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- The Role of Extracellular Vesicles in Pandemic Viral Infections
- Woosung Shim, Anjae Lee, Jung-Hyun Lee
- J. Microbiol. 2024;62(6):419-427. Published online June 25, 2024
- DOI: https://doi.org/10.1007/s12275-024-00144-x
- 415 View
- 5 Download
- 2 Web of Science
- 1 Crossref
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Abstract
PDF - Extracellular vesicles (EVs), of diverse origin and content, are membranous structures secreted by a broad range of cell types. Recent advances in molecular biology have highlighted the pivotal role of EVs in mediating intercellular communication, facilitated by their ability to transport a diverse range of biomolecules, including proteins, lipids, DNA, RNA and metabolites. A striking feature of EVs is their ability to exert dual effects during viral infections, involving both proviral and antiviral effects. This review explores the dual roles of EVs, particularly in the context of pandemic viruses such as HIV-1 and SARS-CoV-2. On the one hand, EVs can enhance viral replication and exacerbate pathogenesis by transferring viral components to susceptible cells. On the other hand, they have intrinsic antiviral properties, including activation of immune responses and direct inhibition of viral infection. By exploring these contrasting functions, our review emphasizes the complexity of EV-mediated interactions in viral pathogenesis and highlights their potential as targets for therapeutic intervention. The insights obtained from investigating EVs in the context of HIV-1 and SARS-CoV-2 provide a deeper understanding of viral mechanisms and pathologies, and offer a new perspective on managing and mitigating the impact of these global health challenges.
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Citations
Citations to this article as recorded by
- Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
Tae-Hun Kim, Sojung Bae, Jinjong Myoung
Journal of Microbiology and Biotechnology.2024; 34(12): 2506. CrossRef
- Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
- Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium
- Nakyeong Ha , Eun-Jin Lee
- J. Microbiol. 2023;61(3):289-296. Published online March 2, 2023
- DOI: https://doi.org/10.1007/s12275-023-00027-7
- 442 View
- 1 Download
- 10 Web of Science
- 10 Crossref
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Abstract
PDF
- The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn2+- dependent riboswitch in its 5′ UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcr!ptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.
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Citations
Citations to this article as recorded by- Microbial communities and substrate properties influence the fate of a human pathogen in horticultural substrates with different peat content
Antje Müller, Jasmin Schmidt, Verena Maiberg, Oscar Gehring, Adam Schikora
Frontiers in Horticulture.2025;[Epub] CrossRef - Dietary Manganese Modulates Microbiota and Intestinal N‐Acylethanolamines in a Sex‐Specific Manner in Mice With Diet‐Induced Obesity
Fredy Alexander Guevara Agudelo, Nadine Leblanc, Isabelle Bourdeau‐Julien, Gabrielle St‐Arnaud, Fadil Dahhani, Nicolas Flamand, Alain Veilleux, Vincenzo Di Marzo, Frédéric Raymond
The FASEB Journal.2025;[Epub] CrossRef -
Functional characterization of a TerC family protein of
Riemerella anatipestifer
in manganese detoxification and virulence
Qinyuan Chen, Fang Guo, Li Huang, Mengying Wang, Chunfeng Shi, Shutong Zhang, Yizhou Yao, Mingshu Wang, Dekang Zhu, Renyong Jia, Shun Chen, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Bin Tian, Juan Huang, Xumin Ou, Qun Gao, Di Sun, Ling Zhang, Yanling
Applied and Environmental Microbiology.2024;[Epub] CrossRef - NO enhances the adaptability to high-salt environments by regulating osmotic balance, antioxidant defense, and ion homeostasis in eelgrass based on transcriptome and metabolome analysis
Xianyan Wang, Tongtong Wang, Pei Yu, Yuchun Li, Xinfang Lv
Frontiers in Plant Science.2024;[Epub] CrossRef - High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection
Benjamin X. Wang, Dmitry Leshchiner, Lijuan Luo, Miles Tuncel, Karsten Hokamp, Jay C. D. Hinton, Denise M. Monack
Nature Genetics.2024; 56(6): 1288. CrossRef -
Biological characteristics of manganese transporter MntP in
Klebsiella pneumoniae
Wei Peng, Yafei Xu, Yilin Yin, Jichen Xie, Renhui Ma, Guoyuan Song, Zhiqiang Zhang, Qiuhang Quan, Qinggen Jiang, Moran Li, Bei Li, Michael David Leslie Johnson
mSphere.2024;[Epub] CrossRef -
Exploring resource competition by protective lactic acid bacteria cultures to control
Salmonella
in food: an Achilles’ heel to target?
Ludovico Screpanti, Nathalie Desmasures, Margot Schlusselhuber
Critical Reviews in Food Science and Nutrition.2024; : 1. CrossRef - Substrate-Induced Structural Dynamics and Evolutionary Linkage of Siderophore-Iron ABC Transporters of Mycobacterium tuberculosis
Aisha Farhana, Abdullah Alsrhani, Hasan Ejaz, Muharib Alruwaili, Ayman A. M. Alameen, Emad Manni, Zafar Rasheed, Yusuf Saleem Khan
Medicina.2024; 60(11): 1891. CrossRef - Structures and coordination chemistry of transporters involved in manganese and iron homeostasis
Shamayeeta Ray, Rachelle Gaudet
Biochemical Society Transactions.2023; 51(3): 897. CrossRef - Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef
- Microbial communities and substrate properties influence the fate of a human pathogen in horticultural substrates with different peat content
- Protective and pathogenic role of humoral responses in COVID-19
- Uni Park , Nam-Hyuk Cho
- J. Microbiol. 2022;60(3):268-275. Published online March 2, 2022
- DOI: https://doi.org/10.1007/s12275-022-2037-8
- 378 View
- 0 Download
- 5 Web of Science
- 3 Crossref
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Abstract
PDF
- Since the advent of SARS-CoV-2 in Dec. 2019, the global endeavor to identify the pathogenic mechanism of COVID-19 has been ongoing. Although humoral immunity including neutralizing activity play an important role in protection from the viral pathogen, dysregulated antibody responses may be associated with the pathogenic progression of COVID-19, especially in high-risk individuals. In addition, SARS-CoV-2 spike-specific antibodies acquired by prior infection or vaccination act as immune pressure, driving continuous population turnover by selecting for antibody-escaping mutations. Here, we review accumulating knowledge on the potential role of humoral immune responses in COVID-19, primarily focusing on their beneficial and pathogenic properties. Understanding the multifaceted regulatory mechanisms of humoral responses during SARS-CoV-2 infection can help us to develop more effective therapeutics, as well as protective measures against the ongoing pandemic.
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Citations
Citations to this article as recorded by- Rise in broadly cross-reactive adaptive immunity against human β-coronaviruses in MERS-recovered patients during the COVID-19 pandemic
So-Hee Kim, Yuri Kim, Sangeun Jeon, Uni Park, Ju-Il Kang, Kyeongseok Jeon, Hye-Ran Kim, Songhyeok Oh, Ji-Young Rhee, Jae-Phil Choi, Wan Beom Park, Sang Won Park, Jeong-Sun Yang, Joo-Yeon Lee, Jihye Kang, Hyoung-Shik Shin, Yeonjae Kim, Seungtaek Kim, Yeon-
Science Advances.2024;[Epub] CrossRef - Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef - Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef
- Rise in broadly cross-reactive adaptive immunity against human β-coronaviruses in MERS-recovered patients during the COVID-19 pandemic
- Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models
- Young-Il Kim , Mark Anthony B. Casel , Young Ki Choi
- J. Microbiol. 2022;60(3):255-267. Published online March 2, 2022
- DOI: https://doi.org/10.1007/s12275-022-2033-z
- 389 View
- 0 Download
- 12 Web of Science
- 9 Crossref
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Abstract
PDF
- As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV- 2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.
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Citations
Citations to this article as recorded by- In vivo characterization of ACE2 expression in Sprague-Dawley rats and cultured primary brain pericytes highlights the utility of Rattus norvegicus in the study of COVID-19 brain pathophysiology
Eugene Park, Elaine Liu, Andrew J. Baker
Brain Research.2025; 1848: 149333. CrossRef - Utilizing non‐human primate models to combat recent COVID‐19/SARS‐CoV‐2 and viral infectious disease outbreaks
Taeho Kwon
Journal of Medical Primatology.2024;[Epub] CrossRef - Early detection of highly transmissible viral variants using phylogenomics
Michael R. May, Bruce Rannala
Science Advances.2024;[Epub] CrossRef - Animal Models, Zoonotic Reservoirs, and Cross-Species Transmission of Emerging Human-Infecting Coronaviruses
Yakhouba Kane, Gary Wong, George F. Gao
Annual Review of Animal Biosciences.2023; 11(1): 1. CrossRef - SARS-CoV-2 Aerosol and Intranasal Exposure Models in Ferrets
Elizabeth E. Zumbrun, Samantha E. Zak, Eric D. Lee, Philip A. Bowling, Sara I. Ruiz, Xiankun Zeng, Jeffrey W. Koehler, Korey L. Delp, Russel R. Bakken, Shannon S. Hentschel, Holly A. Bloomfield, Keersten M. Ricks, Tamara L. Clements, April M. Babka, John
Viruses.2023; 15(12): 2341. CrossRef - The Isolation and In Vitro Differentiation of Primary Fetal Baboon Tracheal Epithelial Cells for the Study of SARS-CoV-2 Host-Virus Interactions
Bharathiraja Subramaniyan, Sunam Gurung, Manish Bodas, Andrew R. Moore, Jason L. Larabee, Darlene Reuter, Constantin Georgescu, Jonathan D. Wren, Dean A. Myers, James F. Papin, Matthew S. Walters
Viruses.2023; 15(4): 862. CrossRef - Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef - Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef - SARS CoV-2 (Delta Variant) Infection Kinetics and Immunopathogenesis in Domestic Cats
Miruthula Tamil Selvan, Sachithra Gunasekara, Ping Xiao, Kristen Griffin, Shannon R. Cowan, Sai Narayanan, Akhilesh Ramachandran, Darren E. Hagen, Jerry W. Ritchey, Jennifer M. Rudd, Craig A. Miller
Viruses.2022; 14(6): 1207. CrossRef
- In vivo characterization of ACE2 expression in Sprague-Dawley rats and cultured primary brain pericytes highlights the utility of Rattus norvegicus in the study of COVID-19 brain pathophysiology
Journal Articles
- Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae)
- Cely T. González , Kristin Saltonstall , Hermógenes Fernández-Marín
- J. Microbiol. 2019;57(10):842-851. Published online August 3, 2019
- DOI: https://doi.org/10.1007/s12275-019-8639-0
- 440 View
- 0 Download
- 6 Web of Science
- 6 Crossref
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Abstract
PDF
- Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllobacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enterobacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.
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Citations
Citations to this article as recorded by- Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission
Victoria A. Sadowski, Panagiotis Sapountzis, Pepijn W. Kooij, Jacobus J. Boomsma, Rachelle M. M. Adams, Nicolas Chaline
PLOS One.2025; 20(10): e0306011. CrossRef - The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates
Elias Eduardo Barbosa da Rosa, Frederico Schmitt Kremer
Brazilian Journal of Microbiology.2024; 55(4): 3603. CrossRef - Pharmacological potential of ants and their symbionts – a review
Surbhi Agarwal, Garima Sharma, Kavita Verma, Narayanan Latha, Vartika Mathur
Entomologia Experimentalis et Applicata.2022; 170(12): 1032. CrossRef - Disease management in two sympatric Apterostigma fungus‐growing ants for controlling the parasitic fungus Escovopsis
Yuliana Christopher, William T. Wcislo, Sergio Martínez‐Luis, William O.H. Hughes, Nicole M. Gerardo, Hermógenes Fernández‐Marín
Ecology and Evolution.2021; 11(11): 6041. CrossRef - The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification
Anakena M. Castillo, Kristin Saltonstall, Carlos F. Arias, Karina A. Chavarria, Luis A. Ramírez-Camejo, Luis C. Mejía, Luis F. De León
Insects.2020; 11(9): 578. CrossRef - Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System
Charlotte B. Francoeur, Lily Khadempour, Rolando D. Moreira-Soto, Kirsten Gotting, Adam J. Book, Adrián A. Pinto-Tomás, Ken Keefover-Ring, Cameron R. Currie, Margaret J. McFall-Ngai
mBio.2020;[Epub] CrossRef
- Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission
- Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China
- Pengyu Zhao , Jinxian Liu , Tong Jia , Zhengming Luo , Cui Li , Baofeng Chai
- J. Microbiol. 2019;57(6):461-469. Published online May 27, 2019
- DOI: https://doi.org/10.1007/s12275-019-8373-7
- 327 View
- 0 Download
- 8 Web of Science
- 8 Crossref
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Abstract
PDF
- Microbial community assembly is affected by trade-offs between deterministic and stochastic processes. However, the mechanisms underlying the relative influences of the two processes remain elusive. This knowledge gap limits our ability to understand the effects of community assembly processes on microbial community structures and functions. To better understand community assembly mechanisms, the community dynamics of bacterial ecological groups were investigated based on niche breadths in 23 soil plots from subalpine coniferous forests on the Loess Plateau in Shanxi, China. Here, the overall community was divided into the ecological groups that corresponded to habitat generalists, ‘other taxa’ and specialists. Redundancy analysis based on Bray-Curtis distances (db-RDA) and multiple regression tree (MRT) analysis indicated that soil organic carbon (SOC) was a general descriptor that encompassed the environmental gradients by which the communities responded to, because it can explain more significant variations in community diversity patterns. The three ecological groups exhibited different niche optima and degrees of specialization (i.e., niche breadths) along the SOC gradient, suggesting the presence of a gradient in tolerance for environmental heterogeneity. The inferred community assembly processes varied along the SOC gradient, wherein a transition was observed from homogenizing dispersal to variable selection that reflects increasing deterministic processes. Moreover, the ecological groups were inferred to perform different community functions that varied with community composition, structure. In conclusion, these results contribute to our understanding of the trade-offs between community assembly mechanisms and the responses of community structure and function to environmental gradients.
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Citations
Citations to this article as recorded by- Effects of Thinning of the Infected Trees and Cultivating of the Resistant Pines on Soil Microbial Diversity and Function
Xiaorui Zhang, Zhuo Liu, Mu Cao, Tingting Dai
Forests.2025; 16(5): 813. CrossRef - The restoration of soil multifunctionality in the later stages of biocrust succession is related to bacterial niche expansion: a case study of ion-adsorption rare earth tailings in southern China
Sheng Xu, Shifeng Sun, Huimin Qiu, Dan Lu, Yizhen Liu, Jun Ye, Hui Zhong, Tao Wang, Yanan Zhang, Lan Wu, Chi Yao, Qiying Cai, Gang Ge
Plant and Soil.2025; 513(2): 2553. CrossRef - Stochastic Processes Dominate the Assembly of Soil Bacterial Communities of Land Use Patterns in Lesser Khingan Mountains, Northeast China
Junnan Ding, Shaopeng Yu
Life.2024; 14(11): 1407. CrossRef - Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef - Community assembly of bacterial generalists and specialists and their network characteristics in different altitudinal soils on Fanjing Mountain in Southwest China
Zhenming Zhang, Xianliang Wu, Jiachun Zhang, Yingying Liu, Wenmin Luo, Guiting Mou
CATENA.2024; 238: 107863. CrossRef - Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts
Qing Li, Xiaoyu Cheng, Xiaoyan Liu, Pengfei Gao, Hongmei Wang, Chuntian Su, Qibo Huang
Frontiers in Microbiology.2024;[Epub] CrossRef - Full-length 16S rRNA gene sequencing reveals the operating mode and chlorination-aggravated SWRO biofouling at a nuclear power plant
Kaijia Ren, Hongxia Ming, Siyu Liu, Xianlong Lang, Yuan Jin, Jingfeng Fan
Water Science & Technology.2024; 90(1): 1. CrossRef - Kalidium cuspidatum colonization changes the structure and function of salt crust microbial communities
Yaqing Pan, Peng Kang, Yaqi Zhang, Xinrong Li
Environmental Science and Pollution Research.2024; 31(13): 19764. CrossRef
- Effects of Thinning of the Infected Trees and Cultivating of the Resistant Pines on Soil Microbial Diversity and Function
- Cecal microbiome divergence of broiler chickens by sex and body weight
- Kyu-Chan Lee , Dong Yong Kil , Woo Jun Sul
- J. Microbiol. 2017;55(12):939-945. Published online December 7, 2017
- DOI: https://doi.org/10.1007/s12275-017-7202-0
- 392 View
- 0 Download
- 83 Crossref
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Abstract
PDF
- The divergence of gut bacterial community on broiler chickens has been reported as potentially possible keys to enhancing nutrient absorption, immune systems, and increasing poultry health and performance. Thus, we compared cecal bacterial communities and functional predictions by sex and body weight regarding the association between cecal microbiota and chicken growth performance. In this study, a total of 12 male and 12 female 1-day-old broiler chickens were raised for 35 days in 2 separate cages. Chickens were divided into 3 subgroups depending on body weight (low, medium, and high) by each sex. We compared chicken cecal microbiota compositions and its predictive functions by sex and body weight difference. We found that bacterial 16S rRNA genes were classified as 3 major phyla (Bacteroidetes, Firmicutes, and Proteobacteria), accounting for > 98% of the total bacterial community. The profiling of different bacterial taxa and predictive metagenome functions derived from 16S rRNA genes were performed over chicken sex and bodyweight. Male chickens were related to the enrichment of Bacteroides while female chickens were to the enrichment of Clostridium and Shigella. Male chickens with high body weight were associated with the enrichment of Faecalibacterium and Shuttleworthia. Carbohydrate and lipid metabolisms were suggested as candidate functions for weight gain in the males. This suggests that the variation of cecal bacterial communities and their functions by sex and body weight may be associated with the differences in the growth potentials of broiler chickens.
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Citations
Citations to this article as recorded by- Anticoccidial activities of a multicomplex mineral-based diet in broilers infected with Eimeria acervulina
Binh T. Nguyen, Rochelle A. Flores, Paula Leona T. Cammayo-Fletcher, Suk Kim, Woo H. Kim, Wongi Min
Parasites, Hosts and Diseases.2025; 63(2): 135. CrossRef - Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights
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Poultry Science.2025; 104(8): 105275. CrossRef - Impact of stocking densities on growth, organ index, serum biochemistry, gut morphology and microbiota of young ducks in a rice-duck-crayfish coculture system
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Animal Bioscience.2025; 38(5): 1067. CrossRef - Niacin mitigates heat stress-induced reduction in performance of Taihe black-boned silky fowl through modulation of gut microorganisms and short-chain fatty acids
Wenliang Mei, Chuanbin Chen, Xiaona Gao, Wenyan Zhang, Ziyu Hu, Mingren Qu, Gen Wan, Lanjiao Xu
Frontiers in Veterinary Science.2025;[Epub] CrossRef -
Impact of
attapulgite
loaded with
essential oil
in diets on the growth performance and gut microbiota of broilers: a correlation analysis
Changqing He, Hanxiang Du, Lingyun He, Yi Liu, Jing Shan, Xiangyong Qu, Songchang Guo, Meichun Li, Jia Tang
Italian Journal of Animal Science.2025; 24(1): 1155. CrossRef - Effects of purple corn anthocyanin on slaughter performance, immune function, the caecal microbiota and the transcriptome in chickens
Xingzhou Tian, Chao Ban, Di Zhou, Hui Li, Jiaxuan Li, Xu Wang, Qi Lu
Poultry Science.2025; 104(6): 105104. CrossRef - Impact of Chlorella vulgaris and probiotic supplementation on performance, immunity and intestinal microbiota of broiler chickens
Verena Pereira Dinalli, Marcio Carvalho Costa, Emerson José Venâncio, João Antônio Barbosa Filho, José Antônio Bessegatto, Augusto Tasch Holkem, Amauri Alcindo Alfieri, Caio Abercio da Silva, Alexandre Oba, Arda Yildirim
PLOS ONE.2025; 20(1): e0313736. CrossRef - Gut response to the dietary supplementation with sodium butyrate in broiler chickens: morphology and microbiota composition and predictive functional groups
Giulia Zardinoni, Almudena Huerta, Marija Boskovic Cabrol, Angela Trocino, Elisa Fonsatti, Cristina Ballarin, Martina Bortoletti, Marco Birolo, Francesco Bordignon, Piergiorgio Stevanato, Daniel Julian, Gerolamo Xiccato
Italian Journal of Animal Science.2025; 24(1): 123. CrossRef - Red seaweed Chondracanthus chamissoi supplementation improved the growth performance of broiler chickens partially through effects on intestinal morphology and cecal microbiota
O.S. Olowe, T. Johnson, O. Adeola
Poultry Science.2025; 104(9): 105402. CrossRef - Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecal microbiome
Yong Yue, Bingnong Yao, Fuyou Liao, Zhiqiang He, Papungkorn Sangsawad, Shenglin Yang
Scientific Reports.2025;[Epub] CrossRef - Breast muscle myopathies: twists and turns in modern broilers
Elizabeth S. Greene, Sunoh Che, Francesca Soglia, Tomohito Iwasaki, Takafumi Watanabe, Takeshi Kawasaki, Leonardo Susta, Massimiliano Petracci, Colin Scanes, Sami Dridi
Avian Pathology.2025; 54(6): 669. CrossRef - Broiler chickens’ responses to a diet incorporating fermented or unfermented palm kernel cake on intestinal morphology, antioxidant indices, caecal microbiota composition, and liver metabolomic profiles
Sindaye Daniel, Shehata Zeid, Liao Jinghong, Suqin Hang
Italian Journal of Animal Science.2025; : 1. CrossRef - Dietary ethylenediamine dihydroiodide mitigated Escherichia coli O78-induced immune and intestinal damage of ducks via suppression of NF-κB signal
Yanru Liang, Yaqi Chang, Yueqin Xie, Qinteng Hou, Hua Zhao, Guangmang Liu, Xiaoling Chen, Gang Tian, Jingyi Cai, Gang Jia
Poultry Science.2024; 103(5): 103610. CrossRef - The effect of sex and dietary crude protein level on nutrient transporter gene expression and cecal microbiota populations in broiler chickens
Ashley D. England, Sara de las Heras-Saldana, Kosar Gharib-Naseri, Sarbast K. Kheravii, Shu-Biao Wu
Poultry Science.2024; 103(2): 103268. CrossRef - Morphological features of the feral pigeon’s (Columba livia f. urbana) digestive system
I. O. Кolomak
Journal for Veterinary Medicine, Biotechnology and Biosafety.2024; 10(1): 7. CrossRef - Microbial community profiling in intestinal tract of indigenous chickens from different villages
Mokoma Eunice Mootane, Thendo Mafuna, Tondani Madeleine Ramantswana, Dikeledi Petunia Malatji
Scientific Reports.2024;[Epub] CrossRef - The Effect of including a Mixed-Enzyme Product in Broiler Diets on Performance, Metabolizable Energy, Phosphorus and Calcium Retention
Harriet Walker, Suvi Vartiainen, Juha Apajalahti, Jules Taylor-Pickard, Ivana Nikodinoska, Colm A. Moran
Animals.2024; 14(2): 328. CrossRef - Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome
Yongxian Yang, Fuping Zhang, Xuan Yu, Liqi Wang, Zhong Wang
Frontiers in Microbiology.2024;[Epub] CrossRef - Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens
Calvin Ho-Fung Lau, Sabrina Capitani, Yuan-Ching Tien, Lou Ann Verellen, Munene Kithama, Hellen Kang, Elijah G. Kiarie, Edward Topp, Moussa S. Diarra, Michael Fruci
Animal Microbiome.2024;[Epub] CrossRef - Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers
Muhammad Zeeshan Akram, Ester Arévalo Sureda, Luke Comer, Matthias Corion, Nadia Everaert
Animal Microbiome.2024;[Epub] CrossRef - Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?
Kateřina Marková, Jakub Kreisinger, Michal Vinkler
Poultry Science.2024; 103(6): 103752. CrossRef - Sex‐specific genetic parameter estimates of body weight in Mazandaran indigenous chickens
Mohammad Esmaeili, Mohsen Gholizadeh, Hasan Hafezian, Ayoub Farhadi
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- Jeong Myeong Kim , An-Sung Roh , Seung-Chul Choi , Eun-Jeong Kim , Moon-Tae Choi , Byung-Koo Ahn , Sun-Kuk Kim , Young-Han Lee , Jae-Ho Joa , Seong-Soo Kang , Shin Ae Lee , Jae-Hyung Ahn , Jaekyeong Song , Hang-Yeon Weon
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- DOI: https://doi.org/10.1007/s12275-016-6526-5
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Abstract
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- Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis. A total of 11,865 operational taxonomic units at a 97% similarity cutoff level were detected from 847,560 sequences. Among nine soil factors evaluated; pH, electrical conductivity (EC), exchangeable cations (Ca2+, Mg2+, Na+, and K+), available P2O5, organic matter, and NO3-N, soil pH was most strongly correlated with bacterial richness (polynomial regression, pH: R2 = 0.1683, P < 0.001) and diversity (pH: R2 = 0.1765, P < 0.001). Community dissimilarities (Bray-Curtis distance) were positively correlated with Euclidean distance for pH and EC (Mantel test, pH: r = 0.2672, P < 0.001; EC: r = 0.1473, P < 0.001). Among dominant phyla (> 1%), the relative abundances of Proteobacteria, Gemmatimonadetes, Acidobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were also more strongly correlated with pH and EC values, compared with other soil cation contents, such as Ca2+, Mg2+, Na+, and K+. Our results suggest that, despite the heterogeneity of various environmental variables, the bacterial communities of the intensively cultivated greenhouse soils were particularly influenced by soil pH and EC. These findings therefore shed light on the soil microbial ecology of greenhouse cultivation, which should be helpful for devising effective management strategies to enhance soil microbial diversity and improving crop productivity.
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Microbial Ecology.2023; 86(4): 3027. CrossRef - Predicting microbial responses to changes in soil physical and chemical properties under different land management
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Applied Soil Ecology.2023; 188: 104878. CrossRef - Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico
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Pedosphere.2023; 33(2): 312. CrossRef - Heavy Metal Distribution and Microbial Diversity of the Surrounding Soil and Tailings of Two Cu Mines in China
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Frontiers in Microbiology.2023;[Epub] CrossRef - Plant ash prevents acid mine drainage from sulfur-bearing tailings through multiple actions — A low-cost alkaline material
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- DOI: https://doi.org/10.1007/s12275-016-6463-3
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- 28 Crossref
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Abstract
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- Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.
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- DOI: https://doi.org/10.1007/s12275-016-6294-2
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Abstract
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- The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.
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- Dominant genera of cyanobacteria in Lake Taihu and their relationships with environmental factors
- Lijun Feng , Shiyou Liu , Wenxian Wu , Jiawen Ma , Pei Li , Hailing Xu , Na Li , Yaoyu Feng
- J. Microbiol. 2016;54(7):468-476. Published online June 28, 2016
- DOI: https://doi.org/10.1007/s12275-016-6037-4
- 324 View
- 0 Download
- 16 Crossref
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Abstract
PDF
- Cyanobacterial blooms in freshwaters have become one of the most widespread of environmental problems and threaten water resources worldwide. Previous studies on cyanobacteria in Lake Taihu often collected samples from one site (like Meiliang Bay or Zhushan Bay) and focused on the variation in patterns or abundance of Microcystis during the blooming season. However, the distribution of cyanobacteria in Lake Taihu shows differing pattern in various seasons. In this study, water samples were collected monthly for one year at five sites in Lake Taihu with different trophic status and a physicochemical analysis and denaturing gradient gel electrophoresis (DGGE) were conducted. DGGE fingerprint analysis showed that Microcystis (7/35 bands) and Synechococcus (12/35 bands) were the two most dominant genera present during the study period at all five sites. Cyanobium (3/35 bands) was the third most common genus which has seldom been previously reported in Lake Taihu. Redundancy analysis (RDA) indicated that the cyanobacterial community structure was significantly correlated with NO3 --N, CODMn, and NH4 +-N in the winter and spring, whereas it was correlated with water temperature in the summer and autumn. Limiting the nutrient input (especially of N and C loading) in Lake Taihu would be a key factor in controlling the growth of different genera of cyanobacteria.
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Citations
Citations to this article as recorded by- Harmful Cyanobacterial Blooms: Going beyond the “Green” to Monitor and Predict HCBs
Daniela R. de Figueiredo
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Research Support, Non-U.S. Gov'ts
- Effect of Long-Term Different Fertilization on Bacterial Community Structures and Diversity in Citrus Orchard Soil of Volcanic Ash
- Jae Ho Joa , Hang Yeon Weon , Hae Nam Hyun , Young Chull Jeun , Sang Wook Koh
- J. Microbiol. 2014;52(12):995-1001. Published online November 29, 2014
- DOI: https://doi.org/10.1007/s12275-014-4129-6
- 359 View
- 0 Download
- 28 Crossref
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Abstract
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- This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687–7,330 and 1,790–3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.
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Citations
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- Pyrosequencing Analysis of the Bacterial Communities in the Guts of Honey Bees Apis cerana and Apis mellifera in Korea
- Jae-Hyung Ahn , In-Pyo Hong , Jeung-Im Bok , Byung-Yong Kim , Jaekyeong Song , Hang-Yeon Weon
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- DOI: https://doi.org/10.1007/s12275-012-2188-0
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- 0 Download
- 84 Crossref
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Abstract
- The bacterial communities in the guts of the adults and larvae of the Asian honey bee Apis cerana and the European honey bee Apis mellifera were surveyed by pyrosequencing the 16S rRNA genes. Most of the gut bacterial 16S rRNA gene sequences were highly similar to the known honey bee-specific ones and affiliated with Pasteurellaceae or lactic acid bacteria (LAB). The numbers of operational taxonomic units (OTUs, defined at 97% similarity) were lower in the larval guts (6 or 9) than in the adult guts (18 or 20), and the frequencies of Pasteurellaceae-related OTUs were higher in the larval guts while those of LAB-related OTUs in the adult guts. The frequencies of Lactococcus, Bartonella, Spiroplasma, Enterobacteriaceae, and Flavobacteriaceae-related OTUs were much higher in A. cerana guts while Bifidobacterium and Lachnospiraceae-related OTUs were more abundant in A. mellfera guts. The bacterial community structures in the midguts and hindguts of the adult honey bees were not different for A. cerana, but significantly different for A. mellifera. The above results substantiated the previous observation that honey bee guts are dominated by several specific bacterial groups, and also showed that the relative abundances of OTUs could be markedly changed depending on the developmental stage, the location within the gut, and the honey bee species. The possibility of using the gut bacterial community as an indicator of honey bee health was discussed.
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- 271 View
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- 4 Crossref
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Abstract
PDF
- The bacterial communities in the food, intestines, and feces of earthworms were investigated by PCR-denaturing gradient gel electrophoresis (DGGE). In this study, PCR-DGGE was optimized by testing 6 universal primer sets for microbial 16S rRNA in 6 pure culture strains of intestinal microbes in earthworms. One primer set effectively amplified 16S rRNA from bacterial populations that were found in the food, intestines, and feces of earthworms. Compared with the reference markers from the pure culture strains, the resulting DGGE profiles contained 28 unique DNA fragments. The dominant microorganisms in the food, intestines, and feces of earthworms included Rhodobacterales bacterium, Fusobacteria, Ferrimonas marina, Aeromonas popoffii, and soil bacteria. Other strains, such as Acinetobacter, Clostridium, and Veillonella, as well as rumen bacteria and uncultured bacteria also were present. These results demonstrated that PCR-DGGE analysis can be used to elucidate bacterial diversity and identify unculturable microorganisms.
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Abstract
PDF
- Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.
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Research Support, Non-U.S. Gov'ts
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- 406 View
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Abstract
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- Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3~15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that γ-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured γ-Proteobacteria) were predominant in the community during 0~9 h, while the ratio of α-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured α-Proteobacteria) increased 2.6~4.8 folds during 24~36 h of the biofilm formation, emerging as the most predominant group. Previously, α-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of γ-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.
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PLOS ONE.2019; 14(6): e0217165. CrossRef - Marine biofilms: diversity of communities and of chemical cues
Jorge Antunes, Pedro Leão, Vitor Vasconcelos
Environmental Microbiology Reports.2019; 11(3): 287. CrossRef - Biofilm facilitates metal accumulation onto microplastics in estuarine waters
Heather Richard, Edward J. Carpenter, Tomoko Komada, Peter T. Palmer, Chelsea M. Rochman
Science of The Total Environment.2019; 683: 600. CrossRef - Shear Stress as a Major Driver of Marine Biofilm Communities in the NW Mediterranean Sea
Elisa C. P. Catão, Thomas Pollet, Benjamin Misson, Cédric Garnier, Jean-Francois Ghiglione, Raphaëlle Barry-Martinet, Marine Maintenay, Christine Bressy, Jean-François Briand
Frontiers in Microbiology.2019;[Epub] CrossRef - Spatial Environmental Heterogeneity Determines Young Biofilm Assemblages on Microplastics in Baltic Sea Mesocosms
Katharina Kesy, Sonja Oberbeckmann, Bernd Kreikemeyer, Matthias Labrenz
Frontiers in Microbiology.2019;[Epub] CrossRef - Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific?
Thirumahal Muthukrishnan, Maryam Al Khaburi, Raeid M. M. Abed
Microbial Ecology.2019; 78(2): 361. CrossRef - Analysis of cultivable aerobic bacterial community composition and screening for facultative sulfate-reducing bacteria in marine corrosive steel
Xiaohong Li, Hui Xiao, Wenjun Zhang, Yongqian Li, Xuexi Tang, Jizhou Duan, Zhibo Yang, Jing Wang, Fang Guan, Guoqing Ding
Journal of Oceanology and Limnology.2019; 37(2): 600. CrossRef - Microbial Ecotoxicology of Marine Plastic Debris: A Review on Colonization and Biodegradation by the “Plastisphere”
Justine Jacquin, Jingguang Cheng, Charlène Odobel, Caroline Pandin, Pascal Conan, Mireille Pujo-Pay, Valérie Barbe, Anne-Leila Meistertzheim, Jean-François Ghiglione
Frontiers in Microbiology.2019;[Epub] CrossRef - Marine microplastic-associated bacterial community succession in response to geography, exposure time, and plastic type in China's coastal seawaters
Xiyuan Xu, Shuai Wang, Fenglei Gao, Jingxi Li, Li Zheng, Chengjun Sun, Changfei He, Zongxing Wang, Lingyun Qu
Marine Pollution Bulletin.2019; 145: 278. CrossRef - Colonization of Non-biodegradable and Biodegradable Plastics by Marine Microorganisms
Claire Dussud, Cindy Hudec, Matthieu George, Pascale Fabre, Perry Higgs, Stéphane Bruzaud, Anne-Marie Delort, Boris Eyheraguibel, Anne-Leïla Meistertzheim, Justine Jacquin, Jingguang Cheng, Nolwenn Callac, Charlène Odobel, Sophie Rabouille, Jean-François
Frontiers in Microbiology.2018;[Epub] CrossRef - Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary
Peilin Jiang, Shiye Zhao, Lixin Zhu, Daoji Li
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Lei Zhou, Chengrong Bai, Jian Cai, Yang Hu, Keqiang Shao, Guang Gao, Erik Jeppesen, Xiangming Tang
Environmental Science and Pollution Research.2018; 25(26): 26550. CrossRef - Biofilm early stage development in two nutrient‐rich streams with different urban impacts
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River Research and Applications.2018; 34(7): 755. CrossRef - Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms
Claire Bertelli, Sophie Courtois, Marta Rosikiewicz, Philippe Piriou, Sébastien Aeby, Samuel Robert, Jean-François Loret, Gilbert Greub
Frontiers in Microbiology.2018;[Epub] CrossRef - Partial replacement of cement for waste aggregates in concrete coastal and marine infrastructure: A foundation for ecological enhancement?
Ryan S. McManus, Nicholas Archibald, Sean Comber, Antony M. Knights, Richard C. Thompson, Louise B. Firth
Ecological Engineering.2018; 120: 655. CrossRef - Comparative study of biofilm formation on biocidal antifouling and fouling-release coatings using next-generation DNA sequencing
Mark O. Winfield, Adrian Downer, Jennifer Longyear, Marie Dale, Gary L. A. Barker
Biofouling.2018; 34(4): 464. CrossRef - Lanosterol expressed bio-fouling inhibition on Gulf of Mannar coast, India
Balasubramanian V., Rajaram R., Palanichamy S., Subramanian G., Mathivanan K., Pugazhendhi A.
Progress in Organic Coatings.2018; 115: 100. CrossRef - Design of a rotating disk reactor to assess the colonization of biofilms by free-living amoebae under high shear rates
A. Perrin, P. Herbelin, F. P. A. Jorand, S. Skali-Lami, L. Mathieu
Biofouling.2018; 34(4): 368. CrossRef - Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea
Lucy C. Woodall, Anna D. Jungblut, Kevin Hopkins, Andie Hall, Laura F. Robinson, Claire Gwinnett, Gordon L. J. Paterson, Daniele Daffonchio
PLOS ONE.2018; 13(11): e0206220. CrossRef - Amphiphilic polymer based on fluoroalkyl and PEG side chains for fouling release coating
W W Cong, K Wang, X Y Yu, H Q Zhang, Z Lv, T J Gui
IOP Conference Series: Materials Science and Engineering.2017; 283: 012002. CrossRef - Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing
Xiaohong Li, Jizhou Duan, Hui Xiao, Yongqian Li, Haixia Liu, Fang Guan, Xiaofan Zhai
Frontiers in Microbiology.2017;[Epub] CrossRef - Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea
Caroline De Tender, Lisa I. Devriese, Annelies Haegeman, Sara Maes, Jürgen Vangeyte, André Cattrijsse, Peter Dawyndt, Tom Ruttink
Environmental Science & Technology.2017; 51(13): 7350. CrossRef - Fate of Eight Different Polymers under Uncontrolled Composting Conditions: Relationships Between Deterioration, Biofilm Formation, and the Material Surface Properties
Anne Mercier, Kevin Gravouil, Willy Aucher, Sandra Brosset-Vincent, Linette Kadri, Jenny Colas, Didier Bouchon, Thierry Ferreira
Environmental Science & Technology.2017; 51(4): 1988. CrossRef - Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments
Jean-François Briand, Aude Barani, Cédric Garnier, Karine Réhel, Félix Urvois, Christophe LePoupon, Agnès Bouchez, Didier Debroas, Christine Bressy
Microbial Ecology.2017; 74(3): 585. CrossRef - Cell-bound exopolysaccharides from an axenic culture of the intertidal mudflat Navicula phyllepta diatom affect biofilm formation by benthic bacteria
Ibtissem Doghri, Johann Lavaud, Alain Dufour, Alexis Bazire, Isabelle Lanneluc, Sophie Sablé
Journal of Applied Phycology.2017; 29(1): 165. CrossRef - Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders
Didier Debroas, Anne Mone, Alexandra Ter Halle
Science of The Total Environment.2017; 599-600: 1222. CrossRef - Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films
Evdokia Syranidou, Katerina Karkanorachaki, Filippo Amorotti, Eftychia Repouskou, Kevin Kroll, Boris Kolvenbach, Philippe F-X Corvini, Fabio Fava, Nicolas Kalogerakis, Zhili He
PLOS ONE.2017; 12(8): e0183984. CrossRef - Influence of femtosecond laser produced nanostructures on biofilm growth on steel
Nadja Epperlein, Friederike Menzel, Karin Schwibbert, Robert Koter, Jörn Bonse, Janin Sameith, Jörg Krüger, Jörg Toepel
Applied Surface Science.2017; 418: 420. CrossRef - Microplastics as a vector for the transport of the bacterial fish pathogen species Aeromonas salmonicida
Manca Kovač Viršek, Marija Nika Lovšin, Špela Koren, Andrej Kržan, Monika Peterlin
Marine Pollution Bulletin.2017; 125(1-2): 301. CrossRef - Biofilm Formation and Heat Stress Induce Pyomelanin Production in Deep-Sea Pseudoalteromonas sp. SM9913
Zhenshun Zeng, Xingsheng Cai, Pengxia Wang, Yunxue Guo, Xiaoxiao Liu, Baiyuan Li, Xiaoxue Wang
Frontiers in Microbiology.2017;[Epub] CrossRef - Multi metal assessment on biofilm formation in offshore environment
Muthukumar Krishnan, Hans-Uwe Dahms, Palanichamy Seeni, Subramanian Gopalan, Vignesh Sivanandham, Kim Jin-Hyoung, Rathinam Arthur James
Materials Science and Engineering: C.2017; 73: 743. CrossRef - In Situ Confocal Raman Microscopy of Hydrated Early Stages of Bacterial Biofilm Formation on Various Surfaces in a Flow Cell
Truis Smith-Palmer, Sicheng Lin, Ikenna Oguejiofor, Tianyang Leng, Amanda Pustam, Jin Yang, Lori L. Graham, Russell C. Wyeth, Cory D. Bishop, M. Edwin DeMont, David Pink
Applied Spectroscopy.2016; 70(2): 289. CrossRef - Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages
Amanda R. McCormick, Timothy J. Hoellein, Maxwell G. London, Joshua Hittie, John W. Scott, John J. Kelly
Ecosphere.2016;[Epub] CrossRef - Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment
Yung Mi Lee, Kyung Hee Cho, Kyuin Hwang, Eun Hye Kim, Mincheol Kim, Soon Gyu Hong, Hong Kum Lee
The Korean Journal of Microbiology.2016; 52(1): 49. CrossRef - Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms
Jasmin C. Lawes, Brett A. Neilan, Mark V. Brown, Graeme F. Clark, Emma L. Johnston
Biofouling.2016; 32(1): 57. CrossRef - Marine and estuarine natural microbial biofilms: ecological and biogeochemical dimensions
O. Roger Anderson
AIMS Microbiology.2016; 2(3): 304. CrossRef - Flow Chamber System for the Statistical Evaluation of Bacterial Colonization on Materials
Friederike Menzel, Bianca Conradi, Karsten Rodenacker, Anna Gorbushina, Karin Schwibbert
Materials.2016; 9(9): 770. CrossRef - Bacterial repopulation of drinking water pipe walls after chlorination
Laurence Mathieu, Grégory Francius, Racha El Zein, Edith Angel, Jean-Claude Block
Biofouling.2016; 32(8): 925. CrossRef - Marine bacteria from the French Atlantic coast displaying high forming-biofilm abilities and different biofilm 3D architectures
Ibtissem Doghri, Sophie Rodrigues, Alexis Bazire, Alain Dufour, David Akbar, Valérie Sopena, Sophie Sablé, Isabelle Lanneluc
BMC Microbiology.2015;[Epub] CrossRef - Marine microplastic-associated biofilms – a review
Sonja Oberbeckmann, Martin G. J. Löder, Matthias Labrenz
Environmental Chemistry.2015; 12(5): 551. CrossRef - Low-concentration diffusible molecules affect the formation of biofilms by mixed marine communities
David Ian Walker, Charles William Keevil, Rajni Hatti Kaul
Cogent Biology.2015; 1(1): 1103830. CrossRef - Modulation of violacein production and phenotypes associated with biofilm by exogenous quorum sensing N-acylhomoserine lactones in the marine bacterium Pseudoalteromonas ulvae TC14
Armande Mireille Ayé, Maryse Bonnin-Jusserand, Florence Brian-Jaisson, Annick Ortalo-Magné, Gérald Culioli, Rose Koffi Nevry, Nadia Rabah, Yves Blache, Maëlle Molmeret
Microbiology.2015; 161(10): 2039. CrossRef - Variations in the abundance and structural diversity of microbes forming biofilms in a thermally stressed coral reef system
Huda Mahmoud
Marine Pollution Bulletin.2015; 100(2): 710. CrossRef - Assessing the Antimicrobial Activity of Polyisoprene Based Surfaces
Hope Badawy, Jérôme Brunellière, Marina Veryaskina, Guillaume Brotons, Sophie Sablé, Isabelle Lanneluc, Kelly Lambert, Pascal Marmey, Amy Milsted, Teresa Cutright, Arnaud Nourry, Jean-Luc Mouget, Pamela Pasetto
International Journal of Molecular Sciences.2015; 16(3): 4392. CrossRef - Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea
Caroline A. De Tender, Lisa I. Devriese, Annelies Haegeman, Sara Maes, Tom Ruttink, Peter Dawyndt
Environmental Science & Technology.2015; 49(16): 9629. CrossRef - Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms
Jesse P Harrison, Michaela Schratzberger, Melanie Sapp, A Mark Osborn
BMC Microbiology.2014;[Epub] CrossRef - Identification of Bacterial Strains Isolated from the Mediterranean Sea Exhibiting Different Abilities of Biofilm Formation
Florence Brian-Jaisson, Annick Ortalo-Magné, Linda Guentas-Dombrowsky, Fabrice Armougom, Yves Blache, Maëlle Molmeret
Microbial Ecology.2014; 68(1): 94. CrossRef - Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration
I. Douterelo, R. Sharpe, J. Boxall
Journal of Applied Microbiology.2014; 117(1): 286. CrossRef -
Fluorescence-Based Quasicontinuous and
In Situ
Monitoring of Biofilm Formation Dynamics in Natural Marine Environments
M. Fischer, G. Friedrichs, T. Lachnit, C. R. Lovell
Applied and Environmental Microbiology.2014; 80(12): 3721. CrossRef - Dynamic shift in community structures of biofilm-forming bacteria by the pre-treatment systems of seawater reverse osmosis processes
Hyokwan Bae, Dawoon Jeong, Heesun Kim, Seil Kim, Seockheon Lee
Desalination.2014; 343: 17. CrossRef - Integrated metagenomic and metaproteomic analyses of marine biofilm communities
Dagmar H. Leary, Robert W. Li, Leila J. Hamdan, W. Judson Hervey, Nikolai Lebedev, Zheng Wang, Jeffrey R. Deschamps, Anne W. Kusterbeck, Gary J. Vora
Biofouling.2014; 30(10): 1211. CrossRef - Marine microbes in the Plastic Age
A Mark Osborn, Slobodanka Stojkovic
Microbiology Australia.2014; 35(4): 207. CrossRef - Life under flow: A novel microfluidic device for the assessment of anti-biofilm technologies
Maria Salta, Lorenzo Capretto, Dario Carugo, Julian A. Wharton, Keith R. Stokes
Biomicrofluidics.2013;[Epub] CrossRef - Biological activity in expanded clay (EC) and granulated activated carbon (GAC) seawater filters
F. Xavier Simon, Ywann Penru, María M. Micó, Joan Llorens, Santiago Esplugas, Sylvie Baig
Desalination.2013; 328: 67. CrossRef - Identification of marine bacteria affecting lithium adsorbents in seawater
Joo-Ae Kim, Mihye Kong, Ji-Ho Kim, Kang-Sup Chung, Chi-Yong Eom, Hye-On Yoon
Environmental Geochemistry and Health.2013; 35(3): 311. CrossRef - Marine biofilms on artificial surfaces: structure and dynamics
Maria Salta, Julian A. Wharton, Yves Blache, Keith R. Stokes, Jean‐Francois Briand
Environmental Microbiology.2013; 15(11): 2879. CrossRef - Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corroded carbon steel
Florence Marty, Jean-François Ghiglione, Sandrine Païssé, Hervé Gueuné, Laurent Quillet, Mark C.M. van Loosdrecht, Gerard Muyzer
Biofouling.2012; 28(4): 363. CrossRef - Bacterial communities associated with the decomposition of Fucus vesiculosus in transitional waters
Patrícia Martins, Marta Lobão Lopes, Ana Maria Rodrigues, Newton C.M. Gomes, Victor Quintino
Estuarine, Coastal and Shelf Science.2012; 110: 116. CrossRef - Pioneer marine biofilms on artificial surfaces including antifouling coatings immersed in two contrasting French Mediterranean coast sites
Jean-François Briand, Ikram Djeridi, Dominique Jamet, Stéphane Coupé, Christine Bressy, Maëlle Molmeret, Brigitte Le Berre, Frédéric Rimet, Agnès Bouchez, Yves Blache
Biofouling.2012; 28(5): 453. CrossRef - Community characteristics of early biofilms formed on water distribution pipe materials
Yeong-Kwan Kim, Sung-Gu Park, Dong-Hun Lee, Sung-Chan Choi
Journal of The Korean Society of Water and Wastewater.2012; 26(6): 767. CrossRef - Characterisation of the bacteria associated with barnacle, Balanus amphitrite, shell and their role in gregarious settlement of cypris larvae
T. Bacchetti De Gregoris, L. Khandeparker, A.C. Anil, E. Mesbahi, J.G. Burgess, A.S. Clare
Journal of Experimental Marine Biology and Ecology.2012; 413: 7. CrossRef - Antifouling activity of commercial biocides vs. natural and natural-derived products assessed by marine bacteria adhesion bioassay
Mercedes Camps, Jean-François Briand, Linda Guentas-Dombrowsky, Gérald Culioli, Alexis Bazire, Yves Blache
Marine Pollution Bulletin.2011; 62(5): 1032. CrossRef - Differences Between Bacterial Communities Associated with the Surface or Tissue of Mediterranean Sponge Species
Berna Gerçe, Thomas Schwartz, Christoph Syldatk, Rudolf Hausmann
Microbial Ecology.2011; 61(4): 769. CrossRef - Development of Bacterial Biofilms on Artificial Corals in Comparison to Surface-Associated Microbes of Hard Corals
Michael John Sweet, Aldo Croquer, John Christopher Bythell, Purification Lopez-Garcia
PLoS ONE.2011; 6(6): e21195. CrossRef - Changes in the relative abundance of biofilm-forming bacteria by conventional sand-filtration and microfiltration as pretreatments for seawater reverse osmosis desalination
Hyokwan Bae, Heesun Kim, Seongpil Jeong, Seockheon Lee
Desalination.2011; 273(2-3): 258. CrossRef - Phylogenetic analysis of culturable marine bacteria in sediments from South Korean Yellow Sea
Natarajan Velmurugan, Duraisamy Kalpana, Jae-Young Cho, Geon-Hyoung Lee, Suk-Hwan Park, Yang-Soo Lee
Microbiology.2011; 80(2): 261. CrossRef - Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa
Tristano Bacchetti De Gregoris, Nick Aldred, Anthony S. Clare, J. Grant Burgess
Journal of Microbiological Methods.2011; 86(3): 351. CrossRef - Pioneering bacterial and algal communities and potential extracellular enzyme activities of stream biofilms
Elisabeth Pohlon, Jürgen Marxsen, Kirsten Küsel
FEMS Microbiology Ecology.2010; 71(3): 364. CrossRef -
Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (
Lactuca
Species) Phyllosphere
Paul J. Hunter, Paul Hand, David Pink, John M. Whipps, Gary D. Bending
Applied and Environmental Microbiology.2010; 76(24): 8117. CrossRef - Marine aerobic biofilm as biocathode catalyst
Benjamin Erable, Ilse Vandecandelaere, Marco Faimali, Marie-Line Delia, Luc Etcheverry, Peter Vandamme, Alain Bergel
Bioelectrochemistry.2010; 78(1): 51. CrossRef - Bacterial biofilm-community selection during autohydrogenotrophic reduction of nitrate and perchlorate in ion-exchange brine
Chang Hoon Ahn, Hyangkyun Oh, Dongwon Ki, Steven W. Van Ginkel, Bruce E. Rittmann, Joonhong Park
Applied Microbiology and Biotechnology.2009; 81(6): 1169. CrossRef - Molecular identification of fecal pollution sources in water supplies by host-specific fecal DNA markers and Terminal Restriction Fragment Length Polymorphism profiles of 16S rRNA gene
Ju-Yong Jeong, Kyung-Ik Gil, Kyong-Hee Lee, Jong-Ok Ka
The Journal of Microbiology.2008; 46(6): 599. CrossRef
- Discovery of potentially degrading microflora of different types of plastics based on long-term in-situ incubation in the deep sea
- Phylogenetic Diversity of Bacteria in an Earth-Cave in Guizhou Province, Southwest of China
- JunPei Zhou , YingQi Gu , ChangSong Zou , MingHe Mo
- J. Microbiol. 2007;45(2):105-112.
- DOI: https://doi.org/2526 [pii]
- 207 View
- 0 Download
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Abstract
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- The objective of this study was to analyze the phylogenetic composition of bacterial community in the soil of an earth-cave (Niu Cave) using a culture-independent molecular approach. 16S rRNA genes were amplified directly from soil DNA with universally conserved and Bacteria-specific rRNA gene primers and cloned. The clone library was screened by restriction fragment length polymorphism (RFLP), and representative rRNA gene sequences were determined. A total of 115 bacterial sequence types were found in 190 analyzed clones. Phylogenetic sequence analyses revealed novel 16S rRNA gene sequence types and a high diversity of putative bacterial community. Members of these bacteria included Proteobacteria (42.6%), Acidobacteria (18.6%), Planctomycetes (9.0%), Chloroflexi (Green nonsulfur bacteria, 7.5%), Bacteroidetes (2.1%), Gemmatimonadetes (2.7%), Nitrospirae (8.0%), Actinobacteria (High G+C Gram-positive bacteria, 6.4%) and candidate divisions (including the OP3, GN08, and SBR1093, 3.2%). Thirty-five clones were affiliated with bacteria that were related to nitrogen, sulfur, iron or manganese cycles. The comparison of the present data with the data obtained previously from caves based on 16S rRNA gene analysis revealed similarities in the bacterial community components, especially in the high abundance of Proteobacteria and Acidobacteria. Furthermore, this study provided the novel evidence for presence of Gemmatimonadetes, Nitrosomonadales, Oceanospirillales, and Rubrobacterales in a karstic hypogean environment.
- Monitoring of Bacterial Community in a Coniferous Forest Soil After a Wildfire
- Ok-Sun Kim , Jae-Jun Yoo , Dong-Hun Lee , Tae-Seok Ahn , Hong-Gyu Song
- J. Microbiol. 2004;42(4):278-284.
- DOI: https://doi.org/2110 [pii]
- 169 View
- 0 Download
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Abstract
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- Changes in the soil bacterial community of a coniferous forest were analyzed to assess microbial responses to wildfire. Soil samples were collected from three different depths in lightly and severely burned areas, as well as a nearby unburned control area. Direct bacterial counts ranged from 3.3-22.6 x10^8 cells/(g . soil). In surface soil, direct bacterial counts of unburned soil exhibited a great degree of fluctuation. Those in lightly burned soil changed less, but no significant variation was observed in the severely burned soil. The fluctuations of direct bacterial count were less in the middle and deep soil layers. The structure of the bacterial community was analyzed via the fluorescent in situ hybridization method. The number of bacteria detected with the eubacteria-targeted probe out of the direct bacterial count varied from 30.3 to 84.7%, and these ratios were generally higher in the burned soils than in the unburned control soils. In the surface unburned soil, the ratios of [alpha]-, [beta]- and [gamma]-proteobacteria, Cytophaga-Flavobacterium group, and other eubacteria groups to total eubacteria were 9.9, 10.6, 15.5, 9.0, and 55.0%, respectively, and these ratios were relatively stable. The ratios of [alpha]-, [beta]- and [gamma]-proteobacteria, and Cytophaga-Flavobacterium group to total eubacteria increased immediately after the wildfire, and the other eubacterial proportions decreased in the surface and middle layer soils. By way of contrast, the composition of the 5 groups of eubacteria in the subsurface soil exhibited no significant fluctuations during the entire period. The total bacterial population and bacterial community structure disturbed by wildfire soon began to recover, and original levels seemed to be restored 3 months after the wildfire.
- Monitoring of Soil Bacterial Community and Some Inoculated Bacteria After Prescribed Fire in Microcosm
- Hong-Gyu Song , Ok-Sun Kim , Jae-Jun Yoo , Sun-Ok Jeon , Sun-Hee Hong , Dong-Hun Lee , Tae-Seok Ahn
- J. Microbiol. 2004;42(4):285-291.
- DOI: https://doi.org/2109 [pii]
- 198 View
- 0 Download
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Abstract
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- The soil bacterial community and some inoculated bacteria were monitored to assess the microbial responses to prescribed fire in their microcosm. An acridine orange direct count of the bacteria in the unburned control soil were maintained at a relatively stable level (2.0~2.7 x10^9 cells/g^-1 . soil) during the 180 day study period. The number of bacteria in the surface soil was decreased by fire, but was restored after 3 months. Inoculation of some bacteria increased the number of inoculated bacteria several times and these elevated levels lasted several months. The ratios of eubacteria detected by a fluorescent in situ hybridization (FISH) method to direct bacterial count were in the range of 60~80% during the study period, with the exception of some lower values at the beginning, but there were no definite differences between the burned and unburned soils or the inoculated and uninoculated soils. In the unburned control soil, the ratios of [alpha]-, [beta]- and [gamma]-subgroups of the proteobacteria, Cytophaga-Flavobacterium and other eubacteria groups to that of the entire eubacteria were 13.7, 31.7, 17.1, 16.8 and 20.8%, respectively, at time 0. The overall change on the patterns of the ratios of the 5 subgroups of eubacteria in the uninoculated burned and inoculated soils were similar to those of the unburned control soil, with the exception of some minor variations during the initial period. The proportions of each group of eubacteria became similar in the different microcosms after 6 months, which may indicate the recovery of the original soil microbial community structure after fire or the inoculation of some bacteria. The populations of Azotobacter vinelandii, Bacillus megaterium and Pseudomonas fluorescens, which had been inoculated to enhance the microbial activities, and monitored by FISH method, showed similar changes in the microcosms, and maintained high levels for several months.
- The Genetic Diversity Analysis of the Bacterial Community in Groundwater by Denaturing Gradient Gel Electrophoresis (DGGE)
- Hong-Bum Cho , Jong-Kwang Lee , Yong-Keel Choi
- J. Microbiol. 2003;41(4):327-334.
- 196 View
- 1 Download
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Abstract
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- This study employed two PCR-based 16S rDNA approaches, amplified rDNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis (DGGE), to characterize the bacterial community structure in groundwater. Samples were collected from groundwater for the use by private residences, as well as for industrial and agricultural purposes, in Ansan City. Each PCR product was obtained by PCR with eubacteria 16S rDNA and variable V3 region specific primer sets. After amplification, the 16S rDNA PCR products were digested with 4-base site specific restriction endonucleases, and the restriction pattern analyzed. The genetic diversity and similarity of the groundwater bacterial community was analyzed by eubacteria universal primer sets for the amplification of variable V3 regions of the bacterial 16S rDNA. The result of the bacterial community analysis, by ARDRA and DGGE, revealed the same pattern. The highest diversity was found in groundwater from site G1, which was used in residences. In the DGGE profile, a high intensity band was sequenced, and revealed to be Pseudomonas sp. strain P51.
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