequencing on an Illumina MiSeq platform. Analysis showed that bottlenose dolphins harbor diverse bacterial communities with a unique microbial community at each body system. Additionally, the bottlenose dolphin bacterial microbiome was clearly distinct to the aquatic microbiome from their surrounding habitat. These results are in close agreement with other cetacean microbiome studies, while our study is the first to explore what was found to be a diverse bottlenose dolphin genital microbiome. The core bacterial communities identified in this study in apparently healthy animals might be informative for future health monitoring of bottlenose dolphins.
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Affiliation(s)
- María José Robles-Malagamba
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Michael T. Walsh
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Mohammad Shamim Ahasan
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Department of Medicine, Surgery and Obstetrics, Faculty of Veterinary and Animal Sciences, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Patrick Thompson
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Randall S. Wells
- Chicago Zoological Society's Sarasota Dolphin Research Program, Mote Marine Laboratory, Sarasota, Florida, USA
| | - Christian Jobin
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Division of Gastroenterology, Hepatology, and Nutrition, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Thomas B. Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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31
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Liu CZ, Chen W, Wang MX, Wang Y, Chen LQ, Zhao F, Shi Y, Liu HJ, Dou XB, Liu C, Chen H. Dendrobium officinale Kimura et Migo and American ginseng mixture: A Chinese herbal formulation for gut microbiota modulation. Chin J Nat Med 2020; 18:446-459. [PMID: 32503736 DOI: 10.1016/s1875-5364(20)30052-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Indexed: 02/07/2023]
Abstract
Dendrobium officinale Kimura et Migo (D. officinale) is a famous traditional Chinese medicine (TCM). A mixture of D. officinale and American ginseng has been shown to enhance cell-mediated immunity, humoral immunity, and monocyte/macrophage functions in mice. Here, the effects of a D. officinale and American ginseng mixture on the structure of gut microbial community in dogs were examined using high-throughput 16S rRNA gene amplicon sequencing. The data revealed that while the mixture did not change the diversity of gut microbial community significantly, differences among individuals were significantly reduced. Furthermore, the mixture-responsive operational taxonomic units (OTUs) exhibited a phase-dependent expression pattern. Fifty-five OTUs were found to exhibit a mixture-induced expression pattern, among which one third were short-chain fatty acid (SCFA)-producing genera and the others were probiotic genera included Lactobacillus spp., Sutterella, Alistipes, Anaerovorax, Bilophila, Coprococcus, Gordonibacter, Oscillibacter, among others. By contrast, 36% of the OTUs exhibiting a mixture-repressed expression pattern were disease-associated microorganisms, and six genera, namely Actinomyces, Escherichia/Shigella, Fusobacterium, Slackia, Streptococcus and Solobacterium, were associated with cancer. In addition, five genera were closely associated with diabetes, namely Collinsella, Rothia, Howardella, Slackia and Intestinibacter. Our results indicate that this D. officinale and American ginseng mixture may be used as a prebiotic agent to enhance SCFA-producing genera and prevent gut dysbiosis.
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Affiliation(s)
- Cheng-Zhi Liu
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Wei Chen
- Hangzhou Huqing yu tang Traditional Chinese Medicine Mordernize Institute, Hangzhou 311100, China
| | - Mei-Xia Wang
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Ying Wang
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Li-Qing Chen
- Hangzhou Huqing yu tang Traditional Chinese Medicine Mordernize Institute, Hangzhou 311100, China
| | - Feng Zhao
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China; College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ya Shi
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Hui-Jun Liu
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Xiao-Bing Dou
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Chao Liu
- Department of Orthopaedics, Sir Sun Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.
| | - Huan Chen
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China.
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32
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Reverter M, Sasal P, Suzuki MT, Raviglione D, Inguimbert N, Pare A, Banaigs B, Voisin SN, Bulet P, Tapissier-Bontemps N. Insights into the Natural Defenses of a Coral Reef Fish Against Gill Ectoparasites: Integrated Metabolome and Microbiome Approach. Metabolites 2020; 10:E227. [PMID: 32486312 PMCID: PMC7345202 DOI: 10.3390/metabo10060227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Understanding natural defense mechanisms against parasites can be a valuable tool for the development of innovative therapies. We have previously identified a butterflyfish species (Chaetodon lunulatus) that avoids gill monogenean parasites while living amongst closely related parasitized species. The metabolome and microbiome of several sympatric butterflyfish species from the island of Moorea (French Polynesia) were previously described. In this study, we used the previously generated datasets in an attempt to identify metabolites and bacteria potentially involved in parasite defense mechanisms. We investigated the interplay between the gill mucus metabolome and microbiome of the non-susceptible C. lunulatus versus sympatric butterflyfish species that were always found parasitized in the Central and Eastern Indo-Pacific. After observing significant differences between the metabolome and bacteria of susceptible versus non-susceptible fish, we obtained the discriminant metabolites and operational taxonomic units (OTUs) using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new peptides derived from β-subunit hemoglobin from C. lunulatus (CLHbβ-1, CLHbβ-2, and CLHbβ-3) were purified, characterized and synthesized to confirm their structures. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C. lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C. lunulatus and highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.
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Affiliation(s)
- Miriam Reverter
- Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universität Oldenburg, 26382 Wilhelmshaven, Germany
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Pierre Sasal
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Marcelino T. Suzuki
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, Sorbonne Université, CNRS, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France;
| | - Delphine Raviglione
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
| | - Nicolas Inguimbert
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Alan Pare
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
| | - Bernard Banaigs
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Sébastien N. Voisin
- Plateforme BioPark d’Archamps, ArchParc, 74160 Archamps, France; (S.N.V.); (P.B.)
| | - Philippe Bulet
- Plateforme BioPark d’Archamps, ArchParc, 74160 Archamps, France; (S.N.V.); (P.B.)
- CR UGA, IAB, InsermU1209, CNRS UMR 5309, 38700 La Tronche, France
| | - Nathalie Tapissier-Bontemps
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
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Gilbert MJ, IJsseldijk LL, Rubio-García A, Gröne A, Duim B, Rossen J, Zomer AL, Wagenaar JA. After the bite: bacterial transmission from grey seals ( Halichoerus grypus) to harbour porpoises ( Phocoena phocoena). ROYAL SOCIETY OPEN SCIENCE 2020; 7:192079. [PMID: 32537205 PMCID: PMC7277243 DOI: 10.1098/rsos.192079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Recent population growth of the harbour porpoise (Phocoena phocoena), grey seal (Halichoerus grypus) and common seal (Phoca vitulina) in the North Sea has increased potential interaction between these species. Grey seals are known to attack harbour porpoises. Some harbour porpoises survive initially, but succumb eventually, often showing severely infected skin lesions. Bacteria transferred from the grey seal oral cavity may be involved in these infections and eventual death of the animal. In humans, seal bites are known to cause severe infections. In this study, a 16S rRNA-based microbiome sequencing approach is used to identify the oral bacterial diversity in harbour porpoises, grey seals and common seals; detect the potential transfer of bacteria from grey seals to harbour porpoises by biting and provide insights in the bacteria with zoonotic potential present in the seal oral cavity. β-diversity analysis showed that 12.9% (4/31) of the harbour porpoise skin lesion microbiomes resembled seal oral microbiomes, while most of the other skin lesion microbiomes also showed seal-associated bacterial species, including potential pathogens. In conclusion, this study shows that bacterial transmission from grey seals to harbour porpoises by biting is highly likely and that seal oral cavities harbour many bacterial pathogens with zoonotic potential.
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Affiliation(s)
- Maarten J. Gilbert
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), Nijmegen, The Netherlands
| | - Lonneke L. IJsseldijk
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division of Pathology, Utrecht University, Utrecht, The Netherlands
| | - Ana Rubio-García
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- Sealcentre, Pieterburen, The Netherlands
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andrea Gröne
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division of Pathology, Utrecht University, Utrecht, The Netherlands
| | - Birgitta Duim
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - John Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Aldert L. Zomer
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
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34
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Zhou J, Nelson TM, Rodriguez Lopez C, Sarma RR, Zhou SJ, Rollins LA. A comparison of nonlethal sampling methods for amphibian gut microbiome analyses. Mol Ecol Resour 2020; 20:844-855. [PMID: 31990452 DOI: 10.1111/1755-0998.13139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/03/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022]
Abstract
Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.
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Affiliation(s)
- Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Tiffanie Maree Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, Qld, Australia
| | - Carlos Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Roshmi Rekha Sarma
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
| | - Shao Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
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35
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Gao Y, Yang W, Che D, Adams S, Yang L. Advances in the mechanism of high copper diets in restraining pigs growth. J Anim Physiol Anim Nutr (Berl) 2019; 104:667-678. [PMID: 31840317 DOI: 10.1111/jpn.13213] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
High copper feed has been widely used as an inexpensive and highly effective feed additive to promote growth performance of pigs. However, long-term feeding of high copper feed may reduce the growth-promoting effects of copper, time-dependent accumulation of copper in animal tissues and organs, and copper toxicity thereby reducing the growth performance of pigs. Due to the widespread effects of high copper supplementation in animals' diets, the benefits and drawbacks of high copper feeding in pigs have been reported in several studies. Meanwhile, few of these studies have systematically described the mechanism by which high copper diets restrain pig growth. Therefore, to address the concerns and give a better understanding of the mechanism of high copper diet in restraining pig growth in different systems, this paper reviews the research progress of long-term supplementation of high copper on the growth of pigs and provides some suggestions and further research directions.
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Affiliation(s)
- Yang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Wenyan Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Lab of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, China.,Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Dongsheng Che
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Lab of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, China.,Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Seidu Adams
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Lianyu Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Lab of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, China.,Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
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36
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Wu YF, Xing P, Liu S, Wu QL. Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment. Front Microbiol 2019; 10:2474. [PMID: 31736913 PMCID: PMC6831559 DOI: 10.3389/fmicb.2019.02474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Microcystis biomass remineralization after blooming represents a hotspot of nutrient recycling in eutrophic lakes. Because Microcystis blooms are massively deposited on lake sediments, resulting in anoxic conditions, it is important to understand the response and role of benthic microbial communities during the anoxic decomposition of Microcystis in freshwater lakes. In the present study, we employed a microcosm method, combined with high-throughput sequencing, functional prediction, and network analysis, to investigate microbial succession during the short-term (30 days) anaerobic decomposition of Microcystis in a eutrophic sediment. Continuous accumulation of CH4 and CO2 and increasing relative abundance of methanogens were observed during the incubation. The microbial community composition (MCC) significantly changed after addition of Microcystis biomass, with a shift in the community from a stochastic to a functional, deterministic succession. Families, including Clostridiaceae, Rhodocyclaceae, Rikenellaceae, Peptostreptococcaceae, Syntrophomonadaceae, Lachnospiraceae, and Methanosarcinaceae, were predominantly enriched and formed diverse substitution patterns, suggesting a synergistic action of these family members in the decomposition of Microcystis biomass. Importantly, intense species-to-species interactions and weak resistance to disturbance were observed in the microbial community after Microcystis biomass addition. Collectively, these results suggest that the addition of Microcystis induce phylogenetic clustering and structure instability in the sediment microbial community and the synergistic interactions among saprotrophic bacteria play a key role in Microcystis biomass remineralization.
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Affiliation(s)
- Yu-Fan Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Technology Center of Zhangjiagang Customs, Zhangjiagang, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qinglong L. Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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37
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Cordero J, de Freitas JR, Germida JJ. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can J Microbiol 2019; 66:71-85. [PMID: 31658427 DOI: 10.1139/cjm-2019-0330] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.
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Affiliation(s)
- Jorge Cordero
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - J Renato de Freitas
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - James J Germida
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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38
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Gohar A, Jamous F, Abdallah M. Concurrent fusobacterial pyogenic liver abscess and empyema. BMJ Case Rep 2019; 12:12/10/e231994. [PMID: 31615779 DOI: 10.1136/bcr-2019-231994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We present a very rare case of concurrent empyema and liver abscess caused by Fusobacterium. Our patient presented with 3-month history of subtle abdominal discomfort and cough leading to eventually presenting with marked chest pain, dyspnoea and septic shock. CT revealed a liver abscess and large right-sided pleural effusion. Drainage of the pleural effusion yielded gross pus with the growth of Fusobacterium varium, while drainage of the liver abscess yielded Fusobacterium nucleatum The patient responded to drainage and antibiotic therapy with resolution of symptoms and decrease in the size of empyema and abscess on follow-up imaging. We also include a review if literature of related fusobacterial infections.
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Affiliation(s)
- Ahmed Gohar
- Department of Internal Medicine, Univesity of South Dakota Sanford School of Medicine, Sioux Falls, SD, USA
| | - Fady Jamous
- Department of Internal Medicine, Univesity of South Dakota Sanford School of Medicine, Sioux Falls, SD, USA.,Department of Pulmonary & Sleep Medicine, Avera Medical Group, Sioux Falls, SD, USA
| | - Mohamed Abdallah
- Department of Internal Medicine, Univesity of South Dakota Sanford School of Medicine, Sioux Falls, SD, USA
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39
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Shen F, Zheng Y, Niu M, Zhou F, Wu Y, Wang J, Zhu T, Wu Y, Wu Z, Hu M, Zhu T. Characteristics of biological particulate matters at urban and rural sites in the North China Plain. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 253:569-577. [PMID: 31330349 DOI: 10.1016/j.envpol.2019.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Depending on their concentrations, sizes, and types, particulate matters of biological origins (bioPM) significantly affect human health. However, for different air environments, they are not well characterized and can vary considerably. As an example, we investigated the bioPM differences at an urban (Beijing) site and a rural (Wangdu) site in the North China Plain (NCP) using an online monitoring instrument, an ultraviolet aerodynamic particle sizer (UV-APS), the limulus amebocyte lysate (LAL) assay, and a high-throughput sequencing method. Generally, lower concentrations of viable bioPM (hourly mean: 1.3 × 103 ± 1.6 × 103 m-3) and endotoxin (0.66 ± 0.16 EU/m3) in Beijing were observed compared to viable bioPM (0.79 × 105 ± 1.4 × 105 m-3) and endotoxin (15.1 ± 23.96 EU/m3) at the Wangdu site. The percentage of viable bioPM number concentration in the total PM was 3.1% in Beijing and 6.4% in Wangdu. Approximately 80% of viable bioPM was found to be in the range from 1 to 2.5 μm. Nevertheless, the size distribution patterns for viable bioPM at the Beijing and Wangdu sites differed and were affected by PM pollution, leading to distinct lung deposition profiles. Moreover, the distinct diurnal variations in viable bioPM on clean days were dimmed by the PM pollution at both sites. Distinct bacterial community structures were found in the air from the Beijing and Wangdu sites. The bacterial community in urban Beijing was dominated by genus Lactococcus (49.5%) and Pseudomonas (15.1%), while the rural Wangdu site was dominated by Enterococcus (65%) and Paenibacillus (10%). Human-derived genera, including Myroides, Streptococcus, Propionibacterium, Dietzia, Helcococcus, and Facklamia, were higher in Beijing, suggesting bacterial emission from humans in the urban air environment. Our results show that different air harbors different biological species, and people residing in different environments thus could have very different biological particle exposure.
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Affiliation(s)
- Fangxia Shen
- School of Space and Environment, Beihang University, Beijing, 102206, China.
| | - Yunhao Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mutong Niu
- School of Space and Environment, Beihang University, Beijing, 102206, China
| | - Feng Zhou
- School of Space and Environment, Beihang University, Beijing, 102206, China
| | - Yan Wu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 250100, China
| | - Junxia Wang
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tong Zhu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yusheng Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhijun Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Min Hu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianle Zhu
- School of Space and Environment, Beihang University, Beijing, 102206, China
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Microbial Dynamics of Biosand Filters and Contributions of the Microbial Food Web to Effective Treatment of Wastewater-Impacted Water Sources. Appl Environ Microbiol 2019; 85:AEM.01142-19. [PMID: 31227556 DOI: 10.1128/aem.01142-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Biosand filtration systems are widely used for drinking water treatment, from household-level, intermittently operated filters to large-scale continuous municipal systems. While it is well-established that microbial activity within the filter is essential for the removal of potential pathogens and other contaminants, the microbial ecology of these systems and how microbial succession relates to their performance remain poorly resolved. We determined how different source waters influence the composition, temporal dynamics, and performance of microbial communities in intermittently operated biosand filters. We operated lab-scale biosand filters, adding daily inputs from two contrasting water sources with differing nutrient concentrations and found that total coliform removal increased and became less variable after 4 weeks, regardless of water source. Total effluent biomass was also lower than total influent biomass for both water sources. Bacterial community composition, assessed via cultivation-independent DNA sequencing, varied by water source, sample type (influent, effluent, or sand), and time. Despite these differences, we identified specific taxa that were consistently removed, including common aquatic and wastewater bacteria. In contrast, taxa consistently more abundant in the sand and effluent included predatory, intracellular, and symbiotic bacteria.IMPORTANCE Although microbial activities are known to contribute to the effectiveness of biosand filtration for drinking water treatment, we have a limited understanding of what microbial groups are most effectively removed, colonize the sand, or make it through the filter. This study tracked the microbial communities in the influent, sand, and effluent of lab-scale, intermittently operated biosand filters over 8 weeks. These results represent the most detailed and time-resolved investigation of the microbial communities in biosand filters typical of those implemented at the household level in many developing countries. We show the importance of the microbial food web in biosand filtration, and we identified taxa that are preferentially removed from wastewater-impacted water sources. We found consistent patterns in filter effectiveness from source waters with differing nutrient loads and, likewise, identified specific bacterial taxa that were consistently more abundant in effluent waters, taxa that are important targets for further study and posttreatment.
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Use of Direct Hemoperfusion with Polymyxin B-Immobilized Fiber for the Treatment of Septic Shock Complicated with Lemierre Syndrome Caused by Fusobacterium necrophorum. Case Rep Crit Care 2019; 2019:5740503. [PMID: 31467732 PMCID: PMC6701397 DOI: 10.1155/2019/5740503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/17/2019] [Indexed: 11/17/2022] Open
Abstract
We report a case of septic shock treated with PMX-DHP that was complicated with Lemierre syndrome caused by Fusobacterium necrophorum. The patient was a 31-year-old man who was initially diagnosed with influenza. He received treatment; however, because his symptoms gradually worsened, he was transported to our hospital 10 days following his diagnosis. His initial examination revealed symptoms of respiratory distress and an altered level of consciousness. Based on laboratory and imaging results, it became clear that he suffered from septic shock of unknown etiology, disseminated intravascular coagulation, and acute renal and respiratory failure. We initiated treatment with vasopressors, an antibacterial agent, immunoglobulins as well as an appropriate ventilator management; however, his unstable circulatory condition continued. As soon as PMX-DHP was initiated, 2 days following admission to the ICU, his circulatory instability normalized. F. necrophorum was ultimately detected after a culture examination, and contrast-enhanced computed tomography revealed a jugular vein thrombus, which led to the diagnosis of Lemierre syndrome. The patient's condition gradually improved, and he was discharged from the ICU after 19 days.
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42
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Tang W, Zhu G, Shi Q, Yang S, Ma T, Mishra SK, Wen A, Xu H, Wang Q, Jiang Y, Wu J, Xie M, Yao Y, Li D. Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions. Microbiologyopen 2019; 8:e00789. [PMID: 30848054 PMCID: PMC6612554 DOI: 10.1002/mbo3.789] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
The gut microbiota helps the host to absorb nutrients and generate immune responses that can affect host behavior, development, reproduction, and overall health. However, in most of the previous studies, microbiota was sampled mainly using feces and intestinal contents from mammals but not from wild reptiles. Here, we described the bacterial profile from five different gastrointestinal tract (GIT) segments (esophagus, stomach, small intestine, large intestine, and cloaca) of three wild Rhabdophis subminiatus using 16S rRNA V4 hypervariable amplicon sequencing. Forty-seven bacterial phyla were found in the entire GIT, of which Proteobacteria, Firmicutes, and Bacteroidetes were predominant. The results showed a significant difference in microbial diversity between the upper GIT segments (esophagus and stomach) and lower GIT segments (large intestine and cloaca). An obvious dynamic distribution of Fusobacteria and Bacteroidetes was observed, which mainly existed in the lower GIT segments. Conversely, the distribution of Tenericutes was mainly observed in the upper GIT. We also predicted the microbial functions in the different GIT segments, which showed that microbiota in each segments played an important role in higher membrane transport and carbohydrate and amino acid metabolism. Microbes in the small intestine were also mainly involved in disease-related systems, while in the large intestine, they were associated with membrane transport and carbohydrate metabolism. This is the first study to investigate the distribution of the gut microbiota and to predict the microbial function in R. subminiatus. The composition of the gut microbiota certainly reflects the diet and the living environment of the host. Furthermore, these findings provide vital evidence for the diagnosis and treatment of gut diseases in snakes and offer a direction for a model of energy budget research.
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Affiliation(s)
- Wenjiao Tang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Guangxiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qian Shi
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Shijun Yang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Shailendra Kumar Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Anxiang Wen
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Huailiang Xu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qin Wang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yanzhi Jiang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Jiayun Wu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Meng Xie
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yongfang Yao
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
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Neu AT, Allen EE, Roy K. Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:434-447. [PMID: 30834681 DOI: 10.1111/1758-2229.12743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/02/2019] [Indexed: 06/09/2023]
Abstract
Marine biogeographic boundaries act as barriers to dispersal for many animal species, thereby creating distinctive faunas on either side. However, how such boundaries affect the distributions of microbial taxa remains poorly known. To test whether biogeographic boundaries influence the diversity and composition of host-associated microbiota, we analysed the microbiomes of three species of common intertidal gastropods at two sites separated by the biogeographic boundary at Point Conception (PtC), CA, using 16S rRNA gene sequencing. Our results show that each host species shows microbiome compositional specificity, even across PtC, and that alpha diversity does not change significantly across this boundary for any of the gastropod hosts. However, for two of the host species, beta diversity differs significantly across PtC, indicating that there may be multiple levels of organization of the marine gastropod microbiome. Overall, our results suggest that while biogeographic boundaries do not constrain the distribution of a core set of microbes associated with each host species, they can play a role in structuring the transient portion of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
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Yao Q, Yu K, Liang J, Wang Y, Hu B, Huang X, Chen B, Qin Z. The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea). Front Microbiol 2019; 10:1168. [PMID: 31191489 PMCID: PMC6546719 DOI: 10.3389/fmicb.2019.01168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/07/2019] [Indexed: 11/18/2022] Open
Abstract
Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.
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Affiliation(s)
- Qiucui Yao
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China.,College of Forestry, Guangxi University, Nanning, China.,Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Teachers Education University, Nanning, China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Baoqing Hu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Teachers Education University, Nanning, China
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
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45
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Grosser S, Sauer J, Paijmans AJ, Caspers BA, Forcada J, Wolf JBW, Hoffman JI. Fur seal microbiota are shaped by the social and physical environment, show mother–offspring similarities and are associated with host genetic quality. Mol Ecol 2019; 28:2406-2422. [DOI: 10.1111/mec.15070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/26/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Stefanie Grosser
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- Division of Evolutionary Biology, Faculty of Biology LMU Munich Planegg‐Martinsried Germany
| | - Jan Sauer
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
| | | | | | - Jaume Forcada
- British Antarctic Survey Natural Environment Research Council Cambridge UK
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology LMU Munich Planegg‐Martinsried Germany
- Department of Evolutionary Biology Uppsala University Uppsala Sweden
| | - Joseph I. Hoffman
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- British Antarctic Survey Natural Environment Research Council Cambridge UK
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46
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Shen Y, Chu L, Zhuan R, Xiang X, Sun H, Wang J. Degradation of antibiotics and antibiotic resistance genes in fermentation residues by ionizing radiation: A new insight into a sustainable management of antibiotic fermentative residuals. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 232:171-178. [PMID: 30472560 DOI: 10.1016/j.jenvman.2018.11.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/20/2018] [Accepted: 11/14/2018] [Indexed: 06/09/2023]
Abstract
Antibiotic fermentative residues are categorized into hazardous wastes in China due to the existence of antibiotic resistance genes (ARGs) and residual antibiotics How to treat and manage these wastes is a new challenge. This paper investigated the treatment of erythromycin thiocyanate fermentation (EryTcF) residues using ionizing radiation technology for removing ARGs and antibiotics from the fermentation residues. The results showed that as exposed the EryTcF residues to gamma radiation, the abundance of four macrolide resistance genes (ereA, ermB, mefA and mpfB) decreased 1.0-1.3 log with 90-95% removal, and around 56% of erythromycin was removed at absorbed dose of 30 kGy and room temperature (19-22 °C). Direct action of γ-ray radiation contributed to 42-53% of ARGs removal and indirect action (radicals' reaction) was mainly responsible for erythromycin removal (84%). The positive correlation between total ARGs and Shannon index was observed. The potential ARGs-linked hosts were assigned to genera Aeromonas and Enterobacteriaceae and their abundance decreased by 36-43% at 30 kGy. Radiation has not obvious influence on the nutrient components of residues, such as protein content, suggesting that the radiation treated fermentative residues can be used as fertilizer, which is favorable for the development of recycling economy in antibiotic pharmaceutical factory. The results could provide a new insight into a sustainable management of antibiotic fermentative residuals.
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Affiliation(s)
- Yunpeng Shen
- School of Economics and Management, Center for Innovation Management Research, Xinjiang University, Xinjiang 830047, PR China
| | - Libing Chu
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China
| | - Run Zhuan
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China
| | - Xianhong Xiang
- School of Economics and Management, Center for Innovation Management Research, Xinjiang University, Xinjiang 830047, PR China
| | - Hui Sun
- School of Economics and Management, Center for Innovation Management Research, Xinjiang University, Xinjiang 830047, PR China
| | - Jianlong Wang
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China.
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47
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Campbell IJ, Bennett GN, Silberg JJ. Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. FRONTIERS IN ENERGY RESEARCH 2019; 7:10.3389/fenrg.2019.00079. [PMID: 32095484 PMCID: PMC7039249 DOI: 10.3389/fenrg.2019.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.
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Affiliation(s)
- Ian J. Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, United States
| | - George N. Bennett
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University Houston, TX, United States
- Correspondence: Jonathan J. Silberg
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48
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Gomes BPFDA, Herrera DR. Etiologic role of root canal infection in apical periodontitis and its relationship with clinical symptomatology. Braz Oral Res 2018; 32:e69. [PMID: 30365610 DOI: 10.1590/1807-3107bor-2018.vol32.0069] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/12/2018] [Indexed: 12/16/2022] Open
Abstract
Evidence shows the polymicrobial etiology of endodontic infections, in which bacteria and their products are the main agents for the development, progression, and dissemination of apical periodontitis. Microbial factors in necrotic root canals (e.g., endotoxin) may spread into apical tissue, evoking and supporting a chronic inflammatory load. Thus, apical periodontitis is the result of the complex interplay between microbial factors and host defense against invasion of periradicular tissues. This review of the literature aims to discuss the complex network between endodontic infectious content and host immune response in apical periodontitis. A better understanding of the relationship of microbial factors with clinical symptomatology is important to establish appropriate therapeutic procedures for a more predictable outcome of endodontic treatment.
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Affiliation(s)
| | - Daniel Rodrigo Herrera
- Universidade Estadual de Campinas -Unicamp, Piracicaba Dental School, Department of Restorative Dentistry, Piracicaba, SP, Brazil
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49
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Nam BH, Jang J, Caetano-Anolles K, Kim YO, Park JY, Sohn H, Yoon SH, Kim H, Kwak W. Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis. PLoS One 2018; 13:e0205594. [PMID: 30308038 PMCID: PMC6181387 DOI: 10.1371/journal.pone.0205594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/27/2018] [Indexed: 02/01/2023] Open
Abstract
Haliotis discus hannai, a species of Pacific abalone, is a highly valuable food source throughout Northeast Asia. As H. discus hannai primarily feed on brown algae and largely extract their energy from algal polysaccharides, understanding the mechanisms by which they digest algal polysaccharides is essential for elucidating their energy metabolism. Gut microbes, as well as the host animal, are involved in the process of polysaccharide degradation. To identify algal polysaccharide-digestion mechanisms and their origin, we analyzed the metagenome and metatranscriptome of abalone visceral extracts. Microbial communities were characterized using the 16S rRNA gene sequences in the metagenome and our results differed significantly from those of previous studies using traditional microbiological methods such as bacterial cultivation and cloning. A greater diversity of bacterial taxa was identified here than was previously identified using cultivation methods. Furthermore, the most abundant bacterial taxa also differed from previous studies, which is not common when comparing the results of bacterial culturing with those of molecular methodologies. Based on the metatranscriptome, overall functions were identified and additional analyses were performed on the coding sequences of algal polysaccharide-digestive enzymes, including alginate lyase. Results of the transcriptomic analyses suggest that alginate lyase in the visceral extracts of H. discus hannai was produced by the host itself, not by visceral bacteria. This is the first next-generation sequencing study performed on abalone to characterize the visceral microbiota and the source of the ability to digest algal polysaccharides by analyzing the metagenome and metatranscriptome together.
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Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- C&K Genomics, Seoul, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hawsun Sohn
- Cetacean Research Institute, National Institute of Fisheries Science, Nam-gu, Ulsan, Republic of Korea
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- C&K Genomics, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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50
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Hashemi Goradel N, Heidarzadeh S, Jahangiri S, Farhood B, Mortezaee K, Khanlarkhani N, Negahdari B. Fusobacterium nucleatumand colorectal cancer: A mechanistic overview. J Cell Physiol 2018; 234:2337-2344. [DOI: 10.1002/jcp.27250] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/24/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Nasser Hashemi Goradel
- Department of Medical BiotechnologySchool of Advanced Technologies in Medicine, Tehran University of Medical SciencesTehran Iran
| | - Siamak Heidarzadeh
- Department of Microbiology and VirologyZanjan University of Medical SciencesZanjan Iran
| | - Samira Jahangiri
- Department of Bacteriology and VirologySchool of Medicine, Shiraz University of Medical SciencesShiraz Iran
| | - Bagher Farhood
- Department of Medical Physics and RadiologyFaculty of Paramedical Sciences, Kashan University of Medical SciencesKashan Iran
| | - Keywan Mortezaee
- Department of AnatomySchool of Medicine, Kurdistan University of Medical SciencesSanandaj Iran
| | - Neda Khanlarkhani
- Department of AnatomySchool of Medicine, Tehran University of Medical SciencesTehran Iran
| | - Babak Negahdari
- Department of Medical BiotechnologySchool of Advanced Technologies in Medicine, Tehran University of Medical SciencesTehran Iran
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