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Liu ZX, Lyu YM, Liu Y, Wang YQ, Xiong MM, Tang Y, Li XY, Sun H, Xu JL. Differential spatial responses and assembly mechanisms of soil microbial communities across region-scale Taiga ecosystems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122653. [PMID: 39340882 DOI: 10.1016/j.jenvman.2024.122653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 09/10/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024]
Abstract
Different soil microbial communities play distinct key roles in regulating forest ecosystem processes and functions. However, the differences in spatial variability and assembly mechanisms of various taiga forest soil microbial taxa remain poorly understood. Here, we assessed the spatial patterns of bacterial and fungal communities, their assembly processes, and the influencing factors in taiga forest ecosystems in Xinjiang, China. A significant distance decay pattern was observed in the similarity of bacterial and fungal communities, with bacterial communities exhibiting a more pronounced pattern than fungal communities. Stochastic and deterministic processes governed together to drive soil bacterial community assembly, whereas stochastic processes dominated fungal community assembly. The coexistence networks revealed that the interactions of bacterial and fungal networks in the four regions are primarily based on interspecies symbiosis, with fungal coexistence networks demonstrating greater stability than bacterial networks. Additionally, the study identified a positive relationship between the modularity of bacterial networks and dispersal limitation. Analysis of environmental factors revealed that soil pH primarily affects the characteristics and assembly mechanisms of bacterial communities, while vegetation conditions primarily affect fungal diversity and composition, with other unconsidered environmental variables influencing the fungal community assembly process. This study emphasized the distinct ways in which bacteria and fungi respond to environmental factors and interspecies interactions. Our results suggested that distinct restoration measures should be implemented for bacteria and fungi in future conservation efforts for forest soil microorganisms.
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Affiliation(s)
- Zheng-Xiao Liu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China; School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yue-Ming Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yang Liu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yun-Qi Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ming-Min Xiong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuan Tang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xing-Yue Li
- The College of Forestry, Beijing Forestry University, Beijing, China
| | - Han Sun
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ji-Liang Xu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China; School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
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Feng X, Tao Y, Dai Z, Chu Z, Wei Y, Tao M, He Y, Chen H. Effects of transgenic modification on the bacterial communities in different niches of maize under glyphosate toxicity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 362:125023. [PMID: 39322111 DOI: 10.1016/j.envpol.2024.125023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 09/22/2024] [Accepted: 09/22/2024] [Indexed: 09/27/2024]
Abstract
Transgenic glyphosate-resistant maize has emerged as a way to expand the use of glyphosate for weed control. Studying the microbiome in the tissues and rhizosphere soil of transgenic plants is vital for understanding the glyphosate-resistant mechanism and optimizing the transgenic design of crops. In our study, the expression of a mutant cp4epsps gene in transgenic maize, which confers tolerance to glyphosate, was performed using the maize variety Xianyu 335 as the genetically modified acceptor line. This transgenic modification did not affect the initial bacterial community in the leaf, stem, or root of maize, but promoted a differential bacterial community in the rhizosphere soil. Under glyphosate application, the abundance of beneficial bacteria involved in N fixation and P solubilization in plant tissues and the rhizosphere soil of glyphosate-resistance maize were higher than those in the glyphosate-sensitive maize. In contrast, the abundance of pathogens had the opposite trend, suggesting that the enhanced health of transgenic maize prevented microbiome deterioration under glyphosate. The re-inoculation of bacterial strains isolated from glyphosate-resistance maize into the leaf and rhizosphere soil of glyphosate-sensitive maize resulted in an enhanced photosynthetic capacity in response to glyphosate, demonstrating the vital role of specific bacteria for glyphosate resistance. Our study provides important evidence of how transgenic maize tolerance to herbicides affects the bacterial communities across the maize niches under glyphosate toxicity.
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Affiliation(s)
- Xuping Feng
- The Rural Development Academy at Zhejiang University, Zhejiang University, Hangzhou, 310058, China; College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yimin Tao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zhongmin Dai
- The Rural Development Academy at Zhejiang University, Zhejiang University, Hangzhou, 310058, China; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Zhenjiang Chu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuzhen Wei
- School of Information Engineering, Huzhou University, Huzhou, 313000, China
| | - Mingzhu Tao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510006, China
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3
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Arnaiz-Villena A, Juarez I, Vaquero-Yuste C, Lledo T, Martin-Villa JM, Suarez-Trujillo F. Complex Interactions between the Human Major Histocompatibility Complex (MHC) and Microbiota: Their Roles in Disease Pathogenesis and Immune System Regulation. Biomedicines 2024; 12:1928. [PMID: 39200390 PMCID: PMC11352054 DOI: 10.3390/biomedicines12081928] [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: 07/04/2024] [Revised: 08/19/2024] [Accepted: 08/19/2024] [Indexed: 09/02/2024] Open
Abstract
The relationship between microbiota and the immune system is complex and characterized by the ways in which microbiota directs immune function interactions, both innate and acquired and also keeps activating the immune system throughout an individual's life. In this respect, the human Major Histocompatibility Complex (MHC, referred to as HLA in humans) plays a crucial role and is also established in self-defense against microbes by presenting microbial-derived peptides to the immune cells. However, this assumption has some unclear aspects that should be investigated. For example, how is the microbiota shaped by microbe species diversity, quantity and functions of the immune system, as well as the role and molecular mechanisms of the HLA complex during this process. There are autoimmune diseases related to both HLA and specific microbiota changes or alterations, many of which are mentioned in the present review. In addition, the HLA peptide presenting function should be put in a framework together with its linkage to diseases and also with HLA compatibility necessary for transplants to be successful. These are still quite an enigmatically statistical and phenomenological approach, but no firm pathogenic mechanisms have been described; thus, HLA's real functioning is still to be fully unveiled. After many years of HLA single-genes studies, firm pathogenesis mechanisms underlying disease linkage have been discovered. Finally, microbiota has been defined as conformed by bacteria, protozoa, archaea, fungi, and viruses; notwithstanding, endogenous viral sequences integrated into the human genome and other viral particles (obelisks) recently found in the digestive mucosa should be taken into account because they may influence both the microbiome and the immune system and their interactions. In this context, we propose to integrate these microbial-genetic particle components into the microbiome concept and designate it as "microgenobiota".
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Affiliation(s)
- Antonio Arnaiz-Villena
- Department of Immunology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain; (I.J.); (C.V.-Y.); (T.L.); (J.M.M.-V.); (F.S.-T.)
- Instituto de Investigacion Sanitaria Gegorio Marañon, 28009 Madrid, Spain
| | - Ignacio Juarez
- Department of Immunology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain; (I.J.); (C.V.-Y.); (T.L.); (J.M.M.-V.); (F.S.-T.)
- Instituto de Investigacion Sanitaria Gegorio Marañon, 28009 Madrid, Spain
| | - Christian Vaquero-Yuste
- Department of Immunology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain; (I.J.); (C.V.-Y.); (T.L.); (J.M.M.-V.); (F.S.-T.)
- Instituto de Investigacion Sanitaria Gegorio Marañon, 28009 Madrid, Spain
| | - Tomás Lledo
- Department of Immunology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain; (I.J.); (C.V.-Y.); (T.L.); (J.M.M.-V.); (F.S.-T.)
- Instituto de Investigacion Sanitaria Gegorio Marañon, 28009 Madrid, Spain
| | - José Manuel Martin-Villa
- Department of Immunology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain; (I.J.); (C.V.-Y.); (T.L.); (J.M.M.-V.); (F.S.-T.)
- Instituto de Investigacion Sanitaria Gegorio Marañon, 28009 Madrid, Spain
| | - Fabio Suarez-Trujillo
- Department of Immunology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain; (I.J.); (C.V.-Y.); (T.L.); (J.M.M.-V.); (F.S.-T.)
- Instituto de Investigacion Sanitaria Gegorio Marañon, 28009 Madrid, Spain
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Ahangari H, Bahramian B, Khezerlou A, Tavassoli M, Kiani‐Salmi N, Tarhriz V, Ehsani A. Association between monosodium glutamate consumption with changes in gut microbiota and related metabolic dysbiosis-A systematic review. Food Sci Nutr 2024; 12:5285-5295. [PMID: 39139924 PMCID: PMC11317663 DOI: 10.1002/fsn3.4198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 08/15/2024] Open
Abstract
Monosodium glutamate (MSG) is used as a common food additive in some foods. However, based on our search and knowledge, no comprehensive study discussed the effect of MSG on the human gut microbiome. In this study, the effects of MSG on the gut microbiome, liver, and kidney were performed. Data were collected from databases including PubMed, Scopus, Web of Science, and ScienceDirect using the search strategy and keywords. Finally, 14 eligible studies were selected for systematic review. This study provides a new perspective on the effects of MSG on the gut flora, shedding light on the potential relationship between MSG intake and human health.
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Affiliation(s)
- Hossein Ahangari
- Student Research CommitteeTabriz University of Medical SciencesTabrizIran
- Department of Food Science and Technology, Faculty of Nutrition and Food SciencesTabriz University of Medical SciencesTabrizIran
| | - Behnam Bahramian
- Department of Food Science and Technology, Faculty of Nutrition and Food SciencesTabriz University of Medical SciencesTabrizIran
| | - Arezou Khezerlou
- Department of Food Science and Technology, Faculty of Nutrition and Food SciencesTabriz University of Medical SciencesTabrizIran
| | - Milad Tavassoli
- Department of Food Science and Technology, Faculty of Nutrition and Food SciencesTabriz University of Medical SciencesTabrizIran
| | - Narges Kiani‐Salmi
- Department of Food Science and Technology, Faculty of Nutrition and Food SciencesTabriz University of Medical SciencesTabrizIran
| | - Vahideh Tarhriz
- Cardiovascular Center of ExcellenceLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Ali Ehsani
- Department of Food Science and Technology, Faculty of Nutrition and Food SciencesTabriz University of Medical SciencesTabrizIran
- Nutrition Research CenterTabriz University of Medical SciencesTabrizIran
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5
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Lobos AE, Brandt AM, Gallard-Góngora JF, Korde R, Brodrick E, Harwood VJ. Persistence of sewage-associated genetic markers in advanced and conventional treated recycled water: implications for microbial source tracking in surface waters. mBio 2024; 15:e0065524. [PMID: 38864636 PMCID: PMC11253620 DOI: 10.1128/mbio.00655-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Sewage contamination of environmental waters is increasingly assessed by measuring DNA from sewage-associated microorganisms in microbial source tracking (MST) approaches. However, DNA can persist through wastewater treatment and reach surface waters when treated sewage/recycled water is discharged, which may falsely indicate pollution from untreated sewage. Recycled water discharged from an advanced wastewater treatment (AWT) facility into a Florida stream elevated the sewage-associated HF183 marker 1,000-fold, with a minimal increase in cultured Escherichia coli. The persistence of sewage-associated microorganisms was compared by qPCR in untreated sewage and recycled water from conventional wastewater treatment (CWT) and AWT facilities. E. coli (EC23S857) and sewage-associated markers HF183, H8, and viral crAssphage CPQ_056 were always detected in untreated sewage (6.5-8.7 log10 GC/100 mL). Multivariate analysis found a significantly greater reduction of microbial variables via AWT vs CWT. Bacterial markers decayed ~4-5 log10 through CWT, but CPQ_056 was ~100-fold more persistent. In AWT facilities, the log10 reduction of all variables was ~5. In recycled water, bacterial marker concentrations were significantly correlated (P ≤ 0.0136; tau ≥ 0.44); however, CPQ_056 was not correlated with any marker, suggesting varying drivers of decay. Concentrations of cultured E. coli carrying the H8 marker (EcH8) in untreated sewage were 5.24-6.02 log10 CFU/100 mL, while no E. coli was isolated from recycled water. HF183 and culturable EcH8 were also correlated in contaminated surface waters (odds ratio β1 = 1.701). Culturable EcH8 has a strong potential to differentiate positive MST marker signals arising from treated (e.g., recycled water) and untreated sewage discharged into environmental waters. IMPORTANCE Genes in sewage-associated microorganisms are widely accepted indicators of sewage pollution in environmental waters. However, DNA persists through wastewater treatment and can reach surface waters when recycled water is discharged, potentially causing false-positive indications of sewage contamination. Previous studies have found that bacterial and viral sewage-associated genes persist through wastewater treatment; however, these studies did not compare different facilities or identify a solution to distinguish sewage from recycled water. In this study, we demonstrated the persistence of bacterial marker genes and the greater persistence of a viral marker gene (CPQ_056 of crAssphage) through varying wastewater treatment facilities. We also aim to provide a tool to confirm sewage contamination in surface waters with recycled water inputs. This work showed that the level of wastewater treatment affects the removal of microorganisms, particularly viruses, and expands our ability to identify sewage in surface waters.
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Affiliation(s)
- Aldo E. Lobos
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Amanda M. Brandt
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Javier F. Gallard-Góngora
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, USA
| | - Ruchi Korde
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Eleanor Brodrick
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
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6
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Sun S, Liu C, Zhang Y, Yue Y, Sun S, Bai Y, Zhang P, Ravanbakhsh M, Dini-Andreote F, Li R, Zhang Z, Jousset A, Shen Q, A Kowalchuk G, Xiong W. Divergent impacts of fertilization regimes on below-ground prokaryotic and eukaryotic communities in the Tibetan Plateau. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 364:121379. [PMID: 38870787 DOI: 10.1016/j.jenvman.2024.121379] [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: 12/17/2023] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Chemical nutrient amendment by human activities can lead to environmental impacts contributing to global biodiversity loss. However, the comprehensive understanding of how below- and above-ground biodiversity shifts under fertilization regimes in natural ecosystems remains elusive. Here, we conducted a seven-year field experiment (2011-2017) and examined the effects of different fertilization on plant biodiversity and soil belowground (prokaryotic and eukaryotic) communities in the alpine meadow of the Tibetan Plateau, based on data collected in 2017. Our results indicate that nitrogen addition promoted total plant biomass but reduced the plant species richness. Conversely, phosphorus enrichment did not promote plant biomass and exhibited an unimodal pattern with plant richness. In the belowground realm, distinct responses of soil prokaryotic and eukaryotic communities were observed under fertilizer application. Specifically, soil prokaryotic diversity decreased with nitrogen enrichment, correlating with shifts in soil pH. Similarly, soil eukaryotic diversity decreased with increased phosphorous inputs, aligning with the equilibrium between soil available and total phosphorus. We also established connections between these soil organism communities with above-ground plant richness and biomass. Overall, our study contributes to a better understanding of the sustainable impacts of human-induced nutrient enrichment on the natural environment. Future research should delve deeper into the long-term effects of fertilization on soil health and ecosystem functioning, aiming to achieve a balance between agricultural productivity and environmental conservation.
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Affiliation(s)
- Shuo Sun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chen Liu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yun Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yang Yue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shiqi Sun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yang Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Pengfei Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China; Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA.
| | - Mohammadhossein Ravanbakhsh
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhenhua Zhang
- Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - Wu Xiong
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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7
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Li Z, Xiong W, Liang Z, Wang J, Zeng Z, Kołat D, Li X, Zhou D, Xu X, Zhao L. Critical role of the gut microbiota in immune responses and cancer immunotherapy. J Hematol Oncol 2024; 17:33. [PMID: 38745196 PMCID: PMC11094969 DOI: 10.1186/s13045-024-01541-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiota plays a critical role in the progression of human diseases, especially cancer. In recent decades, there has been accumulating evidence of the connections between the gut microbiota and cancer immunotherapy. Therefore, understanding the functional role of the gut microbiota in regulating immune responses to cancer immunotherapy is crucial for developing precision medicine. In this review, we extract insights from state-of-the-art research to decipher the complicated crosstalk among the gut microbiota, the systemic immune system, and immunotherapy in the context of cancer. Additionally, as the gut microbiota can account for immune-related adverse events, we discuss potential interventions to minimize these adverse effects and discuss the clinical application of five microbiota-targeted strategies that precisely increase the efficacy of cancer immunotherapy. Finally, as the gut microbiota holds promising potential as a target for precision cancer immunotherapeutics, we summarize current challenges and provide a general outlook on future directions in this field.
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Affiliation(s)
- Zehua Li
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, England
| | - Weixi Xiong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Institute of Brain Science and Brain-Inspired Technology of West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Liang
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, England
- Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, England
| | - Jinyu Wang
- Departments of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Ziyi Zeng
- Department of Neonatology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz, Poland
| | - Xi Li
- Department of Urology, Churchill Hospital, Oxford University Hospitals NHS Foundation, Oxford, UK
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Institute of Brain Science and Brain-Inspired Technology of West China Hospital, Sichuan University, Chengdu, China
| | - Xuewen Xu
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Linyong Zhao
- Department of General Surgery and Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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8
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Gaetano AS, Semeraro S, Greco S, Greco E, Cain A, Perrone MG, Pallavicini A, Licen S, Fornasaro S, Barbieri P. Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant. Microorganisms 2024; 12:965. [PMID: 38792794 PMCID: PMC11124041 DOI: 10.3390/microorganisms12050965] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.
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Affiliation(s)
- Anastasia Serena Gaetano
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Sabrina Semeraro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Enrico Greco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Andrea Cain
- ACEGAS APS AMGA S.p.a., Via degli Alti Forni, 11, 34121 Trieste, Italy;
| | | | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Sabina Licen
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Stefano Fornasaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Pierluigi Barbieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
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Liu J, Ding C, Teng C, Zhang W, Su X, Zhu W. Impacts of litter microbial community on litter decomposition in the absence of soil microorganisms. Appl Environ Microbiol 2024; 90:e0023924. [PMID: 38483156 PMCID: PMC11022580 DOI: 10.1128/aem.00239-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/04/2024] [Indexed: 04/18/2024] Open
Abstract
What is the effect of phyllosphere microorganisms on litter decomposition in the absence of colonization by soil microorganisms? Here, we simulated the litter standing decomposition stage in the field to study the differences in the composition and structure of the phyllosphere microbial community after the mixed decomposition of Populus × canadensis and Pinus sylvestris var. mongolica litter. After 15 months of mixed decomposition, we discovered that litters that were not in contact with soil had an antagonistic effect (the actual decomposition rate was 18.18%, which is lower than the expected decomposition rate) and the difference between the litters themselves resulted in a negative response to litter decomposition. In addition, there was no significant difference in bacterial and fungal community diversity after litter decomposition. The litter bacterial community was negatively responsive to litter properties and positively responsive to the fungal community. Importantly, we found that bacterial communities had a greater impact on litter decomposition than fungi. This study has enriched our understanding of the decomposition of litter itself and provided a theoretical basis for further exploring the "additive and non-additive effects" of litter decomposition and the mechanism of microbial drive. IMPORTANCE The study of litter decomposition mechanism plays an important role in the material circulation of the global ecosystem. However, previous studies have often looked at contact with soil as the starting point for decomposition. But actually, standing litter is very common in forest ecosystems. Therefore, we used field simulation experiments to simulate the decomposition of litters without contact with soil for 15 months, to explore the combined and non-added benefits of the decomposition of mixed litters, and to study the influence of microbial community composition on the decomposition rate while comparing the differences of microbial communities.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Chao Teng
- Liaoning Non-Ferrous Geological Exploration and Research Institute Co. Ltd., Shenyang, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
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Qu X, Pan Y, Wang P, Ran L, Qin G, Li Q, Kang P. Response of Phyllosphere and Rhizosphere Microbial Communities to Salt Stress of Tamarix chinensis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1091. [PMID: 38674498 PMCID: PMC11054833 DOI: 10.3390/plants13081091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria-fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.
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Affiliation(s)
- Xuan Qu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Peiqin Wang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Lele Ran
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Guifei Qin
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Qunfang Li
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
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Abdullaeva Y, Ratering S, Rosado-Porto D, Ambika Manirajan B, Glatt A, Schnell S, Cardinale M. Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens. Microbiol Res 2024; 281:127601. [PMID: 38218094 DOI: 10.1016/j.micres.2024.127601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - Andrea Glatt
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany.
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany; Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Lecce, Italy.
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12
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Liu J, Zhang W, Teng C, Pang Z, Peng Y, Qiu J, Lei J, Su X, Zhu W, Ding C. Intercropping changed the soil microbial community composition but no significant effect on alpha diversity. Front Microbiol 2024; 15:1370996. [PMID: 38572232 PMCID: PMC10988756 DOI: 10.3389/fmicb.2024.1370996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Enhancing the planning of the forest-agricultural composite model and increasing the efficiency with which forest land is utilized could benefit from a thorough understanding of the impacts of intercropping between forests and agriculture on soil physicochemical properties and microbial communities. Methods Populus cathayana × candansis cv. Xinlin No.1 and Glycine max intercrop soils, along with their corresponding monocrops, were used in this study's llumina high-throughput sequencing analysis to determine the composition and diversity of soil bacterial and fungal communities. Results The findings indicated that intercropping considerably raised the soil's total phosphorus content and significantly lowered the soil's carbon nitrogen ratio when compared to poplar single cropping. Furthermore, the total carbon and nitrogen content of soil was increased and the soil pH was decreased. The sequencing results showed that intercropping had no significant effect on soil alpha diversity. Intercropping could increase the composition of fungal community and decrease the composition of bacterial community in poplar soil. At the phylum level, intercropping significantly increased the relative abundance of four dominant phyla, i.e., Patescibacteria, Proteobacteria, Patescibacteria and Deinococcus-Thermus. And the relative abundances of only two dominant phyla were significantly increased. It was found that soil total phosphorus and available phosphorus content had the strongest correlation with soil bacterial community diversity, and soil pH had the strongest correlation with soil fungal community diversity. Discussion The results of this study were similar to those of previous studies. This study can serve as a theoretical foundation for the development of a poplar and black bean-based forest-agricultural complex management system in the future.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Chao Teng
- Liaoning Non-Ferrous Geological Exploration and Research Institute Co., Ltd., Shenyang, China
| | | | | | - Jian Qiu
- State-owned Xinbin Manchu Autonomous County Douling Forest Farm, Fushun, China
| | - Jiawei Lei
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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13
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Zhang B, Yu W, Liang J, Yao X, Sun H, Iwata H, Guo J. Seasonal variation in structural and functional distribution of periphyton in a macrolide antibiotics-contaminated river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123495. [PMID: 38342431 DOI: 10.1016/j.envpol.2024.123495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024]
Abstract
Periphyton, a microbial assemblage of autotrophic and heterotrophic organisms, is vital to aquatic ecosystems. While exposure to macrolide antibiotics has been confirmed to reduce the biodiversity and damage the critical ecological functions in indoor microcosm bioassays, the distribution of periphyton along a macrolide antibiotic pollution gradient in a river has yet to be determined. Herein, we established the spatiotemporal distribution of five major macrolides, i.e., azithromycin (AZI), roxithromycin (ROX), erythromycin (ERY), clarithromycin (CLA), and anhydro erythromycin (ERY-H2O) in water and periphyton of Zao River (Xi'an, China), after which we evaluated the effects on the structures, photosynthetic activity, and carbon utilization capacity of periphyton in March, June, and September 2023. In contrast with the reference sites, the macrolides were identified in all sewage treatment plants (STPs) impacted sites with concentrations ranging from 0.05 to 2.18 μg/L in water and from not detected - 9.67 μg/g in periphyton. Regarding community structure, the occurrence of macrolides was negatively linked to FirmicutesExiguobacterium undae and Exiguobacterium sibiricum, CyanobacteriaOscillatoriales and Vischeria sp., and ChlorophytaMonostroma grevillei, Selenastrum sp. LU21 and Desmodesmus subspicatus. At the functional level, only the metabolism of phenolic acids was significantly decreased in river reach with high antibiotic levels in June, compared to the other five carbon sources that were not altered. The overall photosynthetic activity of periphytic photosystem II remained unchanged in both reference and STPs impacted groups throughout three seasons. Overall, the macrolides released from STPs were correlated with the altered periphytic structures in the river, whereas a similar trend was not detected for the community functions owing to the functional redundancy. A mesocosm experiments warrants further consideration to validate the field results.
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Affiliation(s)
- Baihuan Zhang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Wenqian Yu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Jiayi Liang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Xiunan Yao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Hisato Iwata
- Center for Marine Environmental Studies, Ehime University, Bunkyo-cho 2-5, Matsuyama, Ehime prefecture, 790-8577, Japan
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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14
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Jiang R, Wang D, Jia S, Li Q, Liu S, Zhang XX. Dynamics of bacterioplankton communities in the estuary areas of the Taihu Lake: Distinct ecological mechanisms of abundant and rare communities. ENVIRONMENTAL RESEARCH 2024; 242:117782. [PMID: 38036201 DOI: 10.1016/j.envres.2023.117782] [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: 10/07/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
As the crucial confluences of rivers and lakes, the estuary areas with varied hydrodynamic exchanges intensively affect the bacterioplankton communities, whereas the ecological characteristics of the bacterioplankton in the areas have not been well understood. Here, the distribution patterns and assembly mechanisms of bacterioplankton communities in the estuary areas of the Taihu Lake were investigated using high-throughput sequencing and multivariate statistical analyses. Our results showed obvious seasonal variations in bacterioplankton diversity and community composition, which had significant correlations with water temperature. Neutral and null models together revealed that stochastic processes (especially dispersal limitation) were the major processes in shaping the communities across different seasons. By contrast, heterogeneous selection in deterministic processes exhibited increased impacts on community assembly during summer and autumn, which was significantly related to the comprehensive water quality index (WQI) rather than any single factor. In this study, rare communities displayed more pronounced seasonal dynamics compared to abundant communities, likely due to their sensitivity towards environmental factors. Accordingly, the heterogeneous selection of deterministic processes largely shaped the rare communities. These results enriched our understanding of the assembly mechanisms of bacterioplankton communities in estuary areas and emphasized the specific co-occurrence patterns of abundant and rare communities.
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Affiliation(s)
- Ruiming Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China.
| | - Shuyu Jia
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qisheng Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China; China Three Gorges Construction Engineering Corporation, Beijing, 100048, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China.
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Skaraki K, Pavloudi C, Dailianis T, Lagnel J, Pantazidou A, Magoulas A, Kotoulas G. Microbial diversity in four Mediterranean irciniid sponges. Biodivers Data J 2024; 12:e114809. [PMID: 38283142 PMCID: PMC10819633 DOI: 10.3897/bdj.12.e114809] [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: 10/27/2023] [Accepted: 01/14/2024] [Indexed: 01/30/2024] Open
Abstract
This paper describes a dataset of microbial communities from four different sponge species: Irciniaoros (Schmidt, 1864), Irciniavariabilis (Schmidt, 1862), Sarcotragusspinosulus Schmidt, 1862 and Sarcotragusfasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.
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Affiliation(s)
- Katerina Skaraki
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
- Department of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of Athens, Athens, GreeceDepartment of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of AthensAthensGreece
| | - Christina Pavloudi
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris, FranceEuropean Marine Biological Resource Centre (EMBRC-ERIC)ParisFrance
| | - Thanos Dailianis
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
| | - Jacques Lagnel
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Centre de Recherche PACA, Montfavet, FranceINRAE, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Centre de Recherche PACAMontfavetFrance
| | - Adriani Pantazidou
- Department of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of Athens, Athens, GreeceDepartment of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of AthensAthensGreece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
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16
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Pais A, Ristaino J, Whetten R, Xiang QY(J. Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in Cornus florida (Cornaceae). FRONTIERS IN PLANT SCIENCE 2024; 14:1282188. [PMID: 38273942 PMCID: PMC10809005 DOI: 10.3389/fpls.2023.1282188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Introduction Understanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted. The flowering dogwood tree (Cornus florida L.), an ecologically important species in North America, is threatened by powdery mildew and dogwood anthracnose diseases, and knowledge of the microbial diversity harbored within genetically and environmental distinct populations of this species remains largely unknown. Methods We conducted a metagenomics study utilizing the sequences of RAD-tag/genotype-by-sequence libraries from leaf tissues of C. florida to examine such host-fungus interactions across the dogwood's US range. We performed various combinations of alignments to both host and pathogen genomes to obtain filtered sets sequences for metagenomics analysis. Taxonomic assignments were determined on each filtered set of sequences, followed by estimation of microbial diversity and correlation to environment and host-genetic variation. Results Our data showed that microbial community composition significantly differed between visually healthy and diseased sites. Several microbial taxa known to interact with dogwood were identified from these sequences. We found no correlation between microbial diversity and relative abundances of sequences aligning to draft genomes of either pathogen causing powdery mildew or dogwood anthracnose. We found a significant relationship between differences of fungal communities and geographic distances of plant populations, suggesting roles of environments in shaping fungal communities in leaf tissues. Significant correlations between the genetic differentiation of plant samples and fungal community dissimilarity (beta diversity) were also observed in certain sets of our analyses-suggesting the possibility of a relationship between microbial community composition and plant genetic distance. This relationship persisted in significance even after controlling for significant effects of geographic-bioclimatic variation of microbial diversity. Discussion Our results suggest that both genetics and the environment play a significant role in shaping foliar fungal communities. Our findings underscore the power of leveraging hidden microbial sequences within datasets originally collected for plant genetic studies to understand plant-pathogen interactions.
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Affiliation(s)
- Andrew Pais
- Department of Plant and Microbial Biology, North Carolina State University (NCSU), Raleigh, NC, United States
| | - Jean Ristaino
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, United States
| | - Ross Whetten
- Department of Forestry and Environmental Resources, North Carolina State University (NCSU), Raleigh, NC, United States
| | - Qiu-Yun (Jenny) Xiang
- Department of Plant and Microbial Biology, North Carolina State University (NCSU), Raleigh, NC, United States
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Yuan J, Deng X, Xie X, Chen L, Wei C, Feng C, Qiu G. Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems. ISME COMMUNICATIONS 2024; 4:ycae011. [PMID: 38524765 PMCID: PMC10958769 DOI: 10.1093/ismeco/ycae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/26/2024]
Abstract
Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (<36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.
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Affiliation(s)
- Jing Yuan
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xiaojing Xie
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chunhua Feng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
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Alvarez-Zapata M, Franco-Vega A, Rondero AG, Guerra RS, Flores BIJ, Comas-García M, Ovalle CO, Schneider B, Ratering S, Schnell S, Martinez-Gutierrez F. Modulation of the Altered Intestinal Microbiota by Use of Antibiotics with a Novel Synbiotic on Wistar Rats. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10204-0. [PMID: 38127241 DOI: 10.1007/s12602-023-10204-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The use of antibiotics unbalances the intestinal microbiota. Probiotics, prebiotics, and synbiotics are alternatives for these unbalances. The effects of a new synbiotic composed of probiotic Saccharomyces boulardii CNCM I-745 and fructans from Agave salmiana (fAs) as prebiotics were assessed to modulate the intestinal microbiota. Two probiotic presentations, the commercial probiotic (CP) and the microencapsulated probiotic (MP) to improve those effects, were used to prepare the synbiotics and feed Wistar rats subjected to antibiotics (AB). Eight groups were studied, including five controls and three groups to modulate the microbiota after the use of antibiotics: G5: AB + MP-synbiotic, G6: AB + CP-synbiotic, and G8: AB + fAs. All treatments were administered daily for 7 days. On days 7 and 21, euthanasia was performed, cecum tissue was recovered and used to evaluate histological analysis and to study microphotograph by TEM, and finally, bacterial DNA was extracted and 16S rRNA gene metabarcode sequencing was performed. Histological analysis showed less epithelial damage and more abundance of the intestinal microbiota in the groups G5, G6, and G8 in comparison with the AB control group after 7 days. Microphotograph of the cecum at 2 weeks post treatment showed that G5 and G6 presented beneficial effects in epithelial reconstruction. Interestingly, in the groups that used the synbiotic without AB (G3 and G4) in addition to contributing to the recovery of the autochthonous microbiota, it promotes the development of beneficial microorganisms; those results were also achieved in the groups that used the synbiotic with AB enhancing the bacterial diversity and regulating the impact of AB.
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Affiliation(s)
- Miguel Alvarez-Zapata
- Laboratorio de Antimicrobianos, Biopelículas y Microbiota, Facultad de Ciencias Químicas, U.A.S.L.P., Av. Dr. Manuel Nava No. 6 Zona Universitaria, CP 78210, San Luis Potosí, S.L.P., México
| | - Avelina Franco-Vega
- Laboratorio de Tecnologías Emergentes, Facultad de Ciencias Químicas, U.A.S.L.P., San Luis Potosí, México
| | - Adriana Ganem Rondero
- Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica (L-322), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Mexico City, Estado de México, México
| | - Ruth Soria Guerra
- Laboratorio de Biotecnología de plantas, Facultad de Ciencias Químicas, U.A.S.L.P., San Luis Potosí, México
| | | | - Mauricio Comas-García
- Sección de Genómica Médica, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, México
- Sección de Microscopía de Alta Resolución, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, Mexico
- Facultad de Ciencias, U.A.S.L.P., San Luis Potosi, Mexico
| | | | - Belinda Schneider
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Fidel Martinez-Gutierrez
- Laboratorio de Antimicrobianos, Biopelículas y Microbiota, Facultad de Ciencias Químicas, U.A.S.L.P., Av. Dr. Manuel Nava No. 6 Zona Universitaria, CP 78210, San Luis Potosí, S.L.P., México.
- Sección de Genómica Médica, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, México.
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19
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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20
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Zhang Y, Mo C, Pan Y, Yang P, Ding X, Lei Q, Kang P. Responses of Soil Microbial Survival Strategies and Functional Changes to Wet-Dry Cycle Events. Microorganisms 2023; 11:2783. [PMID: 38004794 PMCID: PMC10672765 DOI: 10.3390/microorganisms11112783] [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: 10/17/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant-soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high-throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy-dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α-glucosidase, β-glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K-strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K-strategist bacteria. The co-occurrence network revealed the inter-relationship between r/K-strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α-glucosidase in the composition of soil microbial communities under wet-dry events and revealed significant correlations with r/K-strategist bacteria. Based on the functional predictions of microorganisms, wet-dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems.
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Affiliation(s)
- Yaqi Zhang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Chunyi Mo
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco–Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China;
| | - Pengbin Yang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Xiaodong Ding
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Qian Lei
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
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21
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Teso-Pérez C, Martínez-Bueno M, Peralta Sánchez JM, Valdivia E, Fárez-Vidal ME, Martín-Platero AM. Circular and L50-like leaderless enterocins share a common ABC-transporter immunity gene. BMC Genomics 2023; 24:639. [PMID: 37875795 PMCID: PMC10598978 DOI: 10.1186/s12864-023-09750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023] Open
Abstract
Microbes live within complex communities of interacting populations, either free-living in waters and soils or symbionts of animals and plants. Their interactions include the production of antimicrobial peptides (bacteriocins) to antagonize competitors, and these producers must carry their own immunity gene for self-protection. Whether other coexisting populations are sensitive or resistant to the bacteriocin producer will be key for the population dynamics within the microbial community. The immunity gene frequently consists of an ABC transporter to repel its own bacteriocin but rarely protects against a nonrelated bacteriocin. A case where this cross-resistance occurs mediated by a shared ABC transporter has been shown between enterocins MR10A/B and AS-48. The first is an L50-like leaderless enterocin, while AS-48 is a circular enterocin. In addition, L50-like enterocins such as MR10A/B have been found in E. faecalis and E. faecium, but AS-48 appears only in E. faecalis. Thus, using the ABC transporter of the enterocin MR10A/B gene cluster of Enterococcus faecalis MRR10-3 as a cross-resistance model, we aimed to unravel to what extent a particular ABC transporter can be shared across multiple bacteriocinogenic bacterial populations. To this end, we screened the MR10A/B-ABC transporters in available microbial genomes and analyzed their sequence homologies and distribution. Overall, our main findings are as follows: (i) the MR10A/B-ABC transporter is associated with multiple enterocin gene clusters; (ii) the different enterocins associated with this transporter have a saposin-like fold in common; (iii) the Mr10E component of the transporter is more conserved within its associated enterocin, while the Mr10FGH components are more conserved within the carrying species. This is the least known component of the transporter, but it has shown the greatest specificity to its corresponding enterocin. Bacteriocins are now being investigated as an alternative to antibiotics; hence, the wider or narrower distribution of the particular immunity gene should be taken into account for clinical applications to avoid the selection of resistant strains. Further research will be needed to investigate the mechanistic interactions between the Mr10E transporter component and the bacteriocin as well as the specific ecological and evolutionary mechanisms involved in the spread of the immunity transporter across multiple bacteriocins.
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Affiliation(s)
- Claudia Teso-Pérez
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
| | - Manuel Martínez-Bueno
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
| | - Juan Manuel Peralta Sánchez
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
- Department of Zoology, University of Seville, Avda. Reina Mercedes, 6, Seville, 41012, Spain
| | - Eva Valdivia
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
| | - María Esther Fárez-Vidal
- Department of Biochemistry and Molecular Biology III and Immunology, School of Medicine, University of Granada, Granada, 18016, Spain.
- Biomedical Research Institute of Granada, University Hospital Complex of Granada, University of Granada, Granada, 18071, Spain.
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22
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Wang X, Huang T, Li Y, Zhao G, Zhao J. Elevational characteristics of soil bacterial community and their responses to soil translocation at a mountainside in northwest Sichuan, China. Sci Rep 2023; 13:17906. [PMID: 37863997 PMCID: PMC10589279 DOI: 10.1038/s41598-023-44811-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023] Open
Abstract
How the soil bacterial communities vary with elevation is context-dependent, and the effect of soil translocation between elevations on bacterial community structure and metabolic function was not fully understood yet. Here, the bacterial community composition and diversity at five elevations along a 1600-3000 m elevation gradient on a mountainside in northwest Sichuan were characterized, and the responses of soil bacterial community to simulated climate changes were further studied by soil translocation reciprocally at three elevations for 12 months. Significant differences were found in soil temperature and moisture at different elevations, but there was no observed change in bacterial alpha diversity. The relative abundance of bacterial phyla was significantly different among the five elevations except for Proteobacteria (the dominant bacterial phyla in five elevation), and most bacterial phyla correlated with soil temperature, moisture, pH and soil bulk density. The direct effect of soil properties (pH, soil nutrients and soil bulk density) on soil bacterial community was stronger than the direct effect of temperature and moisture. Soil translocation changed the relative abundance of some bacterial phyla, and taxonomic groups with significant changes were mainly non-dominant phyla rather than the dominant phyla. Metabolism was the primary function of bacterial community at all elevations, which accounted for ~ 80% of relative abundance, and soil translocation had little effect on metabolic function. These findings indicated that soil bacterial dominant taxa and soil bacterial metabolic functions are relatively stable, which contribute to the stability of the ecosystem when response to the climate change in the future.
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Affiliation(s)
- Xuemei Wang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, Sichuan, China
- School of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Tianzhi Huang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, Sichuan, China
- School of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Yunyun Li
- School of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Guang Zhao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jixia Zhao
- College of Resources and Environment, Yunnan Agricultural University, No. 95, Heijin Road, Panlong District, Kunming, 650201, China.
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23
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Jiang Y, Zhu W, Zhu K, Ge Y, Li W, Liao N. Similarities and differences in the microbial structure of surface soils of different vegetation types. PeerJ 2023; 11:e16260. [PMID: 37872953 PMCID: PMC10590577 DOI: 10.7717/peerj.16260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
Background Soil microbial community diversity serves as a highly sensitive indicator for assessing the response of terrestrial ecosystems to various changes, and it holds significant ecological relevance in terms of indicating ecological alterations. At the global scale, vegetation type acts as a major driving force behind the diversity of soil microbial communities, encompassing both bacterial and fungal components. Modifications in vegetation type not only induce transformations in the visual appearance of land, but also influence the soil ecosystem's material cycle and energy flow, resulting in substantial impacts on the composition and performance of soil microbes. Methods In order to examine the disparities in the structure and diversity of soil microbial communities across distinct vegetation types, we opted to utilize sample plots representing four specific vegetation types. These included a woodland with the dominant tree species Drypetes perreticulata, a woodland with the dominant tree species Horsfieldia hainanensis, a Zea mays farmland and a Citrus reticulata fields. Through the application of high-throughput sequencing, the 16S V3_V4 region of soil bacteria and the ITS region of fungi were sequenced in this experiment. Subsequently, a comparative analysis was conducted to explore and assess the structure and dissimilarities of soil bacterial and fungal communities of the four vegetation types were analyzed comparatively. Results Our findings indicated that woodland soil exhibit a higher richness of microbial diversity compared to farmland soils. There were significant differences between woodland and farmland soil microbial community composition. However, all four dominant phyla of soil fungi were Ascomycota across the four vegetation types, but the bacterial dominant phyla were different in the two-farmland soil microbial communities with the highest similarity. Furthermore, we established a significant correlation between the nutrient content of different vegetation types and the relative abundance of soil microorganisms at both phyla and genus levels. This experiment serves as a crucial step towards unraveling the intricate relationships between plants, soil microbes, and soil, as well as understanding the underlying driving mechanism.
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Affiliation(s)
- Yong Jiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultual University, Shenyang, China
| | - Keye Zhu
- College of Forestry, Shenyang Agricultual University, Shenyang, China
| | - Yang Ge
- College of Forestry, Shenyang Agricultual University, Shenyang, China
| | - Wuzheng Li
- Guangxi Fangcheng Golden Camellias National Nature Reserve, Fangchenggang, China
| | - Nanyan Liao
- Guangxi Fangcheng Golden Camellias National Nature Reserve, Fangchenggang, China
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24
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Jiang X, Liu C, Cai J, Hu Y, Shao K, Tang X, Gong Y, Yao X, Xu Q, Gao G. Relationships between environmental factors and N-cycling microbes reveal the indirect effect of further eutrophication on denitrification and DNRA in shallow lakes. WATER RESEARCH 2023; 245:120572. [PMID: 37688860 DOI: 10.1016/j.watres.2023.120572] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023]
Abstract
Traditional views indicate that eutrophication and subsequent algal blooms favor denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in lake ecosystems. However, lakes tend to show an increasing propensity for inorganic nitrogen (N) limitation as they become more eutrophic. Thus, the influence of further eutrophication on denitrification and DNRA in eutrophic lakes are unclear due to the uncertainty of N availability. To fill this gap, we investigated the genes abundance (AOA, AOB, nirS, nirK and nrfA) and the composition of N-cycling microbes through quantitative PCR and 16S rRNA sequencing analysis, respectively, in 15 shallow eutrophic lakes of the Yangtze-Huaihe River basin, China. The results indicated that denitrification and DNRA rates could be modulated mainly by their functional gene abundances (nirS, nirK and nrfA), followed by the environmental factors (sediment total organic carbon and nitrogen). Denitrification rates significantly increased from slightly to highly eutrophic lakes, but DNRA rates were not. An explanation is that nitrification provided ample nitrate for denitrification, and this cooperative interaction was indicated by the positive correlation of their gene abundances. In addition, Pseudomonas and Anaeromyxobacter was the dominant genus mediated denitrification and DNRA, showing the potential to perform facultative anaerobic and strict anaerobic nitrate reduction, respectively. High level of dissolved oxygen might favor the facultatively aerobic denitrifiers over the obligately anaerobic fermentative DNRA bacteria in these shallow lakes. Chlorophyll a had a weak but positive effect on the gene abundances for nitrification (AOA and AOB). Further eutrophication had an indirect effect on denitrification and DNRA rates through modulating the genes abundances of N-cycling microbes.
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Affiliation(s)
- Xingyu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Cai
- Xiangyang Polytechnic, Xiangyang 441050, China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaolong Yao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiujin Xu
- Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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25
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Zhang Z, Tang G, Chai X, Liu B, Gao X, Zeng F, Wang Y, Zhang B. Different Responses of Soil Bacterial and Fungal Communities in Three Typical Vegetations following Nitrogen Deposition in an Arid Desert. Microorganisms 2023; 11:2471. [PMID: 37894130 PMCID: PMC10609353 DOI: 10.3390/microorganisms11102471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
The effects of increased nitrogen (N) deposition on desert ecosystems have been extensively studied from a plant community perspective. However, the response of soil microbial communities, which play a crucial role in nutrient cycling, to N inputs and plant community types remains poorly understood. In this study, we conducted a two-year N-addition experiment with five gradients (0, 10, 30, 60, and 120 kg N ha-1 year-1) to evaluate the effect of increased N deposition on soil bacterial and fungal communities in three plant community types, namely, Alhagi sparsifolia Shap., Karelinia caspia (Pall.) Less. monocultures and their mixed community in a desert steppe located on the southern edge of the Taklimakan Desert, Northwest China. Our results indicate that N deposition and plant community types exerted an independent and significant influence on the soil microbial community. Bacterial α-diversity and community dissimilarity showed a unimodal pattern with peaks at 30 and 60 kg N ha-1 year-1, respectively. By contrast, fungal α-diversity and community dissimilarity did not vary significantly with increased N inputs. Furthermore, plant community type significantly altered microbial community dissimilarity. The Mantel test and redundancy analysis indicated that soil pH and total and inorganic N (NH4+ and NO3-) levels were the most critical factors regulating soil microbial communities. Similar to the patterns observed in taxonomic composition, fungi exhibit stronger resistance to N addition compared to bacteria in terms of their functionality. Overall, our findings suggest that the response of soil microbial communities to N deposition is domain-specific and independent of desert plant community diversity, and the bacterial community has a critical threshold under N enrichment in arid deserts.
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Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Z.Z.)
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Gangliang Tang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Z.Z.)
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Z.Z.)
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Liu
- School of Resources and Environment, Linyi University, Linyi 276000, China
| | - Xiaopeng Gao
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Z.Z.)
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yun Wang
- Life Science and Technology School, Linnan Normal University, Zhanjiang 524048, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Z.Z.)
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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Nayman EI, Schwartz BA, Polanco FC, Firek AK, Gumabong AC, Hofstee NJ, Narasimhan G, Cickovski T, Mathee K. Microbiome depiction through user-adapted bioinformatic pipelines and parameters. J Med Microbiol 2023; 72. [PMID: 37823280 DOI: 10.1099/jmm.0.001756] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Introduction. The role of the microbiome in health and disease continues to be increasingly recognized. However, there is significant variability in the bioinformatic protocols for analysing genomic data. This, in part, has impeded the potential incorporation of microbiomics into the clinical setting and has challenged interstudy reproducibility. In microbial compositional analysis, there is a growing recognition for the need to move away from a one-size-fits-all approach to data processing.Gap Statement. Few evidence-based recommendations exist for setting parameters of programs that infer microbiota community profiles despite these parameters significantly impacting the accuracy of taxonomic inference.Aim. To compare three commonly used programs (DADA2, QIIME2, and mothur) and optimize them into four user-adapted pipelines for processing paired-end amplicon reads. We aim to increase the accuracy of compositional inference and help standardize microbiomic protocol.Methods. Two key parameters were isolated across four pipelines: filtering sequence reads based on a whole-number error threshold (maxEE) and truncating read ends based on a quality score threshold (QTrim). Closeness of sample inference was then evaluated using a mock community of known composition.Results. We observed that raw genomic data lost were proportionate to how stringently parameters were set. Exactly how much data were lost varied by pipeline. Accuracy of sample inference correlated with increased sequence read retention. Falsely detected taxa and unaccounted for microbial constituents were unique to pipeline and parameter. Implementation of optimized parameter values led to better approximation of the known mock community.Conclusions. Microbial compositions generated based on the 16S rRNA marker gene should be interpreted with caution. To improve microbial community profiling, bioinformatic protocols must be user-adapted. Analysis should be performed with consideration for the select target amplicon, pipelines and parameters used, and taxa of interest.
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Affiliation(s)
- Eric I Nayman
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Brooke A Schwartz
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Fantaysia C Polanco
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Alexandra K Firek
- Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Alayna C Gumabong
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Nolan J Hofstee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Trevor Cickovski
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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Dong M, Kuramae EE, Zhao M, Li R, Shen Q, Kowalchuk GA. Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels. ISME COMMUNICATIONS 2023; 3:104. [PMID: 37752280 PMCID: PMC10522649 DOI: 10.1038/s43705-023-00312-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023]
Abstract
Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1-2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats.
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Affiliation(s)
- Menghui Dong
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Eiko E Kuramae
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, The Netherlands
| | - Mengli Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Rong Li
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
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Liu L, Deng L, Wei W, Li C, Lu Y, Bai J, Li L, Zhang H, Jin N, Li C, Zhao C. Lactiplantibacillus plantarum LPJZ-658 Improves Non-Alcoholic Steatohepatitis by Modulating Bile Acid Metabolism and Gut Microbiota in Mice. Int J Mol Sci 2023; 24:13997. [PMID: 37762300 PMCID: PMC10531215 DOI: 10.3390/ijms241813997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is one of the most prevalent diseases worldwide; it is characterized by hepatic lipid accumulation, inflammation, and progressive fibrosis. Here, a Western diet combined with low-dose weekly carbon tetrachloride was fed to C57BL/6J mice for 12 weeks to build a NASH model to investigate the attenuating effects and possible mechanisms of Lactiplantibacillus plantarum LPJZ-658. Hepatic pathology, lipid profiles, and gene expression were assessed. The metabolomic profiling of the serum was performed. The composition structure of gut microbiota was profiled using 16s rRNA sequencing. The results show that LPJZ-658 treatment significantly attenuated liver injury, steatosis, fibrosis, and inflammation in NASH mice. Metabolic pathway analysis revealed that several pathways, such as purine metabolism, glycerophospholipid metabolism, linoleic acid metabolism, and primary bile acid biosynthesis, were associated with NASH. Notably, we found that treatment with LPJZ-658 regulated the levels of bile acids (BAs) in the serum. Moreover, LPJZ-658 restored NASH-induced gut microbiota dysbiosis. The correlation analysis deduced obvious interactions between BAs and gut microbiota. The current study indicates that LPJZ-658 supplementation protects against NASH progression, which is accompanied by alternating BA metabolic and modulating gut microbiota.
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Affiliation(s)
- Liming Liu
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132101, China; (L.L.); (C.L.); (Y.L.)
| | - Liquan Deng
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Wei Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;
| | - Chunhua Li
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132101, China; (L.L.); (C.L.); (Y.L.)
| | - Yuting Lu
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132101, China; (L.L.); (C.L.); (Y.L.)
| | - Jieying Bai
- College of Future Technology, Peking University, Beijing 100871, China;
| | - Letian Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (L.L.); (N.J.)
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Ningyi Jin
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (L.L.); (N.J.)
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (L.L.); (N.J.)
| | - Cuiqing Zhao
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132101, China; (L.L.); (C.L.); (Y.L.)
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Gorrasi S, Franzetti A, Brandt A, Minzlaff U, Pasqualetti M, Fenice M. Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench. ENVIRONMENTAL MICROBIOME 2023; 18:67. [PMID: 37533108 PMCID: PMC10398949 DOI: 10.1186/s40793-023-00522-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. RESULTS As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench. CONCLUSIONS This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.
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Affiliation(s)
- Susanna Gorrasi
- Laboratory of Microbiology, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Andrea Franzetti
- Laboratory of Microbiology, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, 60325, Frankfurt am Main, Germany
- Institute of Ecology, Diversity and Evolution, Goethe University, 60438, Frankfurt am Main, Germany
| | - Ulrike Minzlaff
- Institute of Ecology, Diversity and Evolution, Goethe University, 60438, Frankfurt am Main, Germany
| | - Marcella Pasqualetti
- Laboratory of Ecology of Marine Fungi - CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Massimiliano Fenice
- Laboratory of Microbiology, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
- Laboratory of Applied Marine Microbiology - CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
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Ge L, Song L, Wang L, Li Y, Sun Y, Wang C, Chen J, Wu G, Pan A, Wu Y, Quan Z, Li P. Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130904. [PMID: 36860032 DOI: 10.1016/j.jhazmat.2023.130904] [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: 10/30/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH+4-N), and nitrite (NO2--N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.
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Affiliation(s)
- Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Jun Chen
- East China University of Technology, Nanchang 330013, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yunfei Wu
- The College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Zhexue Quan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
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Wang B, Xiao L, Xu A, Mao W, Wu Z, Hicks LC, Jiang Y, Xu J. Silicon fertilization enhances the resistance of tobacco plants to combined Cd and Pb contamination: Physiological and microbial mechanisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114816. [PMID: 36963187 DOI: 10.1016/j.ecoenv.2023.114816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 06/18/2023]
Abstract
Remediation of soil contaminated with cadmium (Cd) and lead (Pb) is critical for tobacco production. Silicon (Si) fertilizer can relieve heavy metal stress and promote plant growth, however, it remains unknown whether fertilization with Si can mitigate the effects of Cd and Pb on tobacco growth and alter microbial community composition in polluted soils. Here we assessed the effect of two organic (OSiFA, OSiFB) and one mineral Si fertilizer (MSiF) on Cd and Pb accumulation in tobacco plants, together with responses in plant biomass, physiological parameters and soil bacterial communities in pot experiments. Results showed that Si fertilizer relieved Cd and Pb stress on tobacco, thereby promoting plant growth: Si fertilizer reduced available Cd and Pb in the soil by 37.3 % and 28.6 %, respectively, and decreased Cd and Pb contents in the plant tissue by 42.0-55.5 % and 17.2-25.6 %, resulting in increased plant biomass by 13.0-30.5 %. Fertilization with Si alleviated oxidative damage by decreasing malondialdehyde content and increasing peroxidase and ascorbate peroxidase content. In addition, Si fertilization increased photosynthesis, chlorophyll and carotenoid content. Microbial community structure was also affected by Si fertilization. Proteobacteria and Actinobacteria were the dominant phylum in the Cd and Pb contaminated soils, but Si fertilization reduced the abundance of Actinobacteria. Si fertilization also altered microbial metabolic pathways associated with heavy metal resistance. Together, our results suggest that both organic and mineral Si fertilizers can promote tobacco growth by relieving plant physiological stress and favoring a heavy metal tolerant soil microbial community.
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Affiliation(s)
- Bin Wang
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Liang Xiao
- School of Geographic Information and Tourism, Chuzhou University, Chuzhou 239000, China
| | - Anchuan Xu
- Technical Center of China Tobacco Yunnan Industrial Co., Ltd., Kunming 650031, China
| | - Wanchong Mao
- Sichuan Management & Monitoring Center Station of Radioactive Environment, Chengdu 611139, China
| | - Zhen Wu
- School of Geographic Information and Tourism, Chuzhou University, Chuzhou 239000, China
| | - Lettice C Hicks
- Section of Microbial Ecology, Department of Biology, Lund University, Ecology Building, Lund 223 62, Sweden
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
| | - Junju Xu
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China.
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Yan S, Ding N, Yao X, Song J, He W, Rehman F, Guo J. Effects of erythromycin and roxithromycin on river periphyton: Structure, functions and metabolic pathways. CHEMOSPHERE 2023; 316:137793. [PMID: 36640977 DOI: 10.1016/j.chemosphere.2023.137793] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Macrolides have been frequently detected in the surface waters worldwide, posing a threat to the aquatic microbes. Several studies have evaluated the ecotoxicological effects of macrolides on single algal and bacterial strains. However, without considering the species interaction in the aquatic microbial community, these results cannot be extrapolated to the field. Thus, the present study aimed to evaluate the effects of two macrolides (erythromycin and roxithromycin) on the structure, photosynthetic process, carbon utilization capacity, and the antibiotic metabolic pathways in river periphyton. The colonized periphyton was exposed to the graded concentration (0 μg/L (control), 0.5 μg/L (low), 5 μg/L (medium), 50 μg/L (high)) of ERY and ROX, respectively, for 7 days. Herein, high levels of ERY and ROX altered the community composition by reducing the relative abundance of Chlorophyta in the eukaryotic community. Also, the Shannon and Simpson diversity indexes of prokaryotes were reduced, although similar effects were seldomly detected in the low and medium groups. In contrast to the unchanged carbon utilization capacity, the PSII reaction center involved in the periphytic photosynthesis was significantly inhibited by macrolides at high levels. In addition, both antibiotics had been degraded by periphyton, with the removal rate of 51.63-66.87% and 41.85-48.27% for ERY and ROX, respectively, wherein the side chain and ring cleavage were the main degradation pathways. Overall, this study provides an insight into the structural and functional toxicity and degradation processes of macrolides in river periphyton.
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Affiliation(s)
- Shiwei Yan
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Ning Ding
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Xiunan Yao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Wei He
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Fozia Rehman
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Pakistan
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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Bonvegna S, Cilia R. Disease mechanisms as subtypes: Microbiome. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:107-131. [PMID: 36803806 DOI: 10.1016/b978-0-323-85555-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Abnormalities in gut microbiota have been suggested to be involved in the pathophysiology and progression of Parkinson's disease (PD). Gastrointestinal nonmotor symptoms often precede the onset of motor features in PD, suggesting a role for gut dysbiosis in neuroinflammation and α-synuclein (α-syn) aggregation. In the first part of this chapter, we analyze critical features of healthy gut microbiota and factors (environmental and genetic) that modify its composition. In the second part, we focus on the mechanisms underlying the gut dysbiosis and how it alters anatomically and functionally the mucosal barrier, triggering neuroinflammation and subsequently α-syn aggregation. In the third part, we describe the most common alterations in the gut microbiota of PD patients, dividing the gastrointestinal system in higher and lower tract to examine the association between microbiota abnormalities and clinical features. In the final section, we report on current and future therapeutic approaches to gut dysbiosis aiming to either reduce the risk for PD, modify the disease course, or improve the pharmacokinetic profile of dopaminergic therapies. We also suggest that further studies will be needed to clarify the role of the microbiome in PD subtyping and of pharmacological and nonpharmacological interventions in modifying specific microbiota profiles in individualizing disease-modifying treatments in PD.
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Affiliation(s)
- Salvatore Bonvegna
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy.
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Bovio-Winkler P, Guerrero LD, Erijman L, Oyarzúa P, Suárez-Ojeda ME, Cabezas A, Etchebehere C. Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors. BMC Microbiol 2023; 23:45. [PMID: 36809975 PMCID: PMC9942424 DOI: 10.1186/s12866-023-02765-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/10/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor. RESULTS Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization. CONCLUSION Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.
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Affiliation(s)
- Patricia Bovio-Winkler
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Avenida Italia 3318, CP: 11600, Montevideo, Uruguay
| | - Leandro D Guerrero
- Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Buenos Aires, Argentina
| | - Pía Oyarzúa
- GENOCOV Research Group, Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Eugenia Suárez-Ojeda
- GENOCOV Research Group, Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Francisco Antonio Maciel S/N, CP: 97000, Durazno, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Avenida Italia 3318, CP: 11600, Montevideo, Uruguay.
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Rosado-Porto D, Ratering S, Wohlfahrt Y, Schneider B, Glatt A, Schnell S. Elevated atmospheric CO 2 concentrations caused a shift of the metabolically active microbiome in vineyard soil. BMC Microbiol 2023; 23:46. [PMID: 36809988 PMCID: PMC9942357 DOI: 10.1186/s12866-023-02781-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2). RESULTS Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions. CONCLUSIONS The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, 080002, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Yvette Wohlfahrt
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366, Geisenheim, Germany
| | - Bellinda Schneider
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Andrea Glatt
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany.
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Zhao F, Wang B, Huang K, Yin J, Ren X, Wang Z, Zhang XX. Correlations among Antibiotic Resistance Genes, Mobile Genetic Elements and Microbial Communities in Municipal Sewage Treatment Plants Revealed by High-Throughput Sequencing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3593. [PMID: 36834289 PMCID: PMC9965123 DOI: 10.3390/ijerph20043593] [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: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Municipal sewage treatment plants (MSTPs) are environmental pools for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which is cause for growing environmental-health concerns. In this study, the effects of different wastewater treatment processes on microbial antibiotic resistance in four MSTPs were investigated. PCR, q-PCR, and molecular cloning integrally indicated that the tetracycline resistance (tet) genes significantly reduced after activated-sludge treatment. Illumina high-throughput sequencing revealed that the broad-spectrum profile of ARGs and mobile element genes (MGEs) were also greatly decreased by one order of magnitude via activated sludge treatment and were closely associated with each other. Correlations between ARGs and bacterial communities showed that potential ARB, such as Acinetobacter, Bacteroides, and Cloaibacterium, were removed by the activated-sludge process. Sedimentation processes cannot significantly affect the bacterial structure, resulting in the relative abundance of ARGs, MGEs, and ARB in second-clarifier effluent water being similar to activated sludge. A comprehensive study of ARGs associated with MGEs and bacterial structure might be technologically guided for activated sludge design and operation in the MSTPs, to purposefully control ARGs carried by pathogenic hosts and mobility.
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Affiliation(s)
- Fuzheng Zhao
- Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou Jiaotong University, Lanzhou 730070, China
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Bo Wang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jinbao Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xuechang Ren
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Zhu Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Zhang W, Mo Q, Huang Z, Sabar MA, Medunić G, Ivošević T, He H, Urynowicz M, Liu FJ, Guo H, Haider R, Ali MI, Jamal A. Contaminants from a former Croatian coal sludge dictate the structure of microbiota in the estuarine (Raša Bay) sediment and soil. Front Microbiol 2023; 14:1126612. [PMID: 36846805 PMCID: PMC9947854 DOI: 10.3389/fmicb.2023.1126612] [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: 12/18/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Croatian superhigh-organic-sulfur Raša coal had been mined for nearly 400 years. The release of hazardous trace elements (HTEs) and toxic organic pollutants (TOPs) into the local environment by coal mining, preparation, and combustion activities has resulted in pollution. Methods In this study, the diversity and composition of microbial communities in estuarine sediment and soil samples as well as community function responses to the pollutants were investigated. Results The results showed that PAH degradation does occur following 60 years of natural attenuation, the location is still heavily polluted by polycyclic aromatic hydrocarbons (PAHs) and HTEs. Microbial analyses have shown that high concentrations of PAHs have reduced the diversity and abundance of microbial communities. The pollution exerted an adverse, long-term impact on the microbial community structure and function in the brackish aquatic ecosystem. Microorganisms associated with the degradation of PAHs and sulfur-containing compounds have been enriched although the diversity and abundance of the microbial community have reduced. Fungi which are believed to be the main PAH degrader may play an important role initially, but the activity remains lower thereafter. It is the high concentrations of coal-derived PAHs, rather than HTEs, that have reduced the diversity and abundance of microbial communities and shaped the structure of the local microbiota. Discussion This study could provide a basis for the monitoring and restoration of ecosystems impacted by coal mining activities considering the expected decommission of a large number of coal plants on a global scale in the coming years due to growing global climate change concerns.
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Affiliation(s)
- Weiting Zhang
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
| | - Qianyun Mo
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
| | - Zaixing Huang
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
- Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY, United States
| | - Muhammad Adnan Sabar
- Environmental Risk Control Engineering Laboratory, Division of Environmental Design, Kanazawa University, Kanazawa, Japan
| | - Gordana Medunić
- Department of Geology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Tatjana Ivošević
- Faculty of Maritime Studies, University of Rijeka, Rijeka, Croatia
| | - Huan He
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
| | - Michael Urynowicz
- Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY, United States
| | - Fang-Jing Liu
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
| | - Hongguang Guo
- College of Safety and Emergency Management and Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Rizwan Haider
- Institute of Energy & Environmental Engineering, University of the Punjab, Lahore, Pakistan
| | | | - Asif Jamal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Wang WF, Cheng CX, Liu H, Chen XL, Wang HL. 6His-tatritin promotes antimicrobial defense via regulating immune ability and intestinal microbial community in grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2023; 133:108532. [PMID: 36639064 DOI: 10.1016/j.fsi.2023.108532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Antimicrobial peptides are small, cationic, and amphiphilic peptides found in most organisms, and many of these peptides have broad antimicrobial activity against Gram-negative, -positive bacteria and fungi. In the present study, a derivative of antimicrobial peptide Tatritin, 6His-Tatritin, was designed and expressed by Pichia pastoris using a constitutive vector pGAPZαA with the promoter of pGAP. The 6His-Tatritin had a broad-spectrum antibacterial activity based on the Oxford cup method and the micro broth dilution test. In addition, to explore the role of 6His-Tatritin in vivo, grass carps (Ctenopharyngodon idellus) were infected with Aeromonas hydrophila after they were fed with 6His-Tatritin as feed additives for 28 days. The results revealed that 6His-Tatritin could significantly up-regulate the expression levels of Hepcidin, Leap-2b, Nrf-2, CuZn-SOD and LZM (P < 0.05). In addition, 6His-Tatritin could significantly reduce the mortality (P < 0.05) and the intestinal injury of grass carps infected with bacteria. The 16S sequencing analysis showed that the structure of microbial community in intestine of fish was more diversified compared with control after treatment with 6His-Tatritin. In summary, the peptide of 6His-Tatritin could promote antimicrobial defense via regulating immune ability and intestinal microbial community in grass carp. This study provides an effective method and approach for the application of antimicrobial peptide Tatritin in aquaculture, and also provides insights into the function of antimicrobial peptides in immunity against pathogens in fish.
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Affiliation(s)
- Wei-Feng Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chu-Xing Cheng
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiu-Li Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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Huo Q, Li R, Chen C, Wang C, Long T, Liu X. Study on potential microbial community to the waste water treatment from bauxite desilication process. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:15438-15453. [PMID: 36169826 DOI: 10.1007/s11356-022-23150-1] [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: 01/19/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.
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Affiliation(s)
- Qiang Huo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Ruoyang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Chunqiang Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Chenquan Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Tengfa Long
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Xi Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China.
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China.
- School of Economics and Management, Guangxi Normal University, Guilin, 541006, China.
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Yu Z, Henderson IR, Guo J. Non-caloric artificial sweeteners modulate conjugative transfer of multi-drug resistance plasmid in the gut microbiota. Gut Microbes 2023; 15:2157698. [PMID: 36524841 PMCID: PMC9762752 DOI: 10.1080/19490976.2022.2157698] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Non-caloric artificial sweeteners have been widely permitted as table sugar substitutes with high intensities of sweetness. They can pass through the intestinal tract without significant metabolization and frequently encounter the gut microbiome, which is composed of diverse bacterial species and is a pool of antibiotic resistance genes (ARGs). However, little is known about whether these sweeteners could accelerate the spread of ARGs in the gut microbiome. Here, we established an in vitro conjugation model by using Escherichia coli that carries chromosome-inserted Tn7 lacIq-pLpp-mCherry and plasmid-encoded gfpmut3b gene as the donor and murine fecal bacteria as the recipient. We found that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) can increase reactive oxygen species (ROS) production and promote plasmid-mediated conjugative transfer to the gut microbiome. Cell sorting and 16S rRNA gene amplicon sequencing analysis of fecal samples reveal that the tested sweeteners can promote the broad-host-range plasmid permissiveness to both Gram-negative and Gram-positive gut bacteria. The increased plasmid permissiveness was also validated with a human pathogen Klebsiella pneumoniae. Collectively, our study demonstrates that non-caloric artificial sweeteners can induce oxidative stress and boost the plasmid-mediated conjugative transfer of ARGs among the gut microbiota and a human pathogen. Considering the soaring consumption of these sweeteners and the abundance of mobile ARGs in the human gut, our results highlight the necessity of performing a thorough risk assessment of antibiotic resistance associated with the usage of artificial sweeteners as food additives.
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Affiliation(s)
- Zhigang Yu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
| | - Ian R Henderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
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Li C, Li Y, Tang L, Ikenaga M, Liu R, Xu G. Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective. Ecol Evol 2023; 13:e9727. [PMID: 36620424 PMCID: PMC9810793 DOI: 10.1002/ece3.9727] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in the habitat heterogeneity in the two Haloxylon species from a nutrient perspective. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0-20, 20-40, and 40-60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g., eukarya, bacteria, and nitrogen-fixing microbes). The rhizosphere effect of H. ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H. persicum. However, the fertile island effect of H. ammodendron was weaker than that of H. persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil available nitrogen, especially nitrate nitrogen, was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H. ammodendron recruited more copiotrophs (e.g., Firmicutes, Bacteroidetes, and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. Haloxylon persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea), and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.
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Affiliation(s)
- Chenhua Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina
- Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina
- Univerisity of Chinese Academy of SciencesBeijingChina
| | - Yan Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina
- Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina
- Univerisity of Chinese Academy of SciencesBeijingChina
| | - Lisong Tang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina
- Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina
- Univerisity of Chinese Academy of SciencesBeijingChina
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine AreaKagoshima UniversityKagoshimaJapan
| | - Ran Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina
- Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina
- Univerisity of Chinese Academy of SciencesBeijingChina
| | - Guiqing Xu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina
- Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina
- Univerisity of Chinese Academy of SciencesBeijingChina
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Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations. mBio 2022; 13:e0241422. [PMID: 36214570 PMCID: PMC9765137 DOI: 10.1128/mbio.02414-22] [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] [Indexed: 11/20/2022] Open
Abstract
Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.
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Karampatsas K, Faal A, Jaiteh M, Garcia-Perez I, Aller S, Shaw AG, Kopytek A, Witney AA, Le Doare K. Gastrointestinal, vaginal, nasopharyngeal, and breast milk microbiota profiles and breast milk metabolomic changes in Gambian infants over the first two months of lactation: A prospective cohort study. Medicine (Baltimore) 2022; 101:e31419. [PMID: 36401392 PMCID: PMC9678627 DOI: 10.1097/md.0000000000031419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microbiota composition in breast milk affects intestinal and respiratory microbiota colonization and the mucosal immune system's development in infants. The metabolomic content of breast milk is thought to interact with the microbiota and may influence developing infant immunity. One hundred seven Gambian mothers and their healthy, vaginally delivered, exclusively breastfed infants were included in our study. We analyzed 32 breast milk samples, 51 maternal rectovaginal swabs and 30 infants' rectal swabs at birth. We also analyzed 9 breast milk samples and 18 infants' nasopharyngeal swabs 60 days post-delivery. We used 16S rRNA gene sequencing to determine the microbiota composition. Metabolomic profiling analysis was performed on colostrum and mature breast milk samples using a multiplatform approach combining 1-H Nuclear Magnetic Resonance Spectroscopy and Gas Chromatography-Mass Spectrometry. Bacterial communities were distinct in composition and diversity across different sample types. Breast milk composition changed over the first 60 days of lactation. α-1,4- and α-1,3-fucosylated human milk oligosaccharides, and other 33 key metabolites in breast milk (monosaccharides, sugar alcohols and fatty acids) increased between birth and day 60 of life. This study's results indicate that infant gut and respiratory microbiota are unique bacterial communities, distinct from maternal gut and breast milk, respectively. Breast milk microbiota composition and metabolomic profile change throughout lactation. These changes may contribute to the infant's immunological, metabolic, and neurological development and could consist the basis for future interventions to correct disrupted early life microbial colonization.
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Affiliation(s)
- Konstantinos Karampatsas
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
- * Correspondence: Konstantinos Karampatsas, Institute for Infection and Immunity, St George’s, University of London, Jenner Wing, Level 2, SW17 0RE London, UK (e-mail: )
| | - Amadou Faal
- Medical Research Council The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Mustapha Jaiteh
- Medical Research Council The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Isabel Garcia-Perez
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Sean Aller
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
| | - Alexander G. Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Aleksandra Kopytek
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Adam A. Witney
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
| | - Kirsty Le Doare
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
- Medical Research Council The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Medical Research Council Uganda, Virus Research Institute, Uganda
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Gorrasi S, Pasqualetti M, Muñoz-Palazon B, Novello G, Mazzucato A, Campiglia E, Fenice M. Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich "Sun Black" and Wild-Type Tomatoes under Organic and Conventional Farming. Microorganisms 2022; 10:2240. [PMID: 36422310 PMCID: PMC9694333 DOI: 10.3390/microorganisms10112240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 07/30/2023] Open
Abstract
Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79-91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3-47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.
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Affiliation(s)
- Susanna Gorrasi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Marcella Pasqualetti
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Laboratory of Ecology of Marine Fungi, CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Barbara Muñoz-Palazon
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Institute of Water Research, University of Granada, 18071 Granada, Spain
| | - Giorgia Novello
- Department of Science, Technology and Innovation (DISIT), Università del Piemonte Orientale, Viale Teresa Michel, 11, 15121 Alessandria, Italy
| | - Andrea Mazzucato
- Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Enio Campiglia
- Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Massimiliano Fenice
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Laboratory of Applied Marine Microbiology, CoNISMa, University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
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Liu J, Ding C, Zhang W, Wei Y, Zhou Y, Zhu W. Litter mixing promoted decomposition rate through increasing diversities of phyllosphere microbial communities. Front Microbiol 2022; 13:1009091. [PMID: 36425041 PMCID: PMC9678933 DOI: 10.3389/fmicb.2022.1009091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Decomposition of forest litter is an essential process for returning nutrients to the soil, which is crucial for preserving soil fertility and fostering the regular biological cycle and nutrient balance of the forest ecosystem. About 70% of the land-based forest litter is made up primarily of leaf litter. However, research on the complex effects and key determinants of leaf litter decomposition is still lacking. In this study, we examined the characteristics of nutrient release and microbial diversity structure during the decomposition of three types of litter in arid and semi-arid regions using 16S rRNA and ITS sequencing technology as well as nutrient content determination. It was revealed that the nutrient content and rate of decomposition of mixed litters were significantly different from those of single species. Following litter mixing, the richness and diversity of the microbial community on leaves significantly increased. It was determined that there was a significant correlation between bacterial diversity and content (Total N, Total P, N/P, and C/P). This study provided a theoretical framework for investigating the decomposition mechanism of mixed litters by revealing the microbial mechanism of mixed decomposition of litters from the microbial community and nutrient levels.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Changjun Ding,
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yawei Wei
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Tsai KY, Wu DC, Wu WJ, Wang JW, Juan YS, Li CC, Liu CJ, Lee HY. Exploring the Association between Gut and Urine Microbiota and Prostatic Disease including Benign Prostatic Hyperplasia and Prostate Cancer Using 16S rRNA Sequencing. Biomedicines 2022; 10:2676. [PMID: 36359196 PMCID: PMC9687995 DOI: 10.3390/biomedicines10112676] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 07/22/2023] Open
Abstract
Numerous microorganisms residing in the gastrointestinal and genitourinary tracts affect host health. We investigated stool and voided urine samples collected from patients with benign prostatic hyperplasia (BPH) or prostate cancer (PC) and a control group to explore the potential relationship between human microbiota and prostatic disease, and aimed to identify correlations and pathogenic taxonomic units. We studied microbial composition using 16S rRNA sequencing to identify operational taxonomic units (OTUs). Extracted genome was amplified and filtered sequences were used to classify OTUs based on their specific taxonomy. No statistically significant differences were observed in stool samples among the groups. However, urine samples indicated different microbiota compositions in different patient populations. The top five microbial genera that showed significant differences between the BPH and control groups were Alcaligenes, Pseudomonas, Lactobacillus, Akkermansia, and Cetobacterium. Faecalibacterium, Staphylococcus, Ruminococcaceae_UCG_002, Neisseria, and Agathobacter were the genera with the largest proportion differences when comparing the PC and control groups. We discovered that the urine microbiota composition of the BPH and PC groups was distinct from that of the control group. Due to the impact of microbiota on prostatic disease, it is necessary to identify specific microbes for further research.
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Affiliation(s)
- Kai-Yen Tsai
- Department of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Wen-Jeng Wu
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Jiunn-Wei Wang
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yung-Shun Juan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ching-Chia Li
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chung-Jung Liu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Hsiang-Ying Lee
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Urology Department, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan
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Zhou X, Wang B, Demkowicz PC, Johnson JS, Chen Y, Spakowicz DJ, Zhou Y, Dorsett Y, Chen L, Sodergren E, Kuchel GA, Weinstock GM. Exploratory studies of oral and fecal microbiome in healthy human aging. FRONTIERS IN AGING 2022; 3:1002405. [PMID: 36338834 PMCID: PMC9631447 DOI: 10.3389/fragi.2022.1002405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
Growing evidence has linked an altered host fecal microbiome composition with health status, common chronic diseases, and institutionalization in vulnerable older adults. However, fewer studies have described microbiome changes in healthy older adults without major confounding diseases or conditions, and the impact of aging on the microbiome across different body sites remains unknown. Using 16S ribosomal RNA gene sequencing, we reconstructed the composition of oral and fecal microbiomes in young (23-32; mean = 25 years old) and older (69-94; mean = 77 years old) healthy community-dwelling research subjects. In both body sites, we identified changes in minor bacterial operational taxonomic units (OTUs) between young and older subjects. However, the composition of the predominant bacterial species of the healthy older group in both microbiomes was not significantly different from that of the young cohort, which suggests that dominant bacterial species are relatively stable with healthy aging. In addition, the relative abundance of potentially pathogenic genera, such as Rothia and Mycoplasma, was enriched in the oral microbiome of the healthy older group relative to the young cohort. We also identified several OTUs with a prevalence above 40% and some were more common in young and others in healthy older adults. Differences with aging varied for oral and fecal samples, which suggests that members of the microbiome may be differentially affected by aging in a tissue-specific fashion. This is the first study to investigate both oral and fecal microbiomes in the context of human aging, and provides new insights into interactions between aging and the microbiome within two different clinically relevant sites.
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Affiliation(s)
- Xin Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Baohong Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, Hangzhou City, China
| | - Patrick C. Demkowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Yale University School of Medicine, New Haven, CT, United States
| | - Jethro S. Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Yanfei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, Hangzhou City, China
| | - Daniel J. Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - George A. Kuchel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, United States
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Bamola VD, Dubey D, Samanta P, Kedia S, Ahuja V, Madempudi RS, Neelamraju J, Chaudhry R. Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease. Anaerobe 2022; 78:102652. [PMID: 36198385 DOI: 10.1016/j.anaerobe.2022.102652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients. METHOD Patients were randomly allocated to either placebo or probiotic Bacillus clausii UBBC-07 for four weeks along with the standard medical treatment (SMT). Enrolled patients were evaluated before and after intervention for presence of the given probiotic, change in gut microbiota, change in serum cytokines, serotonin and dopamine, symptoms of disease, physical, behavioral and psychological parameters. RESULTS Probiotic strain Bacillus clausii UBBC-07 showed good survival in IBD patients in the treatment group (p < 0.01) without any reported adverse event. Metagenomic analysis showed that the given probiotic strain was able to modulate the gut microbiota in treated group. Phylum Firmicutes was increased and phylum Bacteroidetes was decreased in the probiotic treated group. A significant increase was observed in the abundance of anaerobic bacterial genera Lactobacillus, Bifidobacterium and Faecalibacterium in the probiotic treated group (p < 0.01) as compared to placebo group. Significant increase was observed in IL-10 (p < 0.05) and variable decrease in the secretion of IL-1β, TNF- α, IL-6, IL -17 and IL -23 in probiotic treated group. In the treatment group a significant decrease in the symptoms of IBD and improvement in the psychological parameter to various degrees was noted. CONCLUSION These results indicated that probiotic strain B clausii UBBC-07 affected the gut microbiota and cytokine secretion and shown efficacy in IBD patients.
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Affiliation(s)
- V Deepak Bamola
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Divya Dubey
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Projoyita Samanta
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ratna Sudha Madempudi
- Centre for Research & Development, Unique Biotech Ltd., Plot No. 2, Phase-II, Alexandria Knowledge Park, Hyderabad, Telangana, 500078, India
| | - Jayanthi Neelamraju
- Centre for Research & Development, Unique Biotech Ltd., Plot No. 2, Phase-II, Alexandria Knowledge Park, Hyderabad, Telangana, 500078, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Wojciechowski S, Majchrzak-Górecka M, Biernat P, Odrzywołek K, Pruss Ł, Zych K, Jan Majta, Milanowska-Zabel K. Machine learning on the road to unlocking microbiota's potential for boosting immune checkpoint therapy. Int J Med Microbiol 2022; 312:151560. [PMID: 36113358 DOI: 10.1016/j.ijmm.2022.151560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022] Open
Abstract
The intestinal microbiota is a complex and diverse ecological community that fulfills multiple functions and substantially impacts human health. Despite its plasticity, unfavorable conditions can cause perturbations leading to so-called dysbiosis, which have been connected to multiple diseases. Unfortunately, understanding the mechanisms underlying the crosstalk between those microorganisms and their host is proving to be difficult. Traditionally used bioinformatic tools have difficulties to fully exploit big data generated for this purpose by modern high throughput screens. Machine Learning (ML) may be a potential means of solving such problems, but it requires diligent application to allow for drawing valid conclusions. This is especially crucial as gaining insight into the mechanistic basis of microbial impact on human health is highly anticipated in numerous fields of study. This includes oncology, where growing amounts of studies implicate the gut ecosystems in both cancerogenesis and antineoplastic treatment outcomes. Based on these reports and first signs of clinical benefits related to microbiota modulation in human trials, hopes are rising for the development of microbiome-derived diagnostics and therapeutics. In this mini-review, we're inspecting analytical approaches used to uncover the role of gut microbiome in immune checkpoint therapy (ICT) with the use of shotgun metagenomic sequencing (SMS) data.
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Affiliation(s)
| | | | | | - Krzysztof Odrzywołek
- Ardigen, Podole 76, 30-394 Kraków, Poland; Institute of Computer Science, Faculty of Computer Science, Electronics and Telecommunications, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków, Poland
| | - Łukasz Pruss
- Ardigen, Podole 76, 30-394 Kraków, Poland; Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-373 Wroclaw, Poland
| | | | - Jan Majta
- Ardigen, Podole 76, 30-394 Kraków, Poland; Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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