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Dong X, Jiang F, Duan D, Tian Z, Liu H, Zhang Y, Hou F, Nan Z, Chen T. Contrasting Effects of Grazing in Shaping the Seasonal Trajectory of Foliar Fungal Endophyte Communities on Two Semiarid Grassland Species. J Fungi (Basel) 2023; 9:1016. [PMID: 37888272 PMCID: PMC10608051 DOI: 10.3390/jof9101016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing's impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant-fungal interactions.
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Affiliation(s)
- Xin Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Feifei Jiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Dongdong Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China
| | - Zhen Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Huining Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Yinan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Tao Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
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102
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Li Y, Hou Y, Hou Q, Long M, Wang Z, Rillig MC, Liao Y, Yong T. Soil microbial community parameters affected by microplastics and other plastic residues. Front Microbiol 2023; 14:1258606. [PMID: 37901816 PMCID: PMC10601715 DOI: 10.3389/fmicb.2023.1258606] [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: 07/14/2023] [Accepted: 08/31/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors. Methods We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities. Results and discussion This study indicated that plastics accelerated soil organic carbon loss (effect size = -0.05, p = 0.004) and increased microbial functionality (effect size = 0.04, p = 0.003), but also reduced microbial biomass (effect size = -0.07, p < 0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size = -0.07, p < 0.001) while polypropylene significantly increased it (effect size = 0.17, p < 0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40 g/kg. Approximately 3564.78 μm was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R2 = 0.04-0.73, p < 0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution.
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Affiliation(s)
- Yüze Li
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Northwest A&F University, Xianyang, China
| | - Yuting Hou
- College of Agronomy, Northwest A&F University, Xianyang, China
| | - Quanming Hou
- College of Agronomy, Northwest A&F University, Xianyang, China
| | - Mei Long
- College of Agronomy, Northwest A&F University, Xianyang, China
| | - Ziting Wang
- College of Agronomy, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China
| | - Matthias C. Rillig
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Xianyang, China
| | - Taiwen Yong
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy, Sichuan Agricultural University, Chengdu, China
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103
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Yuan H, Zhang R, Li Q, Han Q, Lu Q, Wu J. Unveiling the ecological significance of phosphorus fractions in shaping bacterial and archaeal beta diversity in mesotrophic lakes. Front Microbiol 2023; 14:1279751. [PMID: 37886062 PMCID: PMC10598868 DOI: 10.3389/fmicb.2023.1279751] [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: 08/25/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
Both community variation and phosphorus (P) fractions have been extensively studied in aquatic ecosystems, but how P fractions affect the mechanism underlying microbial beta diversity remains elusive, especially in sediment cores. Here, we obtained two sediment cores to examine bacterial and archaeal beta diversity from mesotrophic lakes Hongfeng Lake and Aha Lake, having historically experienced severe eutrophication. Utilizing the Baselga's framework, we partitioned bacterial and archaeal total beta diversity into two components: species turnover and nestedness, and then examined their sediment-depth patterns and the effects of P fractions on them. We found that total beta diversity, species turnover or nestedness consistently increased with deeper sediment layers regarding bacteria and archaea. Notably, there were parallel patterns between bacteria and archaea for total beta diversity and species turnover, which is largely underlain by equivalent processes such as environmental selection. For both microbial taxa, total beta diversity and species turnover were primarily constrained by metal oxide-bound inorganic P (NaOH-Pi) and sediment total phosphorus (STP) in Hongfeng Lake, while largely affected by reductant-soluble total P or calcium-bound inorganic P in Aha Lake. Moreover, NaOH-Pi and STP could influence bacterial total beta diversity by driving species nestedness in Hongfeng Lake. The joint effects of organic P (Po), inorganic P (Pi) and total P fractions indicated that P fractions are important to bacterial and archaeal beta diversity. Compared to Po fractions, Pi fractions had greater pure effects on bacterial beta diversity. Intriguingly, for total beta diversity and species turnover, archaea rather than bacteria are well-explained by Po fractions in both lakes, implying that the archaeal community may be involved in Po mineralization. Overall, our study reveals the importance of P fractions to the mechanism underlying bacterial and archaeal beta diversity in sediments, and provides theoretical underpinnings for controlling P sources in biodiversity conservation.
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Affiliation(s)
- Haijun Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runyu Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Qiuxing Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- College of Earth Science, Chengdu University of Technology, Chengdu, China
| | - Qiao Han
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiping Lu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
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104
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Sheng C, Du W, Liang Y, Xu P, Ding Q, Chen X, Jia S, Wang X. An integrated neuroimaging-omics approach for the gut-brain communication pathways in Alzheimer's disease. Front Aging Neurosci 2023; 15:1211979. [PMID: 37869373 PMCID: PMC10587434 DOI: 10.3389/fnagi.2023.1211979] [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: 04/25/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
A key role of the gut microbiota in the pathogenesis of neurodegenerative diseases, such as Alzheimer's disease (AD), has been identified over the past decades. Increasing clinical and preclinical evidence implicates that there is bidirectional communication between the gut microbiota and the central nervous system (CNS), which is also known as the microbiota-gut-brain axis. Nevertheless, current knowledge on the interplay between gut microbiota and the brain remains largely unclear. One of the primary mediating factors by which the gut microbiota interacts with the host is peripheral metabolites, including blood or gut-derived metabolites. However, mechanistic knowledge about the effect of the microbiome and metabolome signaling on the brain is limited. Neuroimaging techniques, such as multi-modal magnetic resonance imaging (MRI), and fluorodeoxyglucose-positron emission tomography (FDG-PET), have the potential to directly elucidate brain structural and functional changes corresponding with alterations of the gut microbiota and peripheral metabolites in vivo. Employing a combination of gut microbiota, metabolome, and advanced neuroimaging techniques provides a future perspective in illustrating the microbiota-gut-brain pathway and further unveiling potential therapeutic targets for AD treatments.
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Affiliation(s)
- Can Sheng
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Wenying Du
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yuan Liang
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Peng Xu
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Qingqing Ding
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Xue Chen
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Shulei Jia
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoni Wang
- Department of Neurology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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105
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Li W, Cheng F, Zhang J, Li C, Yu D, Simayijiang H, Liu H, Li S, Yan J. Changes in Gut Microbiota and Metabolites in Papillary Thyroid Carcinoma Patients Following Radioactive Iodine Therapy. Int J Gen Med 2023; 16:4453-4464. [PMID: 37808207 PMCID: PMC10557971 DOI: 10.2147/ijgm.s433433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023] Open
Abstract
Purpose Radioactive iodine therapy is administered through oral route, which is accumulated and absorbed in the intestine. However, its effects on the intestine remain unclear. In this study, we investigated the changes in the gut microbiota and metabolites following radioactive iodine therapy. Patients and Methods A total of 76 stool samples from the same 38 patients were collected at the start of radioactive iodine therapy and three days following the therapy. Stool microbiota and metabolites were detected using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry. Results Enterobacteriales, Enterobacteriaceae and Escherichia-Shigella were elevated in most patients (27/38) following the therapy. The levels of 2-hydroxyundec-7-enoylcarnitine were significantly lower, whereas those of 5-dehydroavenasterol, butylisopropylamine, and salsoline-1-carboxylate were higher following the therapy. The relative abundance of Escherichia-Shigella was negatively correlated with 2-hydroxyundec-7-enoylcarnitine level (r2 = -0.661, P = 0.009). Functional pathways were predicted to be involved in amino acid and lipid metabolism following the therapy. Particularly, phenylalanine, linoleic acid, sphingolipid, purine, and alpha-linolenic acid metabolism were the main metabolic pathways. Conclusion Gut microbiota was disturbed following radioactive iodine therapy, with increased Escherichia-Shigella. Processes associated with energy production seems to be impacted following the therapy, with significantly decreased 2-hydroxyundec-7-enoylcarnitine level. Meanwhile, some metabolites and functional pathways may have a positive effect on intestinal homeostasis, and may be related to the repair and promotion of gut recovery following the therapy. This study provides a basic foundation to explore how radioactive iodine affects gut microbiota and metabolites, and how gut function is regulated in response to radioactive iodine therapy.
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Affiliation(s)
- Wanting Li
- Shanxi Key Laboratory of Forensic Medicine, Shanxi Medical University, Jinzhong, People’s Republic of China
| | - Feng Cheng
- Shanxi Key Laboratory of Forensic Medicine, Shanxi Medical University, Jinzhong, People’s Republic of China
| | - Jun Zhang
- Shanxi Key Laboratory of Forensic Medicine, Shanxi Medical University, Jinzhong, People’s Republic of China
| | - Caihong Li
- Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Daijing Yu
- Shanxi Key Laboratory of Forensic Medicine, Shanxi Medical University, Jinzhong, People’s Republic of China
| | - Halimureti Simayijiang
- Shanxi Key Laboratory of Forensic Medicine, Shanxi Medical University, Jinzhong, People’s Republic of China
| | - Haiyan Liu
- Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Sijin Li
- Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Jiangwei Yan
- Shanxi Key Laboratory of Forensic Medicine, Shanxi Medical University, Jinzhong, People’s Republic of China
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106
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Ma X, Ding J, Ren H, Xin Q, Li Z, Han L, Liu D, Zhuo Z, Liu C, Ren Z. Distinguishable Influence of the Delivery Mode, Feeding Pattern, and Infant Sex on Dynamic Alterations in the Intestinal Microbiota in the First Year of Life. MICROBIAL ECOLOGY 2023; 86:1799-1813. [PMID: 36864279 DOI: 10.1007/s00248-023-02188-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/01/2023] [Indexed: 09/13/2023]
Abstract
The delivery mode, the feeding pattern and infant sex significantly influence the development of the infant gut flora. However, the extent to which these factors contribute to the establishment of the gut microbiota at different stages has rarely been studied. The factors that play a dominant role in determining microbial colonization of the infant gut at specific time points are unknown. The purpose of this study was to assess the different contributions of the delivery mode, the feeding pattern and infant sex to the composition of the infant gut microbiome. Here, 213 fecal samples from 55 infants at five ages (0, 1, 3, 6, and 12 months postpartum) were collected, and the composition of the gut microbiota via 16S rRNA sequencing was analyzed. The results showed that the average relative abundances of four genera, Bifidobacterium, Bacteroides, Parabacteroides, and Phascolarctobacterium, were increased in vaginally delivered infants versus cesarean section-delivered infants, while those of ten genera, such as Salmonella and Enterobacter, were reduced. The relative proportions of Anaerococcus and Peptostreptococcaceae were higher in exclusive breastfeeding than in combined feeding, while those of Coriobacteriaceae, Lachnospiraceae and Erysipelotrichaceae were lower. The average relative abundances of two genera, Alistipes and Anaeroglobus, were increased in male infants compared with female infants, whereas those of the phyla Firmicutes and Proteobacteria were reduced. During the first year of life, the average UniFrac distances revealed that the individual difference in the gut microbial composition in vaginally delivered infants was greater than that in cesarean section-delivered infants (P < 0.001) and that infants who received combined feeding had greater individual microbiota differences than exclusively breastfed infants (P < 0.01). The delivery mode, infant sex, and the feeding pattern were the dominant factors determining colonization of the infant gut microbiota at 0 months, from 1 to 6 months, and at 12 months postpartum, respectively. This study demonstrated for the first time that infant sex accounted for the dominant contribution to infant gut microbial development from 1 to 6 months postpartum. More broadly, this study effectively established the extent to which the delivery mode, the feeding pattern and infant sex contribute to the development of the gut microbiota at various time points during the first year of life.
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Affiliation(s)
- Xiao Ma
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Juan Ding
- Department of Quality Control, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Hongyan Ren
- Shanghai Mobio Biomedical Technology Co., Ltd, Shanghai, 201111, China
| | - Qi Xin
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Zhen Li
- Department of Interventional Radiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Liping Han
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Dingjiandi Liu
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhihong Zhuo
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chao Liu
- Shanghai Mobio Biomedical Technology Co., Ltd, Shanghai, 201111, China
| | - Zhigang Ren
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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107
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Arıkan M, Muth T. Integrated multi-omics analyses of microbial communities: a review of the current state and future directions. Mol Omics 2023; 19:607-623. [PMID: 37417894 DOI: 10.1039/d3mo00089c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Integrated multi-omics analyses of microbiomes have become increasingly common in recent years as the emerging omics technologies provide an unprecedented opportunity to better understand the structural and functional properties of microbial communities. Consequently, there is a growing need for and interest in the concepts, approaches, considerations, and available tools for investigating diverse environmental and host-associated microbial communities in an integrative manner. In this review, we first provide a general overview of each omics analysis type, including a brief history, typical workflow, primary applications, strengths, and limitations. Then, we inform on both experimental design and bioinformatics analysis considerations in integrated multi-omics analyses, elaborate on the current approaches and commonly used tools, and highlight the current challenges. Finally, we discuss the expected key advances, emerging trends, potential implications on various fields from human health to biotechnology, and future directions.
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Affiliation(s)
- Muzaffer Arıkan
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.
- Department of Medical Biology, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.
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108
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Papoutsoglou G, Tarazona S, Lopes MB, Klammsteiner T, Ibrahimi E, Eckenberger J, Novielli P, Tonda A, Simeon A, Shigdel R, Béreux S, Vitali G, Tangaro S, Lahti L, Temko A, Claesson MJ, Berland M. Machine learning approaches in microbiome research: challenges and best practices. Front Microbiol 2023; 14:1261889. [PMID: 37808286 PMCID: PMC10556866 DOI: 10.3389/fmicb.2023.1261889] [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: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommendations on algorithm selection, pipeline creation and evaluation, stemming from the COST Action ML4Microbiome. We compared the suggested approaches on a multi-cohort shotgun metagenomics dataset of colorectal cancer patients, focusing on their performance in disease diagnosis and biomarker discovery. It is demonstrated that the use of compositional transformations and filtering methods as part of data preprocessing does not always improve the predictive performance of a model. In contrast, the multivariate feature selection, such as the Statistically Equivalent Signatures algorithm, was effective in reducing the classification error. When validated on a separate test dataset, this algorithm in combination with random forest modeling, provided the most accurate performance estimates. Lastly, we showed how linear modeling by logistic regression coupled with visualization techniques such as Individual Conditional Expectation (ICE) plots can yield interpretable results and offer biological insights. These findings are significant for clinicians and non-experts alike in translational applications.
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Affiliation(s)
- Georgios Papoutsoglou
- Department of Computer Science, University of Crete, Heraklion, Greece
- JADBio Gnosis DA S.A., Science and Technology Park of Crete, Heraklion, Greece
| | - Sonia Tarazona
- Department of Applied Statistics and Operations Research and Quality, Polytechnic University of Valencia, Valencia, Spain
| | - Marta B. Lopes
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Research and Development Unit for Mechanical and Industrial Engineering (UNIDEMI), Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
| | - Thomas Klammsteiner
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Eliana Ibrahimi
- Department of Biology, University of Tirana, Tirana, Albania
| | - Julia Eckenberger
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Pierfrancesco Novielli
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- National Institute for Nuclear Physics, Bari Division, Bari, Italy
| | - Alberto Tonda
- UMR 518 MIA-PS, INRAE, Paris-Saclay University, Palaiseau, France
- Complex Systems Institute of Paris Ile-de-France (ISC-PIF) - UAR 3611 CNRS, Paris, France
| | - Andrea Simeon
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia
| | - Rajesh Shigdel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stéphane Béreux
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
- MaIAGE, INRAE, Paris-Saclay University, Jouy-en-Josas, France
| | - Giacomo Vitali
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
| | - Sabina Tangaro
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- National Institute for Nuclear Physics, Bari Division, Bari, Italy
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Andriy Temko
- Department of Electrical and Electronic Engineering, University College Cork, Cork, Ireland
| | - Marcus J. Claesson
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Magali Berland
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
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109
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Huang S, Kong Y, Chen Y, Huang X, Ma P, Liu X. Microbial denitrification characteristics of typical decentralized wastewater treatment processes based on 16S rRNA sequencing. Front Microbiol 2023; 14:1242506. [PMID: 37779708 PMCID: PMC10537219 DOI: 10.3389/fmicb.2023.1242506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Despite the widespread application of decentralized wastewater treatment (WWT) facilities in China, relatively few research has used the multi-media biological filter (MMBF) facilities to investigate the microorganism characteristics. This study utilizes 16S rRNA high-throughput sequencing (HTS) technology to examine the microbial biodiversity of a representative wastewater treatment (WWT) system in an expressway service area. The pathways of nitrogen removal along the treatment route were analyzed in conjunction with water quality monitoring. The distribution and composition of microbial flora in the samples were examined, and the dominant flora were identified using LEfSe analysis. The FAPROTAX methodology was employed to investigate the relative abundance of genes associated with the nitrogen cycle and to discern the presence of functional genes involved in nitrogen metabolism. On average, the method has a high level of efficiency in removing COD, TN, NH3-N, and TP from the effluent. The analysis of the microbial community identified a total of 40 phyla, 111 classes, 143 orders, 263 families, and 419 genera. The phyla that were predominantly observed include Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Bacteroidetes. The results show that the system has achieved high performance in nitrogen removal, the abundance of nitrification genes is significantly higher than that of other nitrogen cycle genes such as denitrification, and there are six nitrogen metabolism pathways, primarily nitrification, among which Nitrospirae and Nitrospira are the core differentiated flora that can adapt to low temperature conditions and participate in nitrification, and are the dominant nitrogen removal flora in cold regions. This work aims to comprehensively investigate the diversity and functional properties of the bacterial community in decentralized WWT processes.
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Affiliation(s)
- Shanqian Huang
- Center of Environment Protection, China Academy of Transportation Sciences, Beijing, China
| | - Yaping Kong
- Center of Environment Protection, China Academy of Transportation Sciences, Beijing, China
| | - Yao Chen
- Center of Environment Protection, China Academy of Transportation Sciences, Beijing, China
| | - Xuewen Huang
- Anhui Transportation Holding Group CO., LTD., Hefei, China
| | - Pengfei Ma
- Qinghai Expressway Maintenance Service CO., LTD., Xining, China
| | - Xuexin Liu
- Center of Environment Protection, China Academy of Transportation Sciences, Beijing, China
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Khera HK, Mishra R. Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health. Mol Biotechnol 2023:10.1007/s12033-023-00870-4. [PMID: 37695473 DOI: 10.1007/s12033-023-00870-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Timely and accurate detection of the causal agent of a disease is crucial to restrict suffering and save lives. Mere symptoms are often not enough to detect the root cause of the disease. Better diagnostics applied for screening at a population level and sensitive detection assays remain the crucial component of disease surveillance which may include clinical, plant, and environmental samples, including wastewater. The recent advances in genome sequencing, nucleic acid amplification, and detection methods have revolutionized nucleic acid-based testing (NABing) and screening assays. A typical NABing assay consists of three modules: isolation of the nucleic acid from the collected sample, identification of the target sequence, and final reading the target with the help of a signal, which may be in the form of color, fluorescence, etc. Here, we review current NABing assays covering the different aspects of all three modules. We also describe the frequently used target amplification or signal amplification procedures along with the variety of applications of this fast-evolving technology and challenges in implementation of NABing in the context of disease management especially in low-resource settings.
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Affiliation(s)
- Harvinder Kour Khera
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
| | - Rakesh Mishra
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
- CSIR-Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, Telangana, 500007, India.
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111
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Mao X, Chen H, Peng X, Zhao X, Yu Z, Xu D. Dysbiosis of vaginal and cervical microbiome is associated with uterine fibroids. Front Cell Infect Microbiol 2023; 13:1196823. [PMID: 37743857 PMCID: PMC10513091 DOI: 10.3389/fcimb.2023.1196823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Dysbiosis of the female reproductive tract is closely associated with gynecologic diseases. Here, we aim to explore the association between dysbiosis in the genital tract and uterine fibroids (UFs) to further provide new insights into UF etiology. We present an observational study to profile vaginal and cervical microbiome from 29 women with UFs and 38 healthy women, and 125 samples were obtained and sequenced. By comparing the microbial profiles between different parts of the reproductive tract, there is no significant difference in microbial diversity between healthy subjects and UF patients. However, alpha diversity of UF patients was negatively correlated with the number of fibroids. Increased Firmicutes were observed in both the cervical and vaginal microbiome of UF patients at the phylum level. In differential analysis of relative abundance, some genera were shown to be significantly enriched (e.g., Erysipelatoclostridium, Mucispirillum, and Finegoldia) and depleted (e.g., Erysipelotrichaceae UCG-003 and Sporolactobacillus) in UF patients. Furthermore, the microbial co-occurrence networks of UF patients showed lower connectivity and complexity, suggesting reduced interactions and stability of the cervical and vaginal microbiota in UF patients. In summary, our findings revealed the perturbation of microbiome in the presence of UFs and a distinct pattern of characteristic vaginal and cervical microbiome involved in UFs, offering new options to further improve prevention and management strategies.
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Affiliation(s)
- Xuetao Mao
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xuan Peng
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xingping Zhao
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Dabao Xu
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
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112
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He Z, Liu R, Wang M, Wang Q, Zheng J, Ding J, Wen J, Fahey AG, Zhao G. Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens. MICROBIOME 2023; 11:198. [PMID: 37653442 PMCID: PMC10472625 DOI: 10.1186/s40168-023-01627-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Improving feed efficiency is the most important goal for modern animal production. The regulatory mechanisms of controlling feed efficiency traits are extremely complex and include the functions related to host genetics and gut microbiota. Short-chain fatty acids (SCFAs), as significant metabolites of microbiota, could be used to refine the combined effect of host genetics and gut microbiota. However, the association of SCFAs with the gut microbiota and host genetics for regulating feed efficiency is far from understood. RESULTS In this study, 464 broilers were housed for RFI measuring and examining the host genome sequence. And 300 broilers were examined for cecal microbial data and SCFA concentration. Genome-wide association studies (GWAS) showed that four out of seven SCFAs had significant associations with genome variants. One locus (chr4: 29414391-29417189), located near or inside the genes MAML3, SETD7, and MGST2, was significantly associated with propionate and had a modest effect on feed efficiency traits and the microbiota. The genetic effect of the top SNP explained 8.43% variance of propionate. Individuals with genotype AA had significantly different propionate concentrations (0.074 vs. 0.131 μg/mg), feed efficiency (FCR: 1.658 vs. 1.685), and relative abundance of 14 taxa compared to those with the GG genotype. Christensenellaceae and Christensenellaceae_R-7_group were associated with feed efficiency, propionate concentration, the top SNP genotypes, and lipid metabolism. Individuals with a higher cecal abundance of these taxa showed better feed efficiency and lower concentrations of caecal SCFAs. CONCLUSION Our study provides strong evidence of the pathway that host genome variants affect the cecal SCFA by influencing caecal microbiota and then regulating feed efficiency. The cecal taxa Christensenellaceae and Christensenellaceae_R-7_group were identified as representative taxa contributing to the combined effect of host genetics and SCFAs on chicken feed efficiency. These findings provided strong evidence of the combined effect of host genetics and gut microbial SCFAs in regulating feed efficiency traits. Video Abstract.
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Affiliation(s)
- Zhengxiao He
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Mengjie Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qiao Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jumei Zheng
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jiqiang Ding
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Alan G. Fahey
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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Salas-Espejo E, Terrón-Camero LC, Ruiz JL, Molina NM, Andrés-León E. Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms. Semin Reprod Med 2023; 41:125-143. [PMID: 38320576 DOI: 10.1055/s-0044-1779025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.
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Affiliation(s)
- Eduardo Salas-Espejo
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Laura C Terrón-Camero
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - José L Ruiz
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
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114
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Xue Z, Han Y, Tian W, Zhang W. Metagenome sequencing and 103 microbial genomes from ballast water and sediments. Sci Data 2023; 10:536. [PMID: 37563185 PMCID: PMC10415351 DOI: 10.1038/s41597-023-02447-x] [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: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023] Open
Abstract
The great threat of microbes carried by ballast water calls for figuring out the species composition of the ballast-tank microbial community, where the dark, cold, and anoxic tank environment might select special taxa. In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea, from four vessels on international voyages. Of these MAGs, 60 were 'near complete' (completeness >90%), 34 were >80% complete, and nine were >75% complete. Phylogenomic analysis revealed that over 70% (n = 74) of these MAGs represented new taxa at different taxonomical levels, including one order, three families, 12 genera, and 58 species. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 69), Bacteroidota (n = 17), and Actinobacteriota (n = 7). These draft genomes provided novel data on species diversity and function in the ballast-tank microbial community, which will facilitate ballast water and sediments management.
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Affiliation(s)
- Zhaozhao Xue
- Marine College, Shandong University, Weihai, 264209, China
| | - Yangchun Han
- Integrated Technical Service Center of Jiangyin Customs, Jiangyin, 214441, China
| | - Wen Tian
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, 210001, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, 264209, China.
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115
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Yao S, Zhao Y, Chen H, Sun R, Chen L, Huang J, Yu Z, Chen S. Exploring the Plasticity of Diet on Gut Microbiota and Its Correlation with Gut Health. Nutrients 2023; 15:3460. [PMID: 37571397 PMCID: PMC10420685 DOI: 10.3390/nu15153460] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Dietary habits have been proven to help alter the composition of gut microbiota, and exploring the impact of nutritional patterns on gut microbiota changes can help protect gut health. However, few studies have focused on the dietary impact on the gut microbiota over an experimental timeframe. In this study, 16S rRNA gene sequencing was employed to investigate the gut microbiota of mice under different dietary patterns, including AIN-93G diet (Control), high protein diet (HPD), high fiber diet (HFD), and switch diet (Switch). The alpha diversity of the HPD group significantly decreased, but HFD can restore this decline. During HPD, some genera were significantly upregulated (e.g., Feacalibaculum) and downregulated (e.g., Parabacteroides). However, after receiving HFD, other genera were upregulated (e.g., Akkermansia) and downregulated (e.g., Lactobacillus). In addition, the interaction between pathogenic bacteria was more pronounced during HPD, while the main effect was probiotics during HFD. In conclusion, the plasticity exhibited by the gut microbiota was subject to dietary influences, wherein disparate dietary regimens hold pivotal significance in upholding the well-being of the host. Therefore, our findings provide new ideas and references for the relationship between diets and gut microbiota.
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Affiliation(s)
- Siqi Yao
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha 410008, China;
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Yiming Zhao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha 410078, China; (H.C.); (J.H.)
| | - Ruizheng Sun
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Liyu Chen
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha 410078, China; (H.C.); (J.H.)
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Shuijiao Chen
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha 410008, China;
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha 410008, China
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Deissová T, Zapletalová M, Kunovský L, Kroupa R, Grolich T, Kala Z, Bořilová Linhartová P, Lochman J. 16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling. Sci Rep 2023; 13:12577. [PMID: 37537336 PMCID: PMC10400661 DOI: 10.1038/s41598-023-39575-8] [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: 03/24/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1-V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1-V2M primers. Moreover, the V1-V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1-V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research.
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Affiliation(s)
- Tereza Deissová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 735/5, 62500, Brno, Czech Republic
| | - Martina Zapletalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 735/5, 62500, Brno, Czech Republic
| | - Lumír Kunovský
- Department of Gastroenterology and Internal Medicine, University Hospital Brno, and Faculty of Medicine, Masaryk, University, Jihlavská 20, 62500, Brno, Czech Republic
- Department of Surgery, University Hospital Brno, and Faculty of Medicine, Masaryk University, Jihlavská 20, 62500, Brno, Czech Republic
| | - Radek Kroupa
- Department of Gastroenterology and Internal Medicine, University Hospital Brno, and Faculty of Medicine, Masaryk, University, Jihlavská 20, 62500, Brno, Czech Republic
| | - Tomáš Grolich
- Department of Gastroenterology and Internal Medicine, University Hospital Brno, and Faculty of Medicine, Masaryk, University, Jihlavská 20, 62500, Brno, Czech Republic
| | - Zdeněk Kala
- Department of Surgery, University Hospital Brno, and Faculty of Medicine, Masaryk University, Jihlavská 20, 62500, Brno, Czech Republic
| | - Petra Bořilová Linhartová
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Jihlavská 20, 62500, Brno, Czech Republic
- Faculty of Science, RECETOX, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 735/5, 62500, Brno, Czech Republic.
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Jihlavská 20, 62500, Brno, Czech Republic.
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Xie L, Yu S, Lu X, Liu S, Tang Y, Lu H. Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau. Microorganisms 2023; 11:2002. [PMID: 37630563 PMCID: PMC10458105 DOI: 10.3390/microorganisms11082002] [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: 05/31/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem.
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Affiliation(s)
- Linglu Xie
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Shan Yu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing 100871, China
- National Engineering Research Center for Gas Hydrate Exploration and Development, Guangzhou 511466, China
| | - Xindi Lu
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Siwei Liu
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Yukai Tang
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
| | - Hailong Lu
- School of Earth and Space Sciences, Peking University, Beijing 100871, China; (L.X.)
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing 100871, China
- National Engineering Research Center for Gas Hydrate Exploration and Development, Guangzhou 511466, China
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118
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Munley JA, Kirkpatrick SL, Gillies GS, Bible LE, Efron PA, Nagpal R, Mohr AM. The Intestinal Microbiome after Traumatic Injury. Microorganisms 2023; 11:1990. [PMID: 37630549 PMCID: PMC10459834 DOI: 10.3390/microorganisms11081990] [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: 07/16/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
The intestinal microbiome plays a critical role in host immune function and homeostasis. Patients suffering from-as well as models representing-multiple traumatic injuries, isolated organ system trauma, and various severities of traumatic injury have been studied as an area of interest in the dysregulation of immune function and systemic inflammation which occur after trauma. These studies also demonstrate changes in gut microbiome diversity and even microbial composition, with a transition to a pathobiome state. In addition, sex has been identified as a biological variable influencing alterations in the microbiome after trauma. Therapeutics such as fecal transplantation have been utilized to ameliorate not only these microbiome changes but may also play a role in recovery postinjury. This review summarizes the alterations in the gut microbiome that occur postinjury, either in isolated injury or multiple injuries, along with proposed mechanisms for these changes and future directions for the field.
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Affiliation(s)
- Jennifer A. Munley
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA; (J.A.M.); (S.L.K.); (G.S.G.); (L.E.B.); (P.A.E.)
| | - Stacey L. Kirkpatrick
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA; (J.A.M.); (S.L.K.); (G.S.G.); (L.E.B.); (P.A.E.)
| | - Gwendolyn S. Gillies
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA; (J.A.M.); (S.L.K.); (G.S.G.); (L.E.B.); (P.A.E.)
| | - Letitia E. Bible
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA; (J.A.M.); (S.L.K.); (G.S.G.); (L.E.B.); (P.A.E.)
| | - Philip A. Efron
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA; (J.A.M.); (S.L.K.); (G.S.G.); (L.E.B.); (P.A.E.)
| | - Ravinder Nagpal
- Department of Nutrition & Integrative Physiology, Florida State University College of Health and Human Sciences, Tallahassee, FL 32306, USA;
| | - Alicia M. Mohr
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA; (J.A.M.); (S.L.K.); (G.S.G.); (L.E.B.); (P.A.E.)
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Zhang Z, Guo Y, Zhuang M, Liu F, Xia Z, Zhang Z, Yang F, Zeng H, Wu Y, Huang J, Li J. Potential role of the gut microbiota of bumblebee Bombus pyrosoma in adaptation to high-altitude habitats. Front Microbiol 2023; 14:1218560. [PMID: 37601385 PMCID: PMC10433375 DOI: 10.3389/fmicb.2023.1218560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
The gut microbiota affects the health and overall fitness of bumblebees. It can enhance the host's ecological range by leveraging their metabolic capacities. However, the diversity of the gut microbiota and adaptive functional evolution in high-altitude regions remain unclear. To explore how the gut microbiota helps the host adapt to high-altitude environments, we analyzed the differences in diversity and function of the gut microbiota between high- and low-altitude regions through full-length 16S rRNA sequencing. Our results show that high-altitude regions have a lower abundance of Fructobacillus and Saccharibacter compared to low-altitude regions. Additionally, some individuals in low-altitude regions were invaded by opportunistic pathogens. The gut microbiota in high-altitude regions has a greater number of pathways involved in "Protein digestion and absorption" and "Biosynthesis of amino acids," while fewer carbohydrate pathways are involved in "digestion and absorption" and "Salmonella infection." Our finding suggests that plateau hosts typically reduce energy metabolism and enhance immunity in response to adverse environments. Correspondingly, the gut microbiota also makes changes, such as reducing carbohydrate degradation and increasing protein utilization in response to the host. Additionally, the gut microbiota regulates their abundance and function to help the host adapt to adverse high-altitude environments.
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Affiliation(s)
- Zhengyi Zhang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Yulong Guo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Mingsheng Zhuang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
- Shanghai Suosheng Biotechnology Co., Ltd., Shanghai, China
| | - Fugang Liu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Zhongyan Xia
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Zhihao Zhang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Fan Yang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Huayan Zeng
- Luoping Yunling Bee Industry and Trade Co., Ltd., Qujing, Yunnan, China
| | - Yueguo Wu
- Luoping Yunling Bee Industry and Trade Co., Ltd., Qujing, Yunnan, China
| | - Jiaxing Huang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Jilian Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
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Lu Y, Fu Y, Chen L, Cui J, Huang M, Fu Y, Liu H. Combined effect of simulated microgravity and low-dose ionizing radiation on structure and antibiotic resistance of a synthetic community model of bacteria isolated from spacecraft assembly room. LIFE SCIENCES IN SPACE RESEARCH 2023; 38:29-38. [PMID: 37481305 DOI: 10.1016/j.lssr.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Accepted: 04/25/2023] [Indexed: 07/24/2023]
Abstract
Understanding the structural and antibiotic resistance changes of microbial communities in space environments is critical for identifying potential pathogens that may pose health risks to astronauts and for preventing and controlling microbial contamination. The research to date on microbes under simulated space factors has primarily been carried out on single bacterial species under the individual effects of microgravity or low-dose radiation. However, microgravity (MG) and low-dose ionizing radiation (LDIR) coexist in the actual spacecraft environment, and microorganisms coexist as communities in the spacecraft environment. Thus, the microbial response to the real changes present during space habitation has not been adequately explored. To address this knowledge gap, we compared the dynamics of community composition and antibiotic resistance of synthetic bacterial communities under simulated microgravit, low-dose ionizing radiation, and the conditions combined, as it occurs in spacecraft. To ensure representative bacteria were selected, we co-cultured of 12 bacterial strains isolated from spacecraft cleanrooms. We found that the weakened competition between communities increased the possibility of species coexistence, community diversity, and homogeneity. The number of Bacilli increased significantly, while different species under the combined conditions showed various changes in abundance compared to those under the individual conditions. The resistance of the synthetic community to penicillins increased significantly under low doses of ionizing radiation but did not change significantly under simulated microgravity or the combined conditions. The results of functional predictions revealed that antibiotic biosynthesis and resistance increased dramatically in the community under space environmental stress, which confirmed the results of the drug sensitivity assays. Our results show that combined space environmental factors exert different effects on the microbial community structure and antibiotic resistance, which provides new insights into our understanding of the mechanisms of evolution of microorganisms in spacecraft, and is relevant to effective microbial pollution prevention and control strategies.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Yifan Fu
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; 4+4 M D. Program, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Letian Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Jingjing Cui
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Min Huang
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China.
| | - Hong Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China
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He Y, Pan J, Huang D, Sanford RA, Peng S, Wei N, Sun W, Shi L, Jiang Z, Jiang Y, Hu Y, Li S, Li Y, Li M, Dong Y. Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering. ENVIRONMENT INTERNATIONAL 2023; 178:108067. [PMID: 37393724 DOI: 10.1016/j.envint.2023.108067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca2+ concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H+ antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.
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Affiliation(s)
- Yu He
- School of Environmental Studies, China University of Geosciences, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Studies, Shenzhen University, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, China
| | - Dongmei Huang
- School of Environmental Studies, China University of Geosciences, China; Yejin Geological Team of Hubei Geological Bureau, China
| | - Robert A Sanford
- Department of Earth Science & Environmental Change, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Shuming Peng
- Institute of Ecological Environment, Chengdu University of Technology, China
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Weimin Sun
- Guangdong Institute of Eco-environmental and Soil Science, Guangdong, China
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, China
| | - Yongguang Jiang
- School of Environmental Studies, China University of Geosciences, China
| | - Yidan Hu
- School of Environmental Studies, China University of Geosciences, China
| | - Shuyi Li
- School of Environmental Studies, China University of Geosciences, China
| | - Yongzhe Li
- School of Environmental Studies, China University of Geosciences, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Studies, Shenzhen University, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, China.
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China; Hubei Key Laboratory of Wetland Evolution and Ecology Restoration, China.
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Belli M, Barone L, Longo S, Prandi FR, Lecis D, Mollace R, Margonato D, Muscoli S, Sergi D, Federici M, Barillà F. Gut Microbiota Composition and Cardiovascular Disease: A Potential New Therapeutic Target? Int J Mol Sci 2023; 24:11971. [PMID: 37569352 PMCID: PMC10418329 DOI: 10.3390/ijms241511971] [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] [Received: 06/28/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
A great deal of evidence has revealed an important link between gut microbiota and the heart. In particular, the gut microbiota plays a key role in the onset of cardiovascular (CV) disease, including heart failure (HF). In HF, splanchnic hypoperfusion causes intestinal ischemia resulting in the translocation of bacteria and their metabolites into the blood circulation. Among these metabolites, the most important is Trimethylamine N-Oxide (TMAO), which is responsible, through various mechanisms, for pathological processes in different organs and tissues. In this review, we summarise the complex interaction between gut microbiota and CV disease, particularly with respect to HF, and the possible strategies for influencing its composition and function. Finally, we highlight the potential role of TMAO as a novel prognostic marker and a new therapeutic target for HF.
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Affiliation(s)
- Martina Belli
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
- Cardiovascular Imaging Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Lucy Barone
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
| | - Susanna Longo
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy (R.M.)
| | - Francesca Romana Prandi
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
- Division of Cardiology, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Dalgisio Lecis
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
| | - Rocco Mollace
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy (R.M.)
- Cardiovascular Department, Humanitas Gavazzeni, 24125 Bergamo, Italy
| | - Davide Margonato
- Cardiovascular Imaging Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Saverio Muscoli
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
| | - Domenico Sergi
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
| | - Massimo Federici
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy (R.M.)
| | - Francesco Barillà
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (M.B.)
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Brito BP, Frost MJ, Anantanawat K, Jaya F, Batterham T, Djordjevic SP, Chang WS, Holmes EC, Darling AE, Kirkland PD. Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. MICROBIOME 2023; 11:158. [PMID: 37491320 PMCID: PMC10367309 DOI: 10.1186/s40168-023-01591-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/03/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. RESULTS A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. CONCLUSION This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.
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Affiliation(s)
- Barbara P Brito
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia.
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia.
- Present Address: Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, Australia.
| | - Melinda J Frost
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Kay Anantanawat
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- Illumina Australia, Ultimo, New South Wales, Australia
| | - Frederick Jaya
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | - Steven P Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Aaron E Darling
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- Illumina Australia, Ultimo, New South Wales, Australia
| | - Peter D Kirkland
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
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Ma JW, Wu YQ, Xu CL, Luo ZX, Yu RL, Hu GR, Yan Y. Inhibitory effect of polyethylene microplastics on roxarsone degradation in soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131483. [PMID: 37116328 DOI: 10.1016/j.jhazmat.2023.131483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/19/2023]
Abstract
Roxarsone (3-nitro-4-hydroxyphenylarsonic acid, Rox(V)), an extensively used organoarsenical feed additive, enters soils through the application of Rox(V)-containing manure and further degrades to highly toxic arsenicals. Microplastics, as emerging contaminants, are also frequently detected in soils. However, the effects of microplastics on soil Rox(V) degradation are unknown. A microcosm experiment was conducted to investigate soil Rox(V) degradation responses to polyethylene (PE) microplastics and the underlying mechanisms. PE microplastics inhibited soil Rox(V) degradation, with the main products being 3-amino-4-hydroxyphenylarsonic acid [3-AHPAA(V)], N-acetyl-4-hydroxy-m-arsanilic acid [N-AHPAA(V)], arsenate [As(V)], and arsenite [As(III)]. This inhibition was likely driven by the decline in soil pH by PE microplastic addition, which may directly enhance Rox(V) sorption in soils. The decreased soil pH further suppressed the nfnB gene related to nitroreduction of Rox(V) to 3-AHPAA(V) and nhoA gene associated with acetylation of 3-AHPAA(V) to N-AHPAA(V), accompanied by a decrease in the relative abundance of possible Rox(V)-degrading bacteria (e.g., Pseudomonadales), although the diversity, composition, network complexity, and assembly of soil bacterial communities were largely influenced by Rox(V) rather than PE microplastics. Our study emphasizes microplastic-induced inhibition of Rox(V) degradation in soils and the need to consider the role of microplastics in better risk assessment and remediation of Rox(V)-contaminated soils.
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Affiliation(s)
- Jie-Wen Ma
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Ya-Qing Wu
- Instrumental Analysis Center of Huaqiao University, Huaqiao University, Xiamen 361021, China
| | - Chen-Lu Xu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Zhuan-Xi Luo
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Rui-Lian Yu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Gong-Ren Hu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China.
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125
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Chen X, Shi Y. Determinants of microbial colonization in the premature gut. Mol Med 2023; 29:90. [PMID: 37407941 DOI: 10.1186/s10020-023-00689-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Abnormal microbial colonization in the gut at an early stage of life affects growth, development, and health, resulting in short- and long-term adverse effects. Microbial colonization patterns of preterm infants differ from those of full-term infants in that preterm babies and their mothers have more complicated prenatal and postnatal medical conditions. Maternal complications, antibiotic exposure, delivery mode, feeding type, and the use of probiotics may significantly shape the gut microbiota of preterm infants at an early stage of life; however, these influences subside with age. Although some factors and processes are difficult to intervene in or avoid, understanding the potential factors and determinants will help in developing timely strategies for a healthy gut microbiota in preterm infants. This review discusses potential determinants of gut microbial colonization in preterm infants and their underlying mechanisms.
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Affiliation(s)
- Xiaoyu Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110000, China
| | - Yongyan Shi
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110000, China.
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Serghiou IR, Baker D, Evans R, Dalby MJ, Kiu R, Trampari E, Phillips S, Watt R, Atkinson T, Murphy B, Hall LJ, Webber MA. An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs. Microb Genom 2023; 9:mgen001058. [PMID: 37428148 PMCID: PMC10438817 DOI: 10.1099/mgen.0.001058] [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: 02/27/2023] [Accepted: 06/04/2023] [Indexed: 07/11/2023] Open
Abstract
The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.
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Affiliation(s)
- Iliana R. Serghiou
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Dave Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Matthew J. Dalby
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Raymond Kiu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Sarah Phillips
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Rachel Watt
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Thomas Atkinson
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Barry Murphy
- Unilever R&D Port Sunlight, Bebington, CH63 3JW, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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Sun L, Ke X, Guan A, Jin B, Qu J, Wang Y, Xu X, Li C, Sun H, Xu H, Xu G, Sang X, Feng Y, Sun Y, Yang H, Mao Y. Intratumoural microbiome can predict the prognosis of hepatocellular carcinoma after surgery. Clin Transl Med 2023; 13:e1331. [PMID: 37462602 PMCID: PMC10353526 DOI: 10.1002/ctm2.1331] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND The dismal prognosis of hepatocellular carcinoma (HCC) is closely associated with characteristics of the tumour microenvironment (TME). Recent studies have confirmed the presence and potential influence of the microbiome in TME on cancer progression. Elucidating the relationship between microbes in the TME and cancer could provide valuable insights into novel diagnostic markers and therapeutic strategies for HCC and thus warrants a closer investigation of the role of intratumoural microbiome in the HCC TME. METHODS We determined the presence of intratumoural microbiome using fluorescence in situ hybridisation, and explored the microbial community profiles in the HCC TME in paired tumour and adjacent normal tissues using 16S rDNA sequencing. Microbial signatures were characterised in the paired group, and their correlation with clinical characteristics was further investigated. We clustered the microbial signatures of tumour tissues by hepatotypes, and further analysis was performed to elucidate the independent prognostic value of the hepatotypes. RESULTS This study revealed that microbial profiles and community networks differed notably between tumours and adjacent normal tissues. Proteobacteria and Actinobacteria were the most abundant phyla in the HCC TME. The TME microbial profiles also revealed heterogeneities between individuals and between multiple tumour lesions. Clustering of the microbial profiles into two hepatotypes revealed different microbial network patterns. Additionally, the hepatotypes were revealed to be independent prognostic factors in patients with resected HCC. CONCLUSIONS Our study illuminates the microbial profiles in the TME of HCC and presents the hepatotype as a potential independent biomarker for the prognostic prediction of HCC after surgery.
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Affiliation(s)
- Lejia Sun
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Xindi Ke
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
| | - Ai Guan
- Eight-year MD Program, Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences, Beijing, China
| | - Bao Jin
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
| | - Jiangming Qu
- Eight-year MD Program, Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences, Beijing, China
| | - Yinhan Wang
- Eight-year MD Program, Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences, Beijing, China
| | - Xiang Xu
- Eight-year MD Program, Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences, Beijing, China
| | - Changcan Li
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
| | - Hang Sun
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
| | - Hengyi Xu
- Eight-year MD Program, Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences, Beijing, China
| | - Gang Xu
- Liver Transplant Center, Organ Transplant Center, West China Hospital of Sichuan University, Chengdu, China
- Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital of Sichuan University, Chengdu, China
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
| | - Yifei Feng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Huayu Yang
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
| | - Yilei Mao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, China
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Kashyap N, Singh SK, Yadav N, Singh VK, Kumari M, Kumar D, Shukla L, Bhardwaj N, Kumar A. Biocontrol Screening of Endophytes: Applications and Limitations. PLANTS (BASEL, SWITZERLAND) 2023; 12:2480. [PMID: 37447041 DOI: 10.3390/plants12132480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023]
Abstract
The considerable loss of crop productivity each year due to plant disease or pathogen invasion during pre- or post-harvest storage conditions is one of the most severe challenges to achieving the goals of food security for the rising global population. Although chemical pesticides severally affect the food quality and health of consumers, a large population relies on them for plant disease management. But currently, endophytes have been considered one of the most suitable biocontrol agents due to better colonization and acclimatization potential. However, a very limited number of endophytes have been used commercially as biocontrol agents. Isolation of endophytes and their screening to represent potential characteristics as biocontrol agents are considered challenging by different procedures. Through a web search using the keywords "endophytes as biocontrol agents" or "biocontrol mechanism of endophytes," we have succinctly summarised the isolation strategies and different in vitro and in vivo biocontrol screening methods of endophytic biocontrol agents in the present review. In this paper, biocontrol mechanisms of endophytes and their potential application in plant disease management have also been discussed. Furthermore, the registration and regulatory mechanism of the endophytic biocontrol agents are also covered.
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Affiliation(s)
- Nikhil Kashyap
- Department of Biotechnology, Noida International University, Greater Noida 203201, India
| | - Sandeep Kumar Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Nisha Yadav
- Division of Agriculture Extension, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya 224123, India
| | - Madhuree Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Livleen Shukla
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Nikunj Bhardwaj
- Department of Zoology, Maharaj Singh College, Maa Shakumbhari University, Saharanpur 247001, India
| | - Ajay Kumar
- Department of Botany, M.V. College, Buxar 802101, India
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Bukin YS, Mikhailov IS, Petrova DP, Galachyants YP, Zakharova YR, Likhoshway YV. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton. World J Microbiol Biotechnol 2023; 39:229. [PMID: 37341802 DOI: 10.1007/s11274-023-03678-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.
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Affiliation(s)
- Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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130
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Chen Q, Ma X, Xing Z, Zhao X, Zu H, Guo Z, Li B. Antibiotic Conditioning Shapes Pseudosterile Mouse Models by Deleting Colonic Microbes Rather than Small Intestinal Microbes. Microbiol Spectr 2023; 11:e0081423. [PMID: 37074200 PMCID: PMC10269458 DOI: 10.1128/spectrum.00814-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023] Open
Abstract
A simple model of alternative microbiota in the developing intestinal environment has been highly desirable for the study of health and disease in the gut. The pattern of antibiotic depletion of natural gut microbes is necessary for this model. However, the effects and loci of antibiotic deletion of gut microbes remain unclear. In this study, a mixture of three proven broad-spectrum antibiotics was selected to study their effects on microbial deletions in the jejunum, ileum, and colon of mice. The 16S rRNA sequencing results showed that antibiotics significantly reduced colonic microbial diversity, with limited effects on the jejunum and ileum. At the level of microbial genera, only 93.38% of Burkholderia-Caballeronia-Paraburkholderia and 5.89% of Enterorhabdus were present in the colon after antibiotic treatment. However, such changes were not observed in the microbial composition of the jejunum and ileum. Our results suggest that the antibiotics depleted intestinal microorganisms by acting primarily in the colon and not in the small intestine (jejunum and ileum). IMPORTANCE Many studies have applied antibiotics to delete intestinal microbes to shape pseudosterile mouse models and further used for fecal microbial transplantation. However, few studies have explored the spatial location of antibiotic action in the intestine. This study shows that the selected antibiotics effectively deleted microbiota in the colon of mice, with limited effects on microbes in the jejunum and ileum. Our study provides guidance for the application of a mouse model of antibiotic deletion of intestinal microbes.
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Affiliation(s)
- Qingxue Chen
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Xinming Ma
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Zhishuang Xing
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Xin Zhao
- CABIO Biotech (Wuhan) Co., Ltd., Wuhan, China
| | - Hang Zu
- Heilongjiang Ubayt Dairy Group Co., Ltd., Qiqihaer, China
| | - Zengwang Guo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Bailiang Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
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131
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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132
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González-Reguero D, Robas-Mora M, Fernández-Pastrana VM, Probanza-Lobo A, Jiménez-Gómez PA. Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB. BIOLOGY 2023; 12:801. [PMID: 37372086 DOI: 10.3390/biology12060801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.
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Affiliation(s)
- Daniel González-Reguero
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Marina Robas-Mora
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Vanesa M Fernández-Pastrana
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Agustín Probanza-Lobo
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Pedro Antonio Jiménez-Gómez
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
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133
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Li W, Zhao J, Tian H, Shen Y, Wang Y, Shao M, Xiong T, Yao Y, Zhang L, Chen X, Xiao H, Xiong Y, Yang S, Tan C, Xu H. Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12598-x. [PMID: 37249588 DOI: 10.1007/s00253-023-12598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.
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Affiliation(s)
- Wenhao Li
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Junsong Zhao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Hong Tian
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Yanqiong Shen
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province, Zhaotong, 657000, Yunnan, China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province, Zhaotong, 657000, Yunnan, China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province, Zhaotong, 657000, Yunnan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Lin Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xinyu Chen
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Hongtao Xiao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ying Xiong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Cui Tan
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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134
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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135
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Xiao X, Hu AY, Dong XY, Shen RF, Zhao XQ. Involvement of the 4-coumarate:coenzyme A ligase 4CL4 in rice phosphorus acquisition and rhizosphere microbe recruitment via root growth enlargement. PLANTA 2023; 258:7. [PMID: 37222817 DOI: 10.1007/s00425-023-04158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/14/2023] [Indexed: 05/25/2023]
Abstract
MAIN CONCLUSION The 4-coumarate:coenzyme A ligase 4CL4 is involved in enhancing rice P acquisition and use in acid soil by enlarging root growth and boosting functional rhizosphere microbe recruitment. Rice (Oryza sativa L.) cannot easily acquire phosphorus (P) from acid soil, where root growth is inhibited and soil P is fixed. The combination of roots and rhizosphere microbiota is critical for plant P acquisition and soil P mobilization, but the associated molecular mechanism in rice is unclear. 4CL4/RAL1 encodes a 4-coumarate:coenzyme A ligase related to lignin biosynthesis in rice, and its dysfunction results in a small rice root system. In this study, soil culture and hydroponic experiments were conducted to examine the role of RAL1 in regulating rice P acquisition, fertilizer P use, and rhizosphere microbes in acid soil. Disruption of RAL1 markedly decreased root growth. Mutant rice plants exhibited decreased shoot growth, shoot P accumulation, and fertilizer P use efficiency when grown in soil-but not under hydroponic conditions, where all P is soluble and available for plants. Mutant ral1 and wild-type rice rhizospheres had distinct bacterial and fungal community structures, and wild-type rice recruited some genotype-specific microbial taxa associated with P solubilization. Our results highlight the function of 4CL4/RAL1 in enhancing rice P acquisition and use in acid soil, namely by enlarging root growth and boosting functional rhizosphere microbe recruitment. These findings can inform breeding strategies to improve P use efficiency through host genetic manipulation of root growth and rhizosphere microbiota.
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Affiliation(s)
- Xun Xiao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An Yong Hu
- School of Geographical Science, Nantong University, Nantong, 226019, China
| | - Xiao Ying Dong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue Qiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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136
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Chen H, Sun R, Wang J, Yao S, Batool SS, Yu Z, Huang S, Huang J. Bacillus amyloliquefaciens alleviates the pathological injuries in mice infected with Schistosoma japonicum by modulating intestinal microbiome. Front Cell Infect Microbiol 2023; 13:1172298. [PMID: 37265494 PMCID: PMC10230073 DOI: 10.3389/fcimb.2023.1172298] [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: 02/23/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Schistosoma japonicum causes serious pathological organ damage and alteration of the intestinal microbiome in the mammalian host, threatening the health of millions of people in China. Bacillus amyloliquefaciens has been reported to be able to alleviate the damage to the gut and liver and maintain the homeostasis of the intestinal microenvironment. However, it was unclear whether B. amyloliquefaciens could alleviate the hepatic and intestinal symptoms caused by S. japonicum. In this study, the intragastric administration of B. amyloliquefaciens was performed to treat S. japonicum-infected mice during the acute phase. Histopathological analysis and 16S rRNA gene sequencing were used to evaluate the pathological damage and changes in the intestinal microbiome. The results of the study showed that B. amyloliquefaciens treatment significantly reduced the degree of granuloma and fibrosis in infected mice. Additionally, recovery of diversity in the intestinal microbiome, decrease in the relative abundance of potential pathogenic bacteria such as Escherichia-Shigella, and reshaping of the interactive network between genera in the intestine were also observed after treatment with B. amyloliquefaciens. Our findings indicated that treatment with B. amyloliquefaciens effectively alleviated the pathological injuries of the liver and intestine in mice infected with S. japonicum by modulating the intestinal microbiome, implying that this probiotic can function as an effective therapeutic agent against schistosomiasis. We hope our study will provide auxiliary strategies and methods for the early prevention of schistosomiasis japonica.
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Affiliation(s)
- Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Ruizheng Sun
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jingyan Wang
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Siqi Yao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Syeda Sundas Batool
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Zheng Yu
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Shuaiqin Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
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137
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Liang X, Zhou K, Li P, Wan D, Liu J, Yi X, Peng Y. Characteristics of endophytic bacteria and active ingredients in the Eucommiae cortex from different origins. Front Microbiol 2023; 14:1164674. [PMID: 37266017 PMCID: PMC10229866 DOI: 10.3389/fmicb.2023.1164674] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Objective This study aimed to explore the differences between Eucommiae cortex (EC) endophytic bacteria from different origins and their effects on the active ingredients of EC. Methods A total of 10 samples of Eucommia ulmoides Oliv. (E. ulmoides) bark were collected from each of the following four regions, namely, Zunyi in Guizhou (GZ), Baokang in Hubei (HUB), Cili in Hunan (HUN), and Loyang in Shaanxi (SX). Subsequently, the contents of the main active ingredients of EC were determined by ultra-performance liquid chromatography (UPLC), and the endophytic bacteria of EC were detected by 16S rRNA sequencing. The relationship between the dominant endophytic bacteria and the active ingredients was investigated by correlation analysis. Results A total of 4,551 different operational taxonomic units (OTUs) were delineated in the four groups of samples, of which 585, 439, 957, and 684 genera were annotated from GZ, HUB, HUN, and SX, respectively. The richness and diversity of endophytic bacteria from different origins were ranked as HUN > SX > GZ or HUB. The analysis demonstrated that there was no significant correlation between the diversity and richness of endophytic bacteria in EC and its active ingredients. Nevertheless, notable variations in the community structures of endophytic bacteria were observed across different origins, and they had a considerable impact on certain active ingredients in EC. Comamonas and Cedecea were the dominant genera. Characteristic bacteria of different origins could be clearly distinguished. Simultaneous, significant correlations had been identified between some characteristic endophytic bacteria derived from different origins and active ingredients of EC. For example, Delftia, a characteristic bacterium from GZ, showed a significant positive correlation with pinoresinol diglucoside. Paenibacillus and Klebsiella, two characteristic bacteria from HUB, exhibited significant positive correlations with geniposidic acid. Thauera, a characteristic bacterium from HUN, demonstrated a significant positive correlation with geniposide. Brevundimonas, a characteristic bacterium from SX, displayed a significant positive correlation with pinoresinol diglucoside. Conclusion There was a complex correlation between EC endophytic bacteria and active ingredient content, while EC endophytic bacteria from different origins had significant differences at the genus level.
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Affiliation(s)
- Xuejuan Liang
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Kang Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Penghui Li
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Dan Wan
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jing Liu
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Xin Yi
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Yanmei Peng
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
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138
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Mappa C, Alpha-Bazin B, Pible O, Armengaud J. Mix24X, a Lab-Assembled Reference to Evaluate Interpretation Procedures for Tandem Mass Spectrometry Proteotyping of Complex Samples. Int J Mol Sci 2023; 24:ijms24108634. [PMID: 37239979 DOI: 10.3390/ijms24108634] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Correct identification of the microorganisms present in a complex sample is a crucial issue. Proteotyping based on tandem mass spectrometry can help establish an inventory of organisms present in a sample. Evaluation of bioinformatics strategies and tools for mining the recorded datasets is essential to establish confidence in the results obtained and to improve these pipelines in terms of sensitivity and accuracy. Here, we propose several tandem mass spectrometry datasets recorded on an artificial reference consortium comprising 24 bacterial species. This assemblage of environmental and pathogenic bacteria covers 20 different genera and 5 bacterial phyla. The dataset comprises difficult cases, such as the Shigella flexneri species, which is closely related to Escherichia coli, and several highly sequenced clades. Different acquisition strategies simulate real-life scenarios: from rapid survey sampling to exhaustive analysis. We provide access to individual proteomes of each bacterium separately to provide a rational basis for evaluating the assignment strategy of MS/MS spectra when recorded from complex mixtures. This resource should provide an interesting common reference for developers who wish to compare their proteotyping tools and for those interested in evaluating protein assignment when dealing with complex samples, such as microbiomes.
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Affiliation(s)
- Charlotte Mappa
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
- Laboratoire Innovations Technologiques Pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols sur Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
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139
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Chen X, Wang Y, Wang Y, Zhang Y, Shen Y, He X, Xiao C. A Natural Moisture Gradient Affects Soil Fungal Communities on the South Shore of Hulun Lake, Inner Mongolia, China. J Fungi (Basel) 2023; 9:jof9050549. [PMID: 37233260 DOI: 10.3390/jof9050549] [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: 02/20/2023] [Revised: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 05/27/2023] Open
Abstract
Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we set up a natural moisture gradient that was subdivided into high (HW), medium (MW), and low (LW) water contents. Vegetation was investigated by quadrat method, and aboveground biomass was collected by the mowing method. Soil physicochemical properties were obtained by internal experiments. The composition of the soil fungal community was determined using high-throughput sequencing technology. The results showed significant differences in soil texture, nutrients, and fungal species diversity under the moisture gradients. Although there was significant clustering of fungal communities in different treatments, the fungal community composition was not significantly different. According to the phylogenetic tree, the Ascomycota and Basidiomycota were the most important branches. The fungal species diversity was smaller when SWC was higher, and in this environment (HW), the fungal-dominant species were significantly related to SWC and soil nutrients. At this time, soil clay formed a protective barrier for the survival of the dominant classes Sordariomycetes and Dothideomycetes and increased their relative abundance. In summary, the fungal community responded significantly to SWC on the southern shore of the Hulun Lake ecosystem in Inner Mongolia, China, and the fungal community composition of the HW group was stable and easier to survive.
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Affiliation(s)
- Xin Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yujue Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yushu Zhang
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yuting Shen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing 100038, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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140
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Yang Q, Zhang P, Li X, Yang S, Chao X, Liu H, Ba S. Distribution patterns and community assembly processes of eukaryotic microorganisms along an altitudinal gradient in the middle reaches of the Yarlung Zangbo River. WATER RESEARCH 2023; 239:120047. [PMID: 37167854 DOI: 10.1016/j.watres.2023.120047] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/10/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
Eukaryotic microorganisms play an important role in the biogeochemical cycles of rivers. Dynamic hydrological processes in rivers are thought to influence the assembly processes of eukaryotic microbes, as well as affecting local geomorphology. These processes have not been extensively studied for eukaryotic river microbes in extreme environments on the Tibetan Plateau. This study used 18S rDNA gene amplification sequencing, a neutral community model, and a null model to analyze the spatial and temporal dynamics and assembly processes of eukaryotic microbial communities in the middle reaches of the Yarlung Zangbo River. We conducted analyses across wet and dry seasons, as well as varying altitudinal gradients. Our results showed that the diversity, structure, and taxonomic composition of eukaryotic microbial communities varied more with altitude than season, and the diversity of the communities first increased, then decreased, with increasing elevation. Distance-decay analysis showed that the correlation between eukaryotic microbial communities and environmental distance was stronger than the correlation between the microbial communities and geographical distance. Deterministic processes (homogeneous selection) dominated the construction of eukaryotic microbial communities, and water temperature, pH, and total phosphorus were the primary environmental factors that influenced the construction of eukaryotic microbial communities. These results expand our understanding of the characteristics of eukaryotic microbial communities in rivers on the Tibetan Plateau and provide clues to understanding the mechanisms that maintain eukaryotic microbial diversity in extreme environments.
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Affiliation(s)
- Qing Yang
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China
| | - Peng Zhang
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China
| | - Xiaodong Li
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China
| | - Shengxian Yang
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China
| | - Xin Chao
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China
| | - Huiqiu Liu
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China
| | - Sang Ba
- Laboratory of Wetland and Watershed Ecosystems of Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa 850000, China.
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141
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Fan X, Chen H, Yan G, Ye M, Yin C, Li T, Wakelin SA, Liang Y. Niche Differentiation Among Canonical Nitrifiers and N 2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils. MICROBIAL ECOLOGY 2023; 85:1434-1447. [PMID: 35420314 DOI: 10.1007/s00248-022-02006-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/29/2022] [Indexed: 05/10/2023]
Abstract
The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.
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Affiliation(s)
- Xiaoping Fan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guochao Yan
- Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Mujun Ye
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chang Yin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | | | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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142
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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143
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Wang B, Zhang L, Shi J, Su Y, Wu D, Xie B. Genome-centric metagenomics revealed functional traits in high-solids anaerobic co-digestion of restaurant food waste, household food waste and rice straw. BIORESOURCE TECHNOLOGY 2023; 376:128926. [PMID: 36940870 DOI: 10.1016/j.biortech.2023.128926] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
High-solids anaerobic co-digestion (HS-AcoD) of food waste (FW) and other organic wastes is an effective option to improve the biogas production and system stability compared to mono-digestion. However, the clean and sustainable HS-AcoD strategy for FW and associated microbial functional traits have not been well explored. Here, HS-AcoD of restaurant food waste (RFW), household food waste (HFW) and rice straw (RS) were performed. Results showed that the maximum synergy index (SI) of 1.28 were achieved when the volatile solids ratio of RFW, HFW and RS was 0.45:0.45:0.1. HS-AcoD alleviated the acidification process by regulating metabolism associated with hydrolysis and volatile fatty acids formation. The synergistic relationship between syntrophic bacteria and Methanothrix sp., and the enhanced metabolic capacity associated with the acetotrophic and hydrogenotrophic pathways dominated by Methanothrix sp., provided a further explanation of the synergistic mechanism. These findings advance the knowledge about microbial mechanisms underlying the synergistic effect of HS-AcoD.
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Affiliation(s)
- Binghan Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Liangmao Zhang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Jianhong Shi
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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144
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Wang B, Zhu C, Hu Y, Zhang B, Wang J. Dynamics of microbial community composition during degradation of silks in burial environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163694. [PMID: 37100151 DOI: 10.1016/j.scitotenv.2023.163694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
The silk residues in the soil formed the unique niche, termed "silksphere." Here, we proposed a hypothesis that silksphere microbiota have great potential as a biomarker for unraveling the degradation of the ancient silk textiles with great archaeological and conservation values. To test our hypothesis, in this study, we monitored the dynamics of microbial community composition during silk degradation via both indoor soil microcosmos model and outdoor environment with amplicon sequencing against 16S and ITS gene. Microbial community divergence was evaluated with Welch two sample t-test, PCoA, negative binomial generalized log-linear model and clustering, etc. Community assembly mechanisms differences between silksphere and bulk soil microbiota were compared with dissimilarity-overlap curve (DOC) model, Neutral model and Null model. A well-established machine learning algorithm, random forest, was also applied to the screening of potential biomarkers of silk degradation. The results illustrated the ecological and microbial variability during the microbial degradation of silk. Vast majority of microbes populating the silksphere microbiota strongly diverged from those in bulk soil. Certain microbial flora can serve as an indicator of silk degradation, which would lead to a novel perspective to perform identification of archaeological silk residues in the field. To sum up, this study provides a new perspective to perform the identification of archaeological silk residue through the dynamics of microbial communities.
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Affiliation(s)
- Bowen Wang
- Department of Archaeology, Cultural Heritage and Museology, Zhejiang University, Hangzhou 310028, China
| | - Chengshuai Zhu
- Department of Archaeology, Cultural Heritage and Museology, Zhejiang University, Hangzhou 310028, China
| | - Yulan Hu
- Department of Archaeology, Cultural Heritage and Museology, Zhejiang University, Hangzhou 310028, China.
| | - Bingjian Zhang
- Department of Archaeology, Cultural Heritage and Museology, Zhejiang University, Hangzhou 310028, China
| | - Jianlan Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, 201620, China; School of Conservation, Shanghai Institute of Visual Arts, Shanghai 201620, China; Archaeology Program, Boston University, 675 Commonwealth Avenue, 02215 Boston, MA, USA.
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145
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Xue Z, Tian W, Han Y, Feng Z, Wang Y, Zhang W. The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163666. [PMID: 37094681 DOI: 10.1016/j.scitotenv.2023.163666] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
With the rapid globalization of trade, the worldwide spread of pathogens through ballast water is becoming a major concern. Although the international maritime organization (IMO) convention has been adopted to prevent the spread of harmful pathogens, the limited species resolution of the current microbe-monitoring methods challenged the ballast water and sediments management (BWSM). In this study, we explored metagenomic sequencing to investigate the species composition of microbial communities in four international vessels for BWSM. Our results showed the largest species diversity (14,403) in ballast water and sediments, including bacteria (11,710), eukaryotes (1007), archaea (829), and viruses (790). A total of 129 phyla were detected, among which the Proteobacteria, followed by Bacteroidetes, and Actinobacteria were the most abundant. Notably, 422 pathogens that are potentially harmful to marine environments and aquaculture were identified. The co-occurrence network analysis showed that most of these pathogens were positively correlated with the commonly used indicator bacteria Vibrio cholerae, Escherichia coli, and intestinal Enterococci species, validating the D-2 standard in BWSM. The functional profile showed prominent pathways of methane and sulfur metabolism, indicating that the microbial community in the severe tank environment still utilizes the energy to sustain such a high level of microbe diversity. In conclusion, metagenomic sequencing provides novel information for BWSM.
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Affiliation(s)
- Zhaozhao Xue
- Marine College, Shandong University, Weihai, China
| | - Wen Tian
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Yangchun Han
- Integarted Technical Service Center of Jiangyin Customs, Jiangyin, China
| | - Zhen Feng
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Yu Wang
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, China.
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146
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Li C, Jia Z, Zhang S, Li T, Ma S, Cheng X, Chen M, Nie H, Zhai L, Zhang B, Liu X, Zhang J, Müller C. The positive effects of mineral-solubilizing microbial inoculants on asymbiotic nitrogen fixation of abandoned mine soils are driven by keystone phylotype. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163663. [PMID: 37094687 DOI: 10.1016/j.scitotenv.2023.163663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/03/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Toward the restoration of the increasing numbers of abandoned mines across China, external-soil spray seeding technologies have become more extensively utilized. However, considerable challenges remain that seriously hamper the effectiveness of these technologies, such as inadequate nutrient availability for plants. Previous studies have shown that mineral-solubilizing microbial inoculants can increase the nodules of legumes. However, their effects on symbiotic nitrogen fixation (SNF), asymbiotic nitrogen fixation (ANF), and diazotrophic communities remain unknown. Further, research into the application of functional microorganisms for the restoration of abandoned mines has been conducted either in greenhouses, or their application in the field has been too brief. Thus, we established a four-year field experiment in an abandoned mine and quantified the SNF, ANF, and diazotrophic communities. To the best of our knowledge, this study is the first to describe the long-term application of specific functional microorganisms for the remediation of abandoned mine sites in the field. We revealed that mineral-solubilizing microbial inoculants significantly increased the soil ANF rate and SNF content. There was no significant correlation between the diazotrophic alpha diversity and soil ANF rate; however, there were strong positive associations between the relative abundance and biodiversity of keystone phylotype (module #5) within ecological clusters and the ANF rate. Molecular ecological networks indicated that microbial inoculants increased network complexity and stability. Moreover, the inoculants significantly enhanced the deterministic ratio of diazotrophic communities. Furthermore, homogeneous selection predominantly mediated the assembly of soil diazotrophic communities. It was concluded that mineral-solubilizing microorganisms played a critical role in maintaining and enhancing nitrogen, which offers a new solution with great potential for the restoration of ecosystems at abandoned mine sites.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China; Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany.
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Shuifeng Zhang
- Faculty of Information Technology, Nanjing Forest Police College, Nanjing 210000, China.
| | - Tao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Xuefei Cheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Meiling Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Hui Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK 74078, USA; Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland; Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Germany.
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147
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Han X, Liu D, Zhang M, He M, Li J, Zhu X, Wang M, Thongklang N, Zhao R, Cao B. Macrofungal Diversity and Distribution Patterns in the Primary Forests of the Shaluli Mountains. J Fungi (Basel) 2023; 9:jof9040491. [PMID: 37108945 PMCID: PMC10141676 DOI: 10.3390/jof9040491] [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: 02/27/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The Shaluli Mountains are located in the southeastern part of the Tibetan Plateau at an elevation of 2500-5000 m. They are characterized by a typical vertical distribution of climate and vegetation and are considered a global biodiversity hotspot. We selected ten vegetation types at different elevation gradients representing distinct forests in the Shaluli Mountains to assess the macrofungal diversity, including subalpine shrub, Pinus spp., Populus spp., Pinus spp. and Quercus spp., Quercus spp., Abies spp., Picea spp. and Abies spp., Picea spp., Juniperus spp., and alpine meadow. In total, 1654 macrofungal specimens were collected. All specimens were distinguished by morphology and DNA barcoding, resulting in the identification of 766 species belonging to 177 genera in two phyla, eight classes, 22 orders, and 72 families. Macrofungal species composition varied widely among vegetation types, but ectomycorrhizal fungi were predominant. In this study, the analysis of observed species richness, the Chao1 diversity index, the invsimpson diversity index, and the Shannon diversity index revealed that the vegetation types with higher macrofungal alpha diversity in the Shaluli Mountains were composed of Abies, Picea, and Quercus. The vegetation types with lower macrofungal alpha diversity were subalpine shrub, Pinus spp., Juniperus spp., and alpine meadow. The results of curve-fitting regression analysis showed that macrofungal diversity in the Shaluli Mountains was closely related to elevation, with a trend of increasing and then decreasing with rising elevation. This distribution of diversity is consistent with the hump-shaped pattern. Constrained principal coordinate analysis based on Bray-Curtis distances indicated that macrofungal community composition was similar among vegetation types at similar elevations, while vegetation types with large differences in elevation differed significantly in macrofungal community composition. This suggests that large changes in elevation increase macrofungal community turnover. This study is the first investigation of the distribution pattern of macrofungal diversity under different vegetation types in high-altitude areas, providing a scientific basis for the conservation of macrofungal resources.
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Affiliation(s)
- Xixi Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Dongmei Liu
- Institue of Ecology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Mingzhe Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoqiang He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaxin Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Zhu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Meiqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naritsada Thongklang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Ruilin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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148
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Wen L, Yang L, Chen C, Li J, Fu J, Liu G, Kan Q, Ho CT, Huang Q, Lan Y, Cao Y. Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods. Crit Rev Food Sci Nutr 2023:1-17. [PMID: 37068005 DOI: 10.1080/10408398.2023.2199425] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.
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Affiliation(s)
- Linfeng Wen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lixin Yang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Cong Chen
- Guangdong Eco-engineering Polytechnic, Guangzhou, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Jiangyan Fu
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Guo Liu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qixin Kan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Qingrong Huang
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Yaqi Lan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
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149
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Kumar R, Yadav G, Kuddus M, Ashraf GM, Singh R. Unlocking the microbial studies through computational approaches: how far have we reached? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:48929-48947. [PMID: 36920617 PMCID: PMC10016191 DOI: 10.1007/s11356-023-26220-0] [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: 03/23/2022] [Accepted: 02/24/2023] [Indexed: 04/16/2023]
Abstract
The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.
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Affiliation(s)
- Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Garima Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah , 27272, United Arab Emirates
| | - Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India.
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150
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Liu H, Yao J, Liu B, Li M, Liu J, Jiang S, Yu W, Zhao Y, Duran R. Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161133. [PMID: 36566868 DOI: 10.1016/j.scitotenv.2022.161133] [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: 11/02/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.
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Affiliation(s)
- Houquan Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China.
| | - Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| | - Miaomiao Li
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jianli Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shun Jiang
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Wenjing Yu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Yuhui Zhao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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