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Li W, Zhang Z, Xie B, He Y, He K, Qiu H, Lu Z, Jiang C, Pan X, He Y, Hu W, Liu W, Que T, Hu Y. HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data. Comput Struct Biotechnol J 2024; 23:659-668. [PMID: 38292471 PMCID: PMC10824657 DOI: 10.1016/j.csbj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Analyzing the vast amount of omics data generated comprehensively by high-throughput sequencing technology is of utmost importance for scientists. In this context, we propose HiOmics, a cloud-based platform equipped with nearly 300 plugins designed for the comprehensive analysis and visualization of omics data. HiOmics utilizes the Element Plus framework to craft a user-friendly interface and harnesses Docker container technology to ensure the reliability and reproducibility of data analysis results. Furthermore, HiOmics employs the Workflow Description Language and Cromwell engine to construct workflows, ensuring the portability of data analysis and simplifying the examination of intricate data. Additionally, HiOmics has developed DataCheck, a tool based on Golang, which verifies and converts data formats. Finally, by leveraging the object storage technology and batch computing capabilities of public cloud platforms, HiOmics enables the storage and processing of large-scale data while maintaining resource independence among users.
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Affiliation(s)
- Wen Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Zhining Zhang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Bo Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Yunlin He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Kangming He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Hong Qiu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Zhiwei Lu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Chunlan Jiang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Xuanyu Pan
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuxiao He
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Hu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Wenjian Liu
- Faculty of Data Science, City University of Macau, Macau, China
| | - Tengcheng Que
- Faculty of Data Science, City University of Macau, Macau, China
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Guangxi Zhuang Autonomous Terrestrial Wildlife Rescue Research and Epidemic Diseases Monitoring Center, Nanning, Guangxi, China
| | - Yanling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
- Faculty of Data Science, City University of Macau, Macau, China
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Mo F, Li C, Zhou Q. The pivotal role of phosphorus level gradient in regulating nitrogen cycle in wetland ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173646. [PMID: 38821288 DOI: 10.1016/j.scitotenv.2024.173646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Phosphorus (P) is one of key drivers in Earth's nitrogen (N) cycle, however, the global overview of the P-regulated microbial community structure and gene abundance carrying wetland N process remains to be investigated. The key environmental factors that influenced wetland N cycle were initially screened, verifying the central role P. More complex and stable community interaction can be established in rich (20 mg/kg < P ≤ 100 mg/kg) and surplus P groups (P > 100 mg/kg) compared to that in deficient P group (P ≤ 20 mg/kg), with enhanced participation of betaproteobacteria and actinobacteria (i.e., changed hub microorganisms). Accordingly, P-mediated variations in gene expression patterns can be expected. On the one hand, the gene responses to carbon (C), N, and P factors presented nearly synchronous variation, highlighting the potential C-N-P coupling cycle in wetland ecosystem. On the other hand, the gene sensitivity towards environmental factors was changed at different P levels. Overall, the P level gradient can influence N cycle in direct (i.e., influences on gene abundances) and indirect (i.e., influences on gene response to environmental factors) manners. These findings provide important insights for controlling the N cycle in wetland ecosystems, particularly in cases where P levels are limiting factors.
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Affiliation(s)
- Fan Mo
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Interdisciplinary Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Chenghao Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Interdisciplinary Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Interdisciplinary Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Zheng W, Fan X, Chen H, Ye M, Yin C, Wu C, Liang Y. The response patterns of r- and K-strategist bacteria to long-term organic and inorganic fertilization regimes within the microbial food web are closely linked to rice production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173681. [PMID: 38844210 DOI: 10.1016/j.scitotenv.2024.173681] [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: 03/30/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024]
Abstract
Soil microbial food web is crucial for maintaining crop production, while its community structure varies among fertilization regimes. Currently, the mechanistic understanding of the relationships between microbial food web and crop production under various nutrient fertilizations is poor. This knowledge gap limits our capacity to achieve precision agriculture for ensuring yield stability. In this study, we investigated the abiotic (i.e., soil chemical properties) and biotic factors (i.e., microbial food web, including bacteria, fungi, archaea and nematodes) that were closely associated with rice (Oryza sativa L.) production, using soils from seven fertilization regimes in distinct sampling locations (i.e., bulk vs rhizosphere soil) at a long-term experimental site. Organic manure alone fertilization (M) and integrated fertilization (NPKM) combining manure with inorganic fertilizers increased soil pH by 0.21-0.41 units and organic carbon content by 49.1 %-65.2 % relative to the non-fertilization (CK), which was distinct with inorganic fertilization. The principal coordinate analysis (PCoA) revealed that soil microbial and nematode communities were primarily shaped by fertilization rather than sampling locations. Organic fertilization (M, NPKM) increased the relative abundance of both r-strategist bacteria, specific taxa within the fungal (i.e., Pezizales) and nematode communities (i.e., omnivores-predators), whereas inorganic fertilization increased K-strategist bacteria abundances relative to the CK. Correspondingly, network analysis showed that the keystone taxa in the amplicon sequence variants (ASVs) enriched by organic manure and inorganic fertilization were mainly affiliated with r- and K-strategist bacteria, respectively. Structural equation modeling (SEM) analysis found that r- and K-strategist bacteria were positively correlated with rice production under organic and inorganic fertilization, respectively. Our results demonstrate that the response patterns of r/K-strategists to nutrient fertilization largely regulate rice yield, suggesting that the enhanced soil fertility and r-strategists contribute to the highest crop production in NPKM fertilization.
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Affiliation(s)
- Wanning Zheng
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - 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
| | - 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
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chunyan Wu
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, 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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Lin X, Xu G, Li Y, Yu Y. Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173737. [PMID: 38844214 DOI: 10.1016/j.scitotenv.2024.173737] [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: 03/28/2024] [Revised: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.
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Affiliation(s)
- Xiaolong Lin
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; School of Agriculture, Sun Yat-sen University, Guangzhou 510275, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Chen CY, Wang YF, Lei L, Zhang Y. Impacts of microbiota and its metabolites through gut-brain axis on pathophysiology of major depressive disorder. Life Sci 2024; 351:122815. [PMID: 38866215 DOI: 10.1016/j.lfs.2024.122815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
Major depressive disorder (MDD) is characterized by a high rate of recurrence and disability, which seriously affects the quality of life of patients. That's why a deeper understanding of the mechanisms of MDD pathology is an urgent task, and some studies have found that intestinal symptoms accompany people with MDD. The microbiota-gut-brain axis is the bidirectional communication between the gut microbiota and the central nervous system, which was found to have a strong association with the pathogenesis of MDD. Previous studies have focused more on the communication between the gut and the brain through neuroendocrine, neuroimmune and autonomic pathways, and the role of gut microbes and their metabolites in depression is unclear. Metabolites of intestinal microorganisms (e.g., tryptophan, kynurenic acid, indole, and lipopolysaccharide) can participate in the pathogenesis of MDD through immune and inflammatory pathways or by altering the permeability of the gut and blood-brain barrier. In addition, intestinal microbes can communicate with intestinal neurons and glial cells to affect the integrity and function of intestinal nerves. However, the specific role of gut microbes and their metabolites in the pathogenesis of MDD is not well understood. Hence, the present review summarizes how gut microbes and their metabolites are directly or indirectly involved in the pathogenesis of MDD.
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Affiliation(s)
- Cong-Ya Chen
- Department of Anatomy, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yu-Fei Wang
- Department of Anatomy, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Lan Lei
- Department of Anatomy, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yi Zhang
- Department of Anatomy, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China.
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Chen M, Cao Z, Jing B, Chen W, Wen X, Han M, Wang Y, Liao X, Wu Y, Chen T. The production of methyl mercaptan is the main odor source of chicken manure treated with a vertical aerobic fermenter. ENVIRONMENTAL RESEARCH 2024:119634. [PMID: 39029729 DOI: 10.1016/j.envres.2024.119634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/21/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
The process of harmless treatment of livestock manure produces a large amount of odor, which poses a potential threat to human and livestock health. A vertical fermentation tank system is commonly used for the environmentally sound treatment of chicken manure in China, but the composition and concentration of the odor produced and the factors affecting odor emissions remain unclear. In this study, we investigated the types and concentrations of odors produced in the mixing room (MR), vertical fermenter (VF), and aging room (AR) of the system, and analyzed the effects of bacterial communities and metabolic genes on odor production. The results revealed that 34, 26 and 26 odors were detected in the VF, MR and AR, respectively. The total odor concentration in the VF was 66613 ± 10097, which was significantly greater than that in the MR (1157 ± 675) and AR (1143 ± 1005) (P < 0.001), suggesting that the VF was the main source of odor in the vertical fermentation tank system. Methyl mercaptan had the greatest contribution to the odor produced by VF, reaching 47.82%, and the concentration was 0.6145 ± 0.2164 mg/m3. The abundance of metabolic genes did not correlate significantly with odor production, but PICRUSt analysis showed that cysteine and methionine metabolism involved in methyl mercaptan production was significantly more enriched in MR and VF than in AR. Bacillus was the most abundant genus in the VF, with a relative abundance significantly greater than that in the MR (P < 0.05). The RDA results revealed that Bacillus was significantly and positively correlated with methyl mercaptan. The use of large-scale aerobic fermentation systems to treat chicken manure needs to focused on the production of methyl mercaptan.
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Affiliation(s)
- Majian Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Cao
- Wen's Foodstuff Group Co., Ltd., Yunfu 527400, China
| | - Boyu Jing
- State Environmental Protection Key Laboratory of Odor Pollution Control, Tianjin Academy of Eco-environmental Sciences, Tianjin 300191, China
| | - Wenjun Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Meng Han
- State Environmental Protection Key Laboratory of Odor Pollution Control, Tianjin Academy of Eco-environmental Sciences, Tianjin 300191, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
| | - Tao Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Beibei L, Mengying W, Xiao H, Yuzi J, Lijin M, Ke Z, Shengjie Y, Li L. Dysbiosis and interactions of the mycobiome and bacteriome in mucosal lesions of erosive and non-erosive oral lichen planus patients. J Oral Microbiol 2024; 16:2374639. [PMID: 38979477 PMCID: PMC11229720 DOI: 10.1080/20002297.2024.2374639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
Background Oral lichen planus (OLP) is a common oral mucosal disease, clinically categorized into erosive OLP (EOLP) and non-erosive OLP (NEOLP) based on symptoms, but its pathogenic mechanism remains unclear. This study aims to explore the relationship between OLP and the oral microbiome. Methods We collected oral mucosal samples from 49 patients and 10 healthy individuals and conducted 16S rRNA and ITS gene sequencing to explore the oral fungal and bacterial communities. Results We observed significantly lower α diversity of fungi in the EOLP group, with Candida being significantly enriched as the main dominant genus. In the NEOLP group, Aspergillaceae were significantly enriched. The EOLP group showed significant enrichment of Aggregatibacter and Lactobacillus, but the relative abundance of Streptococcus was notably lower than in the other two groups. In the NEOLP group, two species including Prevotella intermedia were significantly enriched. The microbial co-occurrence and co-exclusion networks display distinct characteristics across the three groups, with Lactobacillus assuming a significant bridging role in the ELOP group. Conclusions Our study indicates that EOLP and NEOLP experience varying degrees of dysbiosis at both the fungal and bacterial levels. Therefore, the pathogenic mechanisms and interactive relationships of these microbiota associated with OLP merit further in-depth investigation.
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Affiliation(s)
- Liang Beibei
- Hebei Key Laboratory of Stomatology, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Wei Mengying
- Department of Dental Pulp, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Huo Xiao
- Department of Oral Mucosa, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Jing Yuzi
- School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Mi Lijin
- Department of Oral Mucosa, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Zhang Ke
- Department of Oral Mucosa, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Yi Shengjie
- School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Liu Li
- Department of Oral Mucosa, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
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Chen C, Yang H, Zhang K, Ye G, Luo H, Zou W. Revealing microbiota characteristics and predicting flavor-producing sub-communities in Nongxiangxing baijiu pit mud through metagenomic analysis and metabolic modeling. Food Res Int 2024; 188:114507. [PMID: 38823882 DOI: 10.1016/j.foodres.2024.114507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum, Caproicibacterium, Petrimonas, Lactobacillus, Clostridium, Aminobacterium, Syntrophomonas, Methanobacterium, Methanoculleus, and Methanosarcina. The important enzymes ofPMwere in bothGH and GT familymetabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium, Sphaerochaeta, Muricomes intestini, Methanobacteriaceae, Synergistaceae, and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite-microbiome association and further bioregulation of baijiu.
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Affiliation(s)
- Cong Chen
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Huibo Luo
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, Sichuan 644005, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China; Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, Sichuan 644005, China.
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Mac Aogáin M, Dicker AJ, Mertsch P, Chotirmall SH. Infection and the microbiome in bronchiectasis. Eur Respir Rev 2024; 33:240038. [PMID: 38960615 PMCID: PMC11220623 DOI: 10.1183/16000617.0038-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.
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Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alison J Dicker
- Respiratory Research Group, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Pontus Mertsch
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center (CPC), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
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Olbrich M, Hartmann AM, Künzel S, Aherrahrou Z, Schilf P, Baines JF, Ibrahim SM, Hirose M. Mitochondrial DNA variants and microbiota: An experimental strategy to identify novel therapeutic potential in chronic inflammatory diseases. Pharmacol Res 2024; 205:107231. [PMID: 38815878 DOI: 10.1016/j.phrs.2024.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/06/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
We previously demonstrated that mice carrying natural mtDNA variants of the FVB/NJ strain (m.7778 G>T in the mt-Atp8 gene in mitochondrial complex V), namely C57BL/6 J-mtFVB/NJ (B6-mtFVB), exhibited (i) partial protection from experimental skin inflammatory diseases in an anti-murine type VII collagen antibody-induced skin inflammation model and psoriasiform dermatitis model; (ii) significantly altered metabolites, including short-chain fatty acids, according to targeted metabolomics of liver, skin and lymph node samples; and (iii) a differential composition of the gut microbiota according to bacterial 16 S rRNA gene sequencing of stool samples compared to wild-type C57BL/6 J (B6) mice. To further dissect these disease-contributing factors, we induced an experimental antibody-induced skin inflammatory disease in gnotobiotic mice. We performed shotgun metagenomic sequencing of caecum contents and untargeted metabolomics of liver, CD4+ T cell, and caecum content samples from conventional B6-mtFVB and B6 mice. We identified D-glucosamine as a candidate mediator that ameliorated disease severity in experimental antibody-induced skin inflammation by modulating immune cell function in T cells, neutrophils and macrophages. Because mice carrying mtDNA variants of the FVB/NJ strain show differential disease susceptibility to a wide range of experimental diseases, including diet-induced atherosclerosis in low-density lipoprotein receptor knockout mice and collagen antibody-induced arthritis in DBA/1 J mice, this experimental approach is valuable for identifying novel therapeutic options for skin inflammatory conditions and other chronic inflammatory diseases to which mice carrying specific mtDNA variants show differential susceptibility.
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Affiliation(s)
- Michael Olbrich
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates; University Heart Centre Lübeck, Lübeck, Germany
| | | | - Sven Künzel
- Max Plank Institute of Evolutionary Biology, Plön, Germany; University Heart Centre Lübeck, Lübeck, Germany
| | - Zouhair Aherrahrou
- Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg / Kiel / Lübeck, Germany; University Heart Centre Lübeck, Lübeck, Germany
| | - Paul Schilf
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; University Heart Centre Lübeck, Lübeck, Germany
| | - John F Baines
- Max Plank Institute of Evolutionary Biology, Plön, Germany; University Heart Centre Lübeck, Lübeck, Germany; Institute of Experimental Medicine, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Saleh M Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates; University Heart Centre Lübeck, Lübeck, Germany; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; University Heart Centre Lübeck, Lübeck, Germany; Lübeck Institute of Neurobiology, University of Lübeck, Germany.
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11
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Rowe L, Dowd SE, Davidson K, Kovarik C, VanAken M, Jarabek A, Taylor C. Comparing microbial populations from diverse hydrothermal features in Yellowstone National Park: hot springs and mud volcanoes. Front Microbiol 2024; 15:1409664. [PMID: 38993494 PMCID: PMC11236564 DOI: 10.3389/fmicb.2024.1409664] [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: 03/30/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Geothermal features, such as hot springs and mud volcanoes, host diverse microbial life, including many extremophile organisms. The physicochemical parameters of the geothermal feature, such as temperature, pH, and heavy metal concentration, can influence the alpha and beta diversity of microbial life in these environments, as can spatiotemporal differences between sites and sampling. In this study, water and sediment samples were collected and analyzed from eight geothermal sites at Yellowstone National Park, including six hot springs, a mud volcano, and an acidic lake within the same week in July 2019, and these geothermal sites varied greatly in their temperature, pH, and chemical composition. All samples were processed and analyzed with the same methodology and taxonomic profiles and alpha and beta diversity metrics determined with 16S rRNA sequencing. These microbial diversity results were then analyzed with respect to pH, temperature, and chemical composition of the geothermal features. Results indicated that predominant microbial species varied greatly depending on the physicochemical composition of the geothermal site, with decreases in pH and increases in dissolved heavy metals in the water corresponding to decreases in alpha diversity, especially in the sediment samples. Similarly, sites with acidic pH values had more similar microbial populations (beta diversity) to one another than to relatively neutral or alkaline pH geothermal sites. This study suggests that pH and/or heavy metal concentration is a more important driver for microbial diversity and population profile than the temperature for these sites and is also the first reported microbial diversity study for multiple geothermal sites in Yellowstone National Park, including the relatively new mud volcano Black Dragon's Caldron, which erupted in 1948.
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Affiliation(s)
- Laura Rowe
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA Lab), Shallowater, TX, United States
| | - Kelly Davidson
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Claire Kovarik
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Michayla VanAken
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Alyssa Jarabek
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Churro Taylor
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
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12
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Li Q, Gu Y, Liang J, Yang Z, Qin J. A long journey to treat epilepsy with the gut microbiota. Front Cell Neurosci 2024; 18:1386205. [PMID: 38988662 PMCID: PMC11233807 DOI: 10.3389/fncel.2024.1386205] [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: 02/14/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
Epilepsy is a common neurological disorder that affects approximately 10.5 million children worldwide. Approximately 33% of affected patients exhibit resistance to all available antiseizure medications, but the underlying mechanisms are unknown and there is no effective treatment. Increasing evidence has shown that an abnormal gut microbiota may be associated with epilepsy. The gut microbiota can influence the function of the brain through multiple pathways, including the neuroendocrine, neuroimmune, and autonomic nervous systems. This review discusses the interactions between the central nervous system and the gastrointestinal tract (the brain-gut axis) and the role of the gut microbiota in the pathogenesis of epilepsy. However, the exact gut microbiota involved in epileptogenesis is unknown, and no consistent results have been obtained based on current research. Moreover, the target that should be further explored to identify a novel antiseizure drug is unclear. The role of the gut microbiota in epilepsy will most likely be uncovered with the development of genomics technology.
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Affiliation(s)
- Qinrui Li
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Youyu Gu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Jingjing Liang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Jiong Qin
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
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13
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Yan Z, Hao T, Yan Y, Zhao Y, Wu Y, Tan Y, Bi Y, Cui Y, Yang R, Zhao Y. Quantitative and dynamic profiling of human gut core microbiota by real-time PCR. Appl Microbiol Biotechnol 2024; 108:396. [PMID: 38922447 PMCID: PMC11208268 DOI: 10.1007/s00253-024-13204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024]
Abstract
The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.
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Affiliation(s)
- Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tongyu Hao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
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14
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Morales ME, Allegrini M, Basualdo J, Iocoli GA, Villamil MB, Zabaloy MC. Winter cover crop suppression methods influence on sunflower growth and rhizosphere communities. Front Microbiol 2024; 15:1405842. [PMID: 38993498 PMCID: PMC11238176 DOI: 10.3389/fmicb.2024.1405842] [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: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
Sunflower (Helianthus annuus L.), a vital crop for global vegetable oil production, encounters sustainability challenges in its cultivation. This study assesses the effects of incorporating a winter cover crop (CC), Avena sativa (L.), on the subsequent growth of sunflower crops and the vitality of their rhizosphere microbial communities over a two-year period. It examines the impact of two methods for suppressing winter CC-chemical suppression using glyphosate and mechanical suppression via rolling-both with and without the addition of phosphorus (P) starter fertilizer. These approaches are evaluated in comparison to the regional best management practices for sunflower cultivation, which involve a preparatory chemical fallow period and the subsequent application of starter P fertilizer. The methodology utilized Illumina sequencing for the analysis of rhizosphere bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) amplicons. Findings indicate a significant improvement (9-37%) in sunflower growth parameters (plant height, stem diameter, head diameter, and head dry weight) when cultivated after glyphosate-suppressed winter CC compared to the chemical fallows. Conversely, rolling of winter CC generally negatively affected sunflower growth. Rhizosphere bacterial communities following chemical suppression of winter CC showed greater Pielou's evenness, indicating a uniform distribution of species. In general, this treatment had more detrimental effects on beneficial sunflower rhizosphere bacteria such as Hymenobacter and Pseudarthrobacter than rolling of the winter CC, suggesting that the overall effect on sunflower growth may be mitigated by the redundancy within the bacterial community. As for fungal diversity, measured by the Chao-1 index, it increased in sunflowers planted after winter CC and receiving P fertilization, underscoring nutrient management's role in microbial community structure. Significant positive correlations between fungal diversity and sunflower growth parameters at the reproductive stage were observed (r = 0.41-0.72; p < 0.05), highlighting the role of fungal communities in plant fitness. The study underscores the positive effects of winter CC inclusion and management for enhancing sunflower cultivation while promoting beneficial microbes in the crop's rhizosphere. We advocate for strategic winter CC species selection, optimization of mechanical suppression techniques, and tailored phosphorus fertilization of sunflower to foster sustainable agriculture.
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Affiliation(s)
- Marianela Estefanía Morales
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Marco Allegrini
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Jessica Basualdo
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Gastón Alejandro Iocoli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | | | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
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15
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Shi H, Hou G, Jiang S, Su X. PM-profiler: a high-resolution and fast tool for taxonomy annotation of amplicon-based microbiome. Microbiol Spectr 2024:e0069524. [PMID: 38912828 DOI: 10.1128/spectrum.00695-24] [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: 03/15/2024] [Accepted: 05/12/2024] [Indexed: 06/25/2024] Open
Abstract
Amplicon sequencing stands as a cornerstone in microbiome profiling, yet concerns persist regarding its resolution and accuracy. The enhancement of reference databases and annotations marks a new era for 16S rRNA-based profiling. Capitalizing on this potential, we introduce PM-profiler, a novel tool for profiling amplicon short reads. PM-profiler is implemented by C++-based advanced algorithms, such as pre-allocated hash for reference construction, hybrid and dynamic short-read matching, big-data-guided dual-mode hierarchical taxonomy annotation strategy, and full-procedure parallel computing. This tool delivers species-level resolution and ultrafast speed for large-scale microbiomes, surpassing alignment-based approaches and the Naïve-Bayesian model. Furthermore, recognizing the global uneven distribution of microbes, we delineate optimal annotation strategies for each sampling habitat based on microbial patterns over 270,000 microbiomes. Integrated with the established workflow of Parallel-Meta Suite and the latest curated reference databases, this endeavor offers a swift and dependable solution for high-precision microbiome surveys.IMPORTANCEOur study introduces PM-profiler, a new tool that deciphers the complexity of microbial communities. With advanced algorithms, flexible annotation strategies, and well-organized big-data, PM-profiler provides a faster and more accurate way to study on microbiomes, paving the way for discoveries that could improve our understanding of microbiomes and their impact on the world.
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Affiliation(s)
- Haobo Shi
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Guosen Hou
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Sikai Jiang
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
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16
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Yan Y, Ma JJ, Liang XP, Yin Y, Wu YQ, Yu RL, Hu GR, Zhu YG, Li H. Occurrence and spatiotemporal distribution of arsenic biotransformation genes in urban dust. ENVIRONMENT INTERNATIONAL 2024; 190:108823. [PMID: 38908273 DOI: 10.1016/j.envint.2024.108823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/18/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Microbially-mediated arsenic biotransformation plays a pivotal role in the biogeochemical cycling of arsenic; however, the presence of arsenic biotransformation genes (ABGs) in urban dust remains unclear. To investigate the occurrence and spatiotemporal distributions of ABGs, a total of one hundred and eighteen urban dust samples were collected from different districts of Xiamen city, China in summer and winter. Although inorganic arsenic species, including arsenate [As(V)] and arsenite [As(III)], were found to be predominant, the methylated arsenicals, particularly trimethylarsine oxide [TMAs(V)O] and dimethylarsenate [DMAs(V)], were detected in urban dust. Abundant ABGs were identified in urban dust via AsChip analysis (a high-throughput qPCR chip for ABGs), of which As(III) S-adenosylmethionine methyltransferase genes (arsM), As(V) reductase genes (arsC), As(III) oxidase genes (aioA), As(III) transporter genes (arsB), and arsenic-sensing regulator genes (arsR) were the most prevalent, collectively constituting more than 90 % of ABGs in urban dust. Microbes involved in arsenic methylation were assigned to bacteria (e.g., Actinomycetes and Alphaproteobacteria), archaea (e.g., Halobacteria), and eukaryotes (e.g., Chlamydomonadaceae) in urban dust via the arsM amplicon sequencing. Temperature, a season-dependent environmental factor, profoundly affected the abundance of ABGs and the composition of microbes involved in arsenic methylation. This study provides new insights into the presence of ARGs within the urban dust.
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Affiliation(s)
- Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jin-Jin Ma
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xiu-Peng Liang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yi Yin
- 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
| | - 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
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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17
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Wang F, Chen Y, Zhou S, Li H, Wan C, Yan K, Zhang H, Xu Z. Aerosol sources and transport paths co-control the atmospheric bacterial diversity over the coastal East China Sea. MARINE POLLUTION BULLETIN 2024; 205:116589. [PMID: 38875970 DOI: 10.1016/j.marpolbul.2024.116589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 06/16/2024]
Abstract
Airborne bacteria along with chemical composition of aerosols were investigated during five sampling seasons at an offshore island of the East China Sea. Bacterial diversity was the lowest in spring, the highest in winter, and similar between the autumns of 2019 and 2020, suggesting remarkably seasonal variation but little interannual change. Geodermatophilus (Actinobacteria) was the indicator genus of mineral dust (MD) showed higher proportion in spring than in other seasons. Mastigocladopsis_PCC-10914 (Cyanobacteria) as the indicator of sea salt (SS) demonstrated the highest percentages in both autumns, when the air masses mainly passed over the ocean prior to the sampling site. The higher proportions of soil-derived genera Rubellimicrobium and Craurococcus (both Proteobacteria) and extremophile Chroococcidiopsis_SAG_2023 (Cyanobacteria) were found in summer and winter, respectively. Our study explores the linkage between aerosol source and transport path and bacterial composition, which has implication to understanding of land-sea transmission of bacterial taxa.
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Affiliation(s)
- Fanghui Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Ying Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; State Environmental Protection Key Laboratory of Land and Sea Ecological Governance and Systematic Regulation, Jinan, Shandong 250101, China; Institute of Eco-Chongming (IEC), National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Shanghai 200062, China.
| | - Shengqian Zhou
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Haowen Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Chunli Wan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Ke Yan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Hongliang Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; State Environmental Protection Key Laboratory of Land and Sea Ecological Governance and Systematic Regulation, Jinan, Shandong 250101, China
| | - Zongjun Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
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18
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Cheng F, Li W, Li J, Ji Z, Hu W, Zhao M, Yu D, Zhang L, Yuan P, Simayijiang H, Yan J. Circadian metabolites for evaluating the timing of bloodstain deposition: A preliminary study. Forensic Sci Int 2024; 361:112102. [PMID: 38889602 DOI: 10.1016/j.forsciint.2024.112102] [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: 02/28/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
Metabolites, as products of cellular metabolism, can provide a wealth of biological information and are less susceptible to degradation than other biomarkers due to their low molecular weight. Due to these properties, metabolites can be used as valuable biomarkers for forensic investigations. Knowing the timing of deposition of bloodstain could help to reconstruct crime scenes, draw conclusions about the time of the crime, and narrow down the circle of possible suspects. Previous studies have indicated that the concentration of some metabolites in blood is subject to circadian changes. However, the circadian metabolites of bloodstains have been still unclear. A total of sixty-four bloodstain samples were prepared under real conditions in three time categories (morning/noon (09:00 h ∼ 17:00 h), afternoon/evening (18:00 h ∼ 23:00 h) and night/early morning (24:00 h ∼ 08:00 h)). Fifty metabolites of bloodstains with significant differences were identified in the three time categories. Twenty-eight of these metabolites exhibited significant circadian changes. Finally, three independently contributing circadian metabolites were selected to build the logistic regression model, with an area under the curve of 0.91, 0.84 and 0.87 for the prediction of bloodstain deposition time in the morning/noon, afternoon/evening and night/early morning, respectively. The study indicated that circadian metabolites can be used for evaluating the timing of bloodstain deposition. This would provide a valuable perspective for analyzing the deposition time of biological traces in forensic investigations.
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Affiliation(s)
- Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Mengyang Zhao
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China; Shanxi Key Laboratory of Forensic Medicine, Taiyuan, Shanxi 030001, PR China.
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19
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Qi Z, Tian L, Zhang H, Zhou X, Lei Y, Tang F. Mycobiome mediates the interaction between environmental factors and mycotoxin contamination in wheat grains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172494. [PMID: 38631642 DOI: 10.1016/j.scitotenv.2024.172494] [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: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
Environmental factors significantly impact grain mycobiome assembly and mycotoxin contamination. However, there is still a lack of understanding regarding the wheat mycobiome and the role of fungal communities in the interaction between environmental factors and mycotoxins. In this study, we collected wheat grain samples from 12 major wheat-producing provinces in China during both the harvest and storage periods. Our aim was to evaluate the mycobiomes in wheat samples with varying deoxynivalenol (DON) contamination levels and to confirm the correlation between environmental factors, the wheat mycobiome, and mycotoxins. The results revealed significant differences in the wheat mycobiome and co-occurrence network between contaminated and uncontaminated wheat samples. Fusarium was identified as the main differential taxon responsible for inducing DON contamination in wheat. Correlation analysis identified key factors affecting mycotoxin contamination. The results indicate that both environmental factors and the wheat mycobiome play significant roles in the production and accumulation of DON. Environmental factors can affect the wheat mycobiome assembly, and wheat mycobiome mediates the interaction between environmental factors and mycotoxin contamination. Furthermore, a random forest (RF) model was developed using key biological indicators and environmental features to predict DON contamination in wheat with accuracies exceeding 90 %. The findings provide data support for the accurate prediction of mycotoxin contamination and lay the foundation for the research on biological control technologies of mycotoxin through the assembly of synthetic microbial communities.
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Affiliation(s)
- Zhihui Qi
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, PR China; National Engineering Research Center of Grain Storage and Logistics, Beijing 102209, PR China
| | - Lin Tian
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, PR China; National Engineering Research Center of Grain Storage and Logistics, Beijing 102209, PR China
| | - Haiyang Zhang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, PR China; National Engineering Research Center of Grain Storage and Logistics, Beijing 102209, PR China
| | - Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuqing Lei
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, PR China; National Engineering Research Center of Grain Storage and Logistics, Beijing 102209, PR China
| | - Fang Tang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, PR China; National Engineering Research Center of Grain Storage and Logistics, Beijing 102209, PR China.
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20
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Yang M, Chen T, Liu Y, Huang L. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. IMETA 2024; 3:e184. [PMID: 38898979 PMCID: PMC11183158 DOI: 10.1002/imt2.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 06/21/2024]
Abstract
Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.
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Affiliation(s)
- Mei Yang
- Institute of Traditional Chinese MedicineTianjin University of Traditional Chinese MedicineTianjinChina
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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21
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Xu Y, Feng T, Ding Z, Li L, Li Z, Cui K, Chen W, Pan H, Zhu P, Liu Q. Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome. Front Microbiol 2024; 15:1342804. [PMID: 38881655 PMCID: PMC11177756 DOI: 10.3389/fmicb.2024.1342804] [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: 11/22/2023] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages. Methods In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes. Results The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways. Discussion This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.
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Affiliation(s)
- Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zixu Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Ling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Buffalo Genetics, Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Weihua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongping Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Peng Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf Marine Ecological Environment Field Observation and Research Station of Guangxi, Beibu Gulf University, Qinzhou, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
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22
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [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: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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23
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Elbakary M, Hammad SF, Youseif SH, Soliman HSM. Revealing the diversity of Jojoba-associated fungi using amplicon metagenome approach and assessing the in vitro biocontrol activity of its cultivable community. World J Microbiol Biotechnol 2024; 40:205. [PMID: 38755302 DOI: 10.1007/s11274-024-03986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/13/2024] [Indexed: 05/18/2024]
Abstract
Jojoba shrubs are wild plants cultivated in arid and semiarid lands and characterized by tolerance to drought, salinity, and high temperatures. Fungi associated with such plants may be attributed to the tolerance of host plants against biotic stress in addition to the promotion of plant growth. Previous studies showed the importance of jojoba as jojoba oil in the agricultural field; however, no prior study discussed the role of jojoba-associated fungi (JAF) in reflecting plant health and the possibility of using JAF in biocontrol. Here, the culture-independent and culture-dependent approaches were performed to study the diversity of the jojoba-associated fungi. Then, the cultivable fungi were evaluated for in-vitro antagonistic activity and in vitro plant growth promotion assays. The metagenome analysis revealed the existence of four fungal phyla: Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota. The phylum Ascomycota was the most common and had the highest relative abundance in soil, root, branch, and fruit samples (59.7%, 50.7%, 49.8%, and 52.4%, respectively). Alternaria was the most abundant genus in aboveground tissues: branch (43.7%) and fruit (32.1%), while the genus Discosia had the highest abundance in the underground samples: soil (24%) and root (30.7%). For the culture-dependent method, a total of 14 fungi were isolated, identified, and screened for their chitinolytic and antagonist activity against three phytopathogenic fungi (Fusarium oxysporum, Alternaria alternata and Rhizoctonia solani) as well as their in vitro plant growth promotion (PGP) activity. Based on ITS sequence analysis, the selected potent isolates were identified as Aspergillus stellatusEJ-JFF3, Aspergillus flavus EJ-JFF4, Stilbocrea sp. EJ-JLF1, Fusarium solani EJ-JRF3, and Amesia atrobrunneaEJ-JSF4. The endophyte strain A. flavus EJ-JFF4 exhibited the highest chitinolytic activity (9 Enzyme Index) and antagonistic potential against Fusarium oxysporum, Alternaria alternata, and Rhizoctonia solani phytopathogens with inhibitory percentages of 72, 70, and 80 respectively. Also, A. flavus EJ-JFF4 had significant multiple PGP properties, including siderophore production (69.3%), phosphate solubilization (95.4 µg ml-1). The greatest production of Indol-3-Acetic Acid was belonged to A. atrobrunnea EJ-JSF4 (114.5 µg ml-1). The analysis of FUNGuild revealed the abundance of symbiotrophs over other trophic modes, and the guild of endophytes was commonly assigned in all samples. For the first time, this study uncovered fungal diversity associated with jojoba plants using a culture-independent approach and in-vitro assessed the roles of cultivable fungal strains in promoting plant growth and biocontrol. The present study indicated the significance of jojoba shrubs as a potential source of diverse fungi with high biocontrol and PGP activities.
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Affiliation(s)
- Mustafa Elbakary
- Biotechnology Program, Basic and Applied Science Institute, Egypt-Japan University of Science and Technology, Alexandria, 21934, Egypt.
- Department of Nucleic Acids and Protein Structure, Agricultural Research Center, Agricultural Genetic Engineering Research Institute, Giza, 12619, Egypt.
| | - Sherif F Hammad
- Pharm D Program, Egypt-Japan University of Science and Technology, New Borg El-Arab City, Alexandria, 21934, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo, 11795, Egypt
| | - Sameh H Youseif
- School of Biotechnology, Nile University, Giza, 12677, Egypt.
- Department of Microbial Genetic Resources, Agricultural Research Center (ARC), National Gene Bank, Giza, 12619, Egypt.
| | - Hesham S M Soliman
- Pharm D Program, Egypt-Japan University of Science and Technology, New Borg El-Arab City, Alexandria, 21934, Egypt
- Pharmacognosy Department, Helwan University, Ain-Helwan, Cairo, 11795, Egypt
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24
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Coskun M, Babayeva A, Barlas T, Muhittin Yalcin M, Akturk M, Balos Toruner F, Ayhan Karakoc M, Karakan T, Cindoruk M, Yetkin I, Eroglu Altinova A. Relationship between gut microbiome and bone deficits in primary hyperparathyroidism: A proof-of-concept pilot study. J Investig Med 2024:10815589241251695. [PMID: 38641855 DOI: 10.1177/10815589241251695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Parathyroid hormone (PTH) interacts with components of the gut microbiota to exert its bone-regulating effects. This study aimed to investigate the gut microbial composition in patients with primary hyperparathyroidism (PHPT). Nine patients with PHPT and nine age-sex and body mass index-matched healthy controls were included. Gut microbial composition was assessed using 16S rRNA gene amplicon sequencing in both groups at baseline and 1 month after parathyroidectomy in the PHPT group. Data were imported into QIIME-2 and both QIIME-2 and R packages were used for microbiome analysis. Alpha and beta diversities were similar between the groups and remained unchanged after parathyroidectomy. The relative abundance of Subdoligranulum was significantly higher, whereas Ruminococcus, Alloprevotella, Phascolarctobacterium, and Clostridium sensu stricto_1 were significantly lower in PHPT than in controls (p < 0.001). After parathyroidectomy, the relative abundance of Subdoligranulum decreased, and Ruminococcus and Alloprevotella increased (p < 0.001). The PHPT group had lower total femoral and lumbar bone mineral density (BMD) than the controls (p < 0.05). At baseline, Alloprevotella abundance was positively correlated with serum phosphorus and Subdoligranulum was positively correlated with total lumbar BMD. Clostridium sensu stricto_1 was negatively correlated with serum calcium and positively correlated with femoral neck BMD. Postoperatively, Alloprevotella was positively correlated with baseline serum phosphorus and Phascolarctobacterium was positively correlated with distal radius BMD. This study demonstrated that the diversity of the gut microbiome was altered, possibly in response to electrolyte changes in PHPT, both before and after parathyroidectomy.
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Affiliation(s)
- Meric Coskun
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Afruz Babayeva
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Tugba Barlas
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Mehmet Muhittin Yalcin
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Mujde Akturk
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Fusun Balos Toruner
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Mehmet Ayhan Karakoc
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Tarkan Karakan
- Department of Gastroenterology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Mehmet Cindoruk
- Department of Gastroenterology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Ilhan Yetkin
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Alev Eroglu Altinova
- Department of Endocrinology and Metabolism, Faculty of Medicine, Gazi University, Ankara, Turkey
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25
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Balakrishnan K, Krishnaa D, Balakrishnan G, Manickam M, Abdulkader AM, Dharumadurai D. Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing. Appl Biochem Biotechnol 2024; 196:2566-2590. [PMID: 37103739 DOI: 10.1007/s12010-023-04527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
Microbial communities' resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.
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Affiliation(s)
- Karthiyayini Balakrishnan
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- National Centre for alternatives to Animal Experiments, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Dheebhashriee Krishnaa
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Gowdhami Balakrishnan
- National Centre for alternatives to Animal Experiments, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Muthuselvam Manickam
- Department of Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Akbarsha Mohammad Abdulkader
- Mahatma Gandhi-Dorenkamp Centre, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- Department of Biotechnology & Research Coordinator, National College (Autonomous), Tiruchirappalli, Tamil Nadu, India
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26
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Wen X, Xu J, Wang Y, Yang X, Peng G, Li S, Ma B, Zou Y, Liao X, Wang Y, Worrich A, Wu Y. Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system. Microbiol Res 2024; 284:127734. [PMID: 38670037 DOI: 10.1016/j.micres.2024.127734] [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: 12/29/2023] [Revised: 03/27/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yiting Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xin Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guoliang Peng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Siming Li
- Shimadzu (China) Co., LTD. Guangzhou Branch, Guangzhou 510656, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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27
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Sharafi R, Salehi Jouzani G, Karimi E, Ghanavati H, Kowsari M. Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw. World J Microbiol Biotechnol 2024; 40:173. [PMID: 38630379 DOI: 10.1007/s11274-024-03959-3] [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: 12/10/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg-1 and in pilot level 65 °C, 72.11%, 310 g kg-1) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.
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Grants
- 2-05-05-017-960740 Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)
- 2-05-05-017-960740 Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)
- 2-05-05-017-960740 Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)
- 2-05-05-017-960740 Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)
- 2-05-05-017-960740 Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)
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Affiliation(s)
- Reza Sharafi
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd, P.O. Box, Karaj, 31535-1897, Iran
| | - Gholamreza Salehi Jouzani
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd, P.O. Box, Karaj, 31535-1897, Iran.
| | - Ebrahim Karimi
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd, P.O. Box, Karaj, 31535-1897, Iran
| | - Hosein Ghanavati
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd, P.O. Box, Karaj, 31535-1897, Iran
| | - Mojegan Kowsari
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd, P.O. Box, Karaj, 31535-1897, Iran
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28
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Ramos Peña DE, Pillet S, Grupioni Lourenço A, Pozzetto B, Bourlet T, Motta ACF. Human immunodeficiency virus and oral microbiota: mutual influence on the establishment of a viral gingival reservoir in individuals under antiretroviral therapy. Front Cell Infect Microbiol 2024; 14:1364002. [PMID: 38660490 PMCID: PMC11039817 DOI: 10.3389/fcimb.2024.1364002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The role of the oral microbiota in the overall health and in systemic diseases has gained more importance in the recent years, mainly due to the systemic effects that are mediated by the chronic inflammation caused by oral diseases, such as periodontitis, through the microbial communities of the mouth. The chronic infection by the human immunodeficiency virus (HIV) interacts at the tissue level (e.g. gut, genital tract, brain) to create reservoirs; the modulation of the gut microbiota by HIV infection is a good example of these interactions. The purpose of the present review is to assess the state of knowledge on the oral microbiota (microbiome, mycobiome and virome) of HIV-infected patients in comparison to that of HIV-negative individuals and to discuss the reciprocal influence of HIV infection and oral microbiota in patients with periodontitis on the potential establishment of a viral gingival reservoir. The influence of different clinical and biological parameters are reviewed including age, immune and viral status, potent antiretroviral therapies, smoking, infection of the airway and viral coinfections, all factors that can modulate the oral microbiota during HIV infection. The analysis of the literature proposed in this review indicates that the comparisons of the available studies are difficult due to their great heterogeneity. However, some important findings emerge: (i) the oral microbiota is less influenced than that of the gut during HIV infection, although some recurrent changes in the microbiome are identified in many studies; (ii) severe immunosuppression is correlated with altered microbiota and potent antiretroviral therapies correct partially these modifications; (iii) periodontitis constitutes a major factor of dysbiosis, which is exacerbated in HIV-infected patients; its pathogenesis can be described as a reciprocal reinforcement of the two conditions, where the local dysbiosis present in the periodontal pocket leads to inflammation, bacterial translocation and destruction of the supporting tissues, which in turn enhances an inflammatory environment that perpetuates the periodontitis cycle. With the objective of curing viral reservoirs of HIV-infected patients in the future years, it appears important to develop further researches aimed at defining whether the inflamed gingiva can serve of viral reservoir in HIV-infected patients with periodontitis.
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Affiliation(s)
- Diana Estefania Ramos Peña
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
| | - Sylvie Pillet
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Alan Grupioni Lourenço
- Department of Basic and Oral Biology, Ribeirão Preto School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Bruno Pozzetto
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Thomas Bourlet
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Ana Carolina Fragoso Motta
- Department of Stomatology, Public Health and Forensic Dentistry, Ribeirão Preto School of Dentistry, University of São Paulo, São Paulo, Brazil
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Zhang M, Zhou Y, Yao S, Zhao Y, Batool SS, Huang J, Jiang L, Yan D, Yan W, Yu Z. Effect of stress urinary incontinence on vaginal microbial communities. BMC Microbiol 2024; 24:112. [PMID: 38575862 PMCID: PMC10993610 DOI: 10.1186/s12866-024-03237-0] [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: 11/10/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Postpartum women often experience stress urinary incontinence (SUI) and vaginal microbial dysbiosis, which seriously affect women's physical and mental health. Understanding the relationship between SUI and vaginal microbiota composition may help to prevent vaginal diseases, but research on the potential association between these conditions is limited. RESULTS This study employed 16S rRNA gene sequencing to explore the association between SUI and vaginal dysbiosis. In terms of the vaginal microbiota, both species richness and evenness were significantly higher in the SUI group. Additionally, the results of NMDS and species composition indicated that there were differences in the composition of the vaginal microbiota between the two groups. Specifically, compared to postpartum women without SUI (Non-SUI), the relative abundance of bacteria associated with bacterial dysbiosis, such as Streptococcus, Prevotella, Dialister, and Veillonella, showed an increase, while the relative abundance of Lactobacillus decreased in SUI patients. Furthermore, the vaginal microbial co-occurrence network of SUI patients displayed higher connectivity, complexity, and clustering. CONCLUSION The study highlights the role of Lactobacillus in maintaining vaginal microbial homeostasis. It found a correlation between SUI and vaginal microbiota, indicating an increased risk of vaginal dysbiosis. The findings could enhance our understanding of the relationship between SUI and vaginal dysbiosis in postpartum women, providing valuable insights for preventing bacterial vaginal diseases and improving women's health.
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Affiliation(s)
- Man Zhang
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yanhua Zhou
- Department of Rehabilitation Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Yao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yiming Zhao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Syeda Sundas Batool
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Li Jiang
- Department of Rehabilitation Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Dayu Yan
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wenguang Yan
- Department of Rehabilitation Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.
| | - Zheng Yu
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
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Li ZT, Song X, Yuan S, Zhao HP. Unveiling the inhibitory mechanisms of chromium exposure on microbial reductive dechlorination: Kinetics and microbial responses. WATER RESEARCH 2024; 253:121328. [PMID: 38382292 DOI: 10.1016/j.watres.2024.121328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Chromium and organochlorine solvents, particularly trichloroethene (TCE), are pervasive co-existing contaminants in subsurface aquifers due to their extensive industrial use and improper disposal practices. In this study, we investigated the microbial dechlorination kinetics under different TCE-Cr(Ⅲ/VI) composite pollution conditions and elucidated microbial response mechanisms based on community shift patterns and metagenomic analysis. Our results revealed that the reductive dechlorinating consortium had high resistance to Cr(III) but extreme sensitivity to Cr(VI) disturbance, resulting in a persistent inhibitory effect on subsequent dechlorination. Interestingly, the vinyl chloride-respiring organohalide-respiring bacteria (OHRB) was notably more susceptible to Cr(III/VI) exposure than the trichloroethene-respiring one, possibly due to inferior competition for growth substrates, such as electron donors. In terms of synergistic non-OHRB populations, Cr(III/VI) exposure had limited impacts on lactate fermentation but significantly interfered with H2-producing acetogenesis, leading to inhibited microbial dechlorination due to electron donor deficiencies. However, this inhibition can be effectively mitigated by the amendment of exogenous H2 supply. Furthermore, being the predominant OHRB, Dehalococcoides have inherent Cr(VI) resistance defects and collaborate with synergistic non-OHRB populations to achieve concurrent bio-detoxication of Cr(VI) and TCE. Our findings expand the understanding of the response patterns of different functional populations towards Cr(III/VI) stress, and provide valuable insights for the development of in situ bioremediation strategies for sites co-contaminated with chloroethene and chromium.
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Affiliation(s)
- Zheng-Tao Li
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310030, PR China
| | - Xin Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, PR China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310030, PR China.
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Bai H, He LY, Gao FZ, Yao KS, Zhang M, Qiao LK, Chen ZY, He LX, Liu YS, Zhao JL, Ying GG. Airborne antibiotic resistome and microbiome in pharmaceutical factories. ENVIRONMENT INTERNATIONAL 2024; 186:108639. [PMID: 38603815 DOI: 10.1016/j.envint.2024.108639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/24/2024] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.
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Affiliation(s)
- Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Kai-Sheng Yao
- Aquatic Ecology and Water Quality Management group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Min Zhang
- Pearl River Water Resources Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou 510610, China
| | - Lu-Kai Qiao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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Wen X, Chen M, Ma B, Xu J, Zhu T, Zou Y, Liao X, Wang Y, Worrich A, Wu Y. Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 177:76-85. [PMID: 38290350 DOI: 10.1016/j.wasman.2024.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
Antibiotic resistance genes (ARGs) are emerging pollutants that enter the farm and surrounding environment via the manure of antibiotic-treated animals. Pretreatment of livestock manure by composting decreases ARGs abundance, but how antibiotic residues affect ARGs removal efficiency remains poorly understood. Here, we explored the fate of the resistome under different doxycycline residue levels during aerobic swine manure composting. Metagenomic sequencing showed that the presence of high levels of doxycycline generally had a higher abundance of tetracycline ARGs, and their dominant host bacteria of Firmicutes, especially Clostridium and Streptococcus, also had limited elimination in composting under high levels of doxycycline stress. Moreover, high levels of doxycycline impaired the removal of the total ARGs number in finished composts, with a removal rate of 51.74 % compared to 63.70 % and 71.52 % for the control and low-level doxycycline manure, respectively. Horizontal gene transfer and strengthened correlations among the bacterial community fostered ARGs preservation at high doxycycline levels during composting. In addition, ARGs carried by both plasmids and chromosomes, such as multidrug ARGs, showed wide host characteristics and rebound during compost maturation. Compared with chromosomes, a greater variety of ARGs on plasmids suggested that the majority of ARGs were characterized by horizontal mobility during composting, and the cross-host characteristics of ARGs during composting deserve further attention. This study provided deep insight into the fate of ARGs under residual antibiotic stress during manure composting and reminded the associated risk for environmental and public health.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Majian Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ting Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
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Li Y, Pan Z, Liao J, Dai R, Lin JG, Ling J, Xu Y. Micro-aeration and low influent C/N are key environmental factors for achieving ANAMMOX in livestock farming wastewater treatment plants. WATER RESEARCH 2024; 253:120141. [PMID: 38377919 DOI: 10.1016/j.watres.2023.120141] [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: 02/03/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 02/22/2024]
Abstract
Anaerobic ammonium oxidation (ANAMMOX)-mediated system is a cost-effective green nitrogen removal process. However, there are few examples of successful application of this advanced wastewater denitrification process in wastewater treatment plants, and the understanding of how to implement anaerobic ammonia oxidation process in full-scale is still limited. In this study, it was found that the abundance of anaerobic ammonia-oxidizing bacteria (AnAOB) in the two livestock wastewater plants named J1 and J2, respectively, showed diametrically opposed trends of waxing and waning with time. The microbial communities of the activated sludge in the two plants at different time were sampled and analyzed by high-throughput sequencing of 16S rRNA genes. Structural equation models (SEMs) were used to reveal the key factors affecting the realization of the ANAMMOX. Changes in the concentration of dissolved oxygen and C/N had a significant effect on the relative abundance of anaerobic ammonia oxidation bacteria (AnAOB). The low concentration of DO (0.2∼0.5 mg/L) could inhibit the activity of nitrifying bacteria (NOB) to achieve partial oxidation of ammonia nitrogen and provide sufficient substrate for the growth of AnAOB, similar to the CANON (Completely Autotrophic Nitrogen removal Over Nitrite). Unlike CANON, heterotrophic denitrification is also a particularly critical part of the livestock wastewater treatment, and a suitable C/N of about 0.6 could reduce the competition risk of heterotrophic microorganisms to AnAOB and ensure a good ecological niche for AnAOB. Based on the results of 16S rRNA and microbial co-occurrence networks, it was discovered that microorganisms in the sludge not only had a richer network interaction, but also achieved a mutually beneficial symbiotic interaction network among denitrifying bacteria (Pseudomonas sp., Terrimonas sp., Dokdonella sp.), AnAOB (Candidatus Brocadia sp.) at DO of 0.2∼0.5 mg/L and C/N of 0.6. Among the top 20 in abundance of genus level, AnAOB had a high relative abundance of 27.66%, followed by denitrifying bacteria of 3.67%, AOB of 0.64% and NOB of 0.26%, which is an essential indicator for the emergence of an AnAOB-dominated nitrogen removal cycle. In conclusion, this study highlights the importance of dissolved oxygen and C/N regulation by analyzing the mechanism of ANAMMOX sludge extinction and growth in two plants under anthropogenic regulation of AnAOB in full-scale wastewater treatment systems.
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Affiliation(s)
- Yuxin Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zhenzhong Pan
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jingsong Liao
- Yikangsheng Environmental Science and Technology Limited Company of Guangdong, Yunfu, 527400, China
| | - Ruizhi Dai
- Yikangsheng Environmental Science and Technology Limited Company of Guangdong, Yunfu, 527400, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City, 30010, Taiwan
| | - Jiayin Ling
- School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing, 526061, China
| | - Yanbin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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Shi T, Lure M, Zhang R, Liu Z, Hu Q, Liu J, Yang S, Jing L. Indole-3-acetic acid improves periphyton's resistance to ultraviolet-B: From physiological-biochemical properties and bacteria community to livestock-polluted water purification. ENVIRONMENTAL RESEARCH 2024; 246:118029. [PMID: 38160980 DOI: 10.1016/j.envres.2023.118029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Livestock-polluted water is a pressing water environmental issue in plateau pastoral regions, necessitating the adoption of eco-friendly solutions. Despite periphyton being a promising alternative, its efficacy is limited by the prevalence of intense ultraviolet radiation, particularly ultraviolet-B (UVB), in these regions. Therefore, this study employs molecular tools and small-scale trials to explore the crucial role of indole-3-acetic acid (IAA) in modulating periphyton characteristics and mediating nutrient removal from livestock-polluted water under UVB exposure. The results revealed that IAA augments periphyton's resilience to UVB stress through several pathways, including increasing periphyton's biomass, producing more extracellular polymeric substances (EPS), and enhancing antioxidant enzyme activities and photosynthetic activity of periphyton. Moreover, IAA addition increased periphyton's bacterial diversity, reshaped bacterial community structure, enhanced community stability, and elevated the R2 value of neutral processes in bacterial assembly from 0.257 to 0.651 under UVB. Practically, an IAA concentration of 50 mg/L was recommended. Small-scale trials confirmed the effectiveness of IAA in assisting UVB-stressed periphyton to remove nitrogen and phosphorus from livestock-polluted water, without the risk of nitrogen accumulation. These findings offer valuable insights into the protection of aquatic ecosystems in plateau pastoral regions based on periphyton property in an eco-friendly manner.
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Affiliation(s)
- Tianyu Shi
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Maobulin Lure
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Run Zhang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Zhiheng Liu
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Qianming Hu
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Jia Liu
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Shengtao Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China
| | - Liandong Jing
- Key Laboratory of Pollution Control Chemistry and Environmental Functional, Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China; Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu, 610041, China.
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Achudhan AB, Kannan P, Gupta A, Saleena LM. A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data. Biochem Genet 2024; 62:621-632. [PMID: 37507643 DOI: 10.1007/s10528-023-10467-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.
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Affiliation(s)
- Arunmozhi Bharathi Achudhan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Priya Kannan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Annapurna Gupta
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.
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36
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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Han L, Chang ZM, Ren CS, Chen XS, Smagghe G, Yuan YG, Long JK. Colony performance of three native bumblebee species from South China and association with their gut microbiome. INSECT SCIENCE 2024. [PMID: 38516802 DOI: 10.1111/1744-7917.13351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/09/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024]
Abstract
Bumblebees play an important ecological economic role as pollinators in nature and agriculture. For reasons of biosecurity, many countries promote the cultivation of native bumblebee species for crop pollination instead of importing "alien" species. In South China, a few bumblebee species are considered useful in this way, particularly, Bombus atripes, Bombus bicoloratus and Bombus breviceps. However, whether they are suitable for artificial rearing and forming healthy colonies for pollination, remains unknown. In this project, queens from the 3 native species of Guizhou Province were collected and colonies were started under standardized conditions. The colonies were scored based on 19 parameters, including the stage of colony development, number and weight of offspring, and diet consumed. The data revealed that B. breviceps had the best performance, produced more workers and consumed the smallest diet. Next, we performed 16S rDNA sequencing of the bacterial communities found in the guts of offspring workers, and then a correlation analysis between colony performance and gut bacteria was conducted. Here, B. breviceps showed the highest diversity in gut bacterial composition, dominated by the bacteria Gilliamella, Snodgrassella, Enterobacter, and Lactobacillus Firm5. The higher the abundance of Snodgrassella, the better the performance of the colony in the foundation stage, and later Lactobacillus Firm5, Apibacter and Bifidobacterium were beneficial during the stages of rapid growth and colony decline. Although we do not understand all of the interactions yet, these correlations explain why B. breviceps demonstrated better colony performance. Our data provide valuable information for breeding local Bombus species and will contribute to developing strong colonies for crop pollination.
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Affiliation(s)
- Lei Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education/College of Animal Science, Guizhou University, Guiyang, China
| | - Zhi-Min Chang
- Institute of Entomology/Provincial Special Key Laboratory for Developing and Utilization of Insect Resources, Guizhou University, Guiyang, China
| | - Chang-Shi Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education/College of Animal Science, Guizhou University, Guiyang, China
| | - Xiang-Sheng Chen
- Institute of Entomology/Provincial Special Key Laboratory for Developing and Utilization of Insect Resources, Guizhou University, Guiyang, China
| | - Guy Smagghe
- Institute of Entomology/Provincial Special Key Laboratory for Developing and Utilization of Insect Resources, Guizhou University, Guiyang, China
| | - Yi-Ge Yuan
- Institute of Entomology/Provincial Special Key Laboratory for Developing and Utilization of Insect Resources, Guizhou University, Guiyang, China
| | - Jian-Kun Long
- Institute of Entomology/Provincial Special Key Laboratory for Developing and Utilization of Insect Resources, Guizhou University, Guiyang, China
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38
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Zulak KG, Farfan-Caceres L, Knight NL, Lopez-Ruiz FJ. Exploiting long read sequencing to detect azole fungicide resistance mutations in Pyrenophora teres using unique molecular identifiers. Sci Rep 2024; 14:6285. [PMID: 38491078 PMCID: PMC10943121 DOI: 10.1038/s41598-024-56801-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Resistance to fungicides is a global challenge as target proteins under selection can evolve rapidly, reducing fungicide efficacy. To manage resistance, detection technologies must be fast and flexible enough to cope with a rapidly increasing number of mutations. The most important agricultural fungicides are azoles that target the ergosterol biosynthetic enzyme sterol 14α-demethylase (CYP51). Mutations associated with azole resistance in the Cyp51 promoter and coding sequence can co-occur in the same allele at different positions and codons, increasing the complexity of resistance detection. Resistance mutations arise rapidly and cannot be detected using traditional amplification-based methods if they are not known. To capture the complexity of azole resistance in two net blotch pathogens of barley we used the Oxford Nanopore MinION to sequence the promoter and coding sequence of Cyp51A. This approach detected all currently known mutations from biologically complex samples increasing the simplicity of resistance detection as multiple alleles can be profiled in a single assay. With the mobility and decreasing cost of long read sequencing, we demonstrate this approach is broadly applicable for characterizing resistance within known agrochemical target sites.
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Affiliation(s)
- Katherine G Zulak
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| | - Lina Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
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Lv PL, Jia C, Wei CH, Zhao HP, Chen R. Efficient perchlorate reduction in microaerobic environment facilitated by partner methane oxidizers. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133683. [PMID: 38310847 DOI: 10.1016/j.jhazmat.2024.133683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
The conventional perchlorate (ClO4-) reduction typically necessitates anaerobic conditions. However, in this study, we observed efficient ClO4- reduction using CH4 as the electron donor in a microaerobic environment. The maximum ClO4- removal flux of 2.18 g/m2·d was achieved in CH4-based biofilm. The kinetics of ClO4- reduction showed significant differences, with trace oxygen increasing the reduction rate of ClO4-, whereas oxygen levels exceeding 2 mg/L decelerated the ClO4- reduction. In the absence of exogenous oxygen, anaerobic methanotrophic (ANME) archaea contribute more than 80% electrons through the reverse methanogenesis pathway for ClO4- reduction. Simultaneously, microorganisms activate CH4 by utilizing oxygen generated from chlorite (ClO2-) disproportionation. In the presence of exogenous oxygen, methane oxidizers predominantly consume oxygen to drive the aerobic oxidation of methane. It is indicated that methane oxidizers and perchlorate reducing bacteria can form aggregates to resist external oxygen shocks and achieve efficient ClO4- reduction under microaerobic condition. These findings provide new insights into biological CH4 mitigation and ClO4- removal in hypoxic environment.
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Affiliation(s)
- Pan-Long Lv
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China
| | - Chuan Jia
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China
| | - Chi-Hang Wei
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China
| | - He-Ping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Rong Chen
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, China.
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40
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Munk K, Ilina D, Ziemba L, Brader G, Molin EM. Holomics - a user-friendly R shiny application for multi-omics data integration and analysis. BMC Bioinformatics 2024; 25:93. [PMID: 38438871 PMCID: PMC10913680 DOI: 10.1186/s12859-024-05719-4] [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: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
An organism's observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic and abiotic stressors, can significantly impact this complex biological system, influencing processes like growth, development and productivity. A comprehensive analysis of the entire biological system and its interactions is thus crucial to identify key components that support adaptation to stressors and to discover biomarkers applicable in breeding programs or disease diagnostics. Since the genomics era, several other 'omics' disciplines have emerged, and recent advances in high-throughput technologies have facilitated the generation of additional omics datasets. While traditionally analyzed individually, the last decade has seen an increase in multi-omics data integration and analysis strategies aimed at achieving a holistic understanding of interactions across different biological layers. Despite these advances, the analysis of multi-omics data is still challenging due to their scale, complexity, high dimensionality and multimodality. To address these challenges, a number of analytical tools and strategies have been developed, including clustering and differential equations, which require advanced knowledge in bioinformatics and statistics. Therefore, this study recognizes the need for user-friendly tools by introducing Holomics, an accessible and easy-to-use R shiny application with multi-omics functions tailored for scientists with limited bioinformatics knowledge. Holomics provides a well-defined workflow, starting with the upload and pre-filtering of single-omics data, which are then further refined by single-omics analysis focusing on key features. Subsequently, these reduced datasets are subjected to multi-omics analyses to unveil correlations between 2-n datasets. This paper concludes with a real-world case study where microbiomics, transcriptomics and metabolomics data from previous studies that elucidate factors associated with improved sugar beet storability are integrated using Holomics. The results are discussed in the context of the biological background, underscoring the importance of multi-omics insights. This example not only highlights the versatility of Holomics in handling different types of omics data, but also validates its consistency by reproducing findings from preceding single-omics studies.
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Affiliation(s)
- Katharina Munk
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Daria Ilina
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Lisa Ziemba
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Günter Brader
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Eva M Molin
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria.
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41
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Wei S, Tang W, Chen D, Xiong J, Xue L, Dai Y, Guo Y, Wu C, Dai J, Wu M, Wang S. Multiomics insights into the female reproductive aging. Ageing Res Rev 2024; 95:102245. [PMID: 38401570 DOI: 10.1016/j.arr.2024.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
The human female reproductive lifespan significantly diminishes with age, leading to decreased fertility, reduced fertility quality and endocrine function disorders. While many aspects of aging in general have been extensively documented, the precise mechanisms governing programmed aging in the female reproductive system remain elusive. Recent advancements in omics technologies and computational capabilities have facilitated the emergence of multiomics deep phenotyping. Through the application and refinement of various high-throughput omics methods, a substantial volume of omics data has been generated, deepening our comprehension of the pathogenesis and molecular underpinnings of reproductive aging. This review highlights current and emerging multiomics approaches for investigating female reproductive aging, encompassing genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics. We elucidate their influence on fundamental cell biology and translational research in the context of reproductive aging, address the limitations and current challenges associated with multiomics studies, and offer a glimpse into future prospects.
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Affiliation(s)
- Simin Wei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Weicheng Tang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Dan Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Jiaqiang Xiong
- Department of Obstetrics and Gynecology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Liru Xue
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yican Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Chuqing Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
| | - Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
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42
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Parida D, Katare K, Ganguly A, Chakraborty D, Konar O, Nogueira R, Bala K. Molecular docking and metagenomics assisted mitigation of microplastic pollution. CHEMOSPHERE 2024; 351:141271. [PMID: 38262490 DOI: 10.1016/j.chemosphere.2024.141271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.
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Affiliation(s)
- Dinesh Parida
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Konica Katare
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Atmaadeep Ganguly
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, West Bengal State University, Kolkata, 700118, India.
| | - Disha Chakraborty
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Oisi Konar
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Regina Nogueira
- Institute of Sanitary Engineering and Waste Management, Leibniz Universität, Hannover, Germany.
| | - Kiran Bala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
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43
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Fan B, Zhao C, Zhao L, Wang M, Sun N, Li Z, Yang F. Biochar application can enhance phosphorus solubilization by strengthening redox properties of humic reducing microorganisms during composting. BIORESOURCE TECHNOLOGY 2024; 395:130329. [PMID: 38224785 DOI: 10.1016/j.biortech.2024.130329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Phosphorus (P) in nature mostly exists in an insoluble state, and humic reducing microorganisms (HRMs) can dissolve insoluble substances through redox properties. This study aimed to investigate the correlations between insoluble P and dominant HRMs amenable to individual culture during biochar composting. These analyses revealed that, in comparison to the control, biochar addition increased the relative abundance of dominant HRMs by 20.3% and decreased redox potential (Eh) levels by 15.4% hence, enhancing the moderately-labile-P and non-labile-P dissolution. The pathways underlying the observed effects were additionally assessed through structural equation modeling, revealing that biochar addition promoted insoluble P dissolution through both the direct effects of bacterial community structure as well as the direct effects of HRMs community structure and indirect effects based on Eh of HRMs community structure. This research offers a better understanding of the effect of HRMs on insoluble P during the composting process.
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Affiliation(s)
- Bowen Fan
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China; College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, China; Key Laboratory of Low-carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang 163319, China; Engineering Research Center of Crop Straw Utilization, Daqing, Heilongjiang 163319, China
| | - Changjiang Zhao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, China; Key Laboratory of Low-carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang 163319, China; Engineering Research Center of Crop Straw Utilization, Daqing, Heilongjiang 163319, China
| | - Liqin Zhao
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mengmeng Wang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ning Sun
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zoutong Li
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, China; Key Laboratory of Low-carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang 163319, China; Engineering Research Center of Crop Straw Utilization, Daqing, Heilongjiang 163319, China
| | - Fengjun Yang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China.
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DI Pierro F, Bertuccioli A, Cazzaniga M, Matera M, Cavecchia I, Gerardi V, Piccirelli S, Salvi D, Pugliano CL, Cesaro P, Spada C, Guasti L, Zerbinati N. Can microbiota analysis help intercept cases of colon cancer in case of occult blood negativity, also suggesting possible pharmacological intervention strategies? Minerva Gastroenterol (Torino) 2024; 70:109-112. [PMID: 37889113 DOI: 10.23736/s2724-5985.23.03578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Affiliation(s)
- Francesco DI Pierro
- Scientific Department, Velleja Research, Milan, Italy -
- Department of Medicine and Surgery, University of Insubria, Varese, Italy -
| | - Alexander Bertuccioli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Pesaro-Urbino, Italy
| | | | | | | | - Viviana Gerardi
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Stefania Piccirelli
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Daniele Salvi
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Cecilia L Pugliano
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Paola Cesaro
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Cristiano Spada
- Unit of Digestive Endoscopy, IRCCS A. Gemelli University Polyclinic Foundation, Rome, Italy
| | - Luigina Guasti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Nicola Zerbinati
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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45
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Ng HJ, Goh KM, Yahya A, Abdul-Wahab MF. Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane. 3 Biotech 2024; 14:91. [PMID: 38419684 PMCID: PMC10897112 DOI: 10.1007/s13205-024-03933-8] [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: 05/17/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024] Open
Abstract
Oil palm processing generates substantial waste materials rich in organic content, posing various environmental challenges. Anaerobic digestion (AD), particularly for palm oil mill effluent (POME), offers a sustainable solution, by converting waste into valuable biomethane for thermal energy or electricity generation. The synergistic activities of the AD microbiota directly affect the biomethane production, and the microbial community involved in biomethane production in POME anaerobic digestion has been reported. The composition of bacterial and archaeal communities varies under different substrate and physicochemical conditions. This review discusses the characteristics of POME, explores the microbial members engaged in each stage of AD, and elucidates the impacts of substrate and physicochemical conditions on the microbial community dynamics, with a specific focus on POME. Finally, the review outlines current research needs and provides future perspectives on optimizing the microbial communities for enhanced biomethane production from oil palm wastes.
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Affiliation(s)
- Hui Jing Ng
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Kian Mau Goh
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Adibah Yahya
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Mohd Firdaus Abdul-Wahab
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
- Taiwan-Malaysia Innovation Centre for Clean Water and Sustainable Energy (WISE Centre), 81310 UTM Johor Bahru, Johor, Malaysia
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46
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Lachmansingh DA, Valderrama B, Bastiaanssen T, Cryan J, Clarke G, Lavelle A. Impact of dietary fiber on gut microbiota composition, function and gut-brain-modules in healthy adults - a systematic review protocol. HRB Open Res 2024; 6:62. [PMID: 38525261 PMCID: PMC10958149 DOI: 10.12688/hrbopenres.13794.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Background The gut microbiota has been extensively implicated in health and disease. The functional outputs of the gut microbiota, such as microbial metabolites, are considered particularly important in this regard. Significant associations exist between alterations in the relative abundance of specific microbial taxa and mental health disorders. Dietary fiber has the potential to alter gut microbiota composition and function, modifying bacterial enzymatic function and the production of metabolites. As many taxa of microorganisms have enzymes capable of producing or degrading neurochemicals i.e. neuroactive gut brain modules, new predictive tools can be applied to existing datasets such as those harvested from dietary fiber interventions. We endeavor to perform a systematic review in order to identify studies reporting compositional gut microbiota alterations after interventions with dietary fiber in healthy individuals. We aim to also extract from the selected studies publicly available microbial genomic sequence datasets for reanalysis with a consistent bioinformatics pipeline, with the ultimate intention of identifying altered gut brain modules following dietary fiber interventions. Methods Interventional trials and randomized controlled studies that are originally published, including cross-over and non-crossover design and involving healthy adult humans will be included. A systematic search of PubMed/MEDLINE and EMBASE, two electronic databases, will be completed. Discussion Various types of dietary fiber have an impact on the gut microbiota composition, with some promoting the growth of particular taxa while others are reduced in relative abundance. Our search focuses on the impact of this food component on the microbiota of healthy individuals. Compositional gut microbial changes have been reported and our review will compile and update these observations after reanalysis of their datasets with a consistent bioinformatic pipeline. From this it may be possible to predict more detailed functional consequences in terms of neuroactive gut brain modules, of the compositional alterations in gut microbial taxa.
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Affiliation(s)
- David Antoine Lachmansingh
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Benjamin Valderrama
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Thomaz Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - John Cryan
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
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47
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Wang M, Ge AH, Ma X, Wang X, Xie Q, Wang L, Song X, Jiang M, Yang W, Murray JD, Wang Y, Liu H, Cao X, Wang E. Dynamic root microbiome sustains soybean productivity under unbalanced fertilization. Nat Commun 2024; 15:1668. [PMID: 38395981 PMCID: PMC10891064 DOI: 10.1038/s41467-024-45925-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.
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Affiliation(s)
- Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xingzhu Ma
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, China
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiujin Xie
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Like Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengchen Jiang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weibing Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jeremy D Murray
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Mthethwa-Hlongwa NP, Amoah ID, Gomez A, Davison S, Reddy P, Bux F, Kumari S. Profiling pathogenic protozoan and their functional pathways in wastewater using 18S rRNA and shotgun metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169602. [PMID: 38154626 DOI: 10.1016/j.scitotenv.2023.169602] [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: 08/20/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Despite extensive research, little is known about the composition of eukaryotic protists in environmental samples. This is due to low parasite concentrations, the complexity of parasite diversity, and a lack of suitable reference databases and standardized protocols. To bridge this knowledge gap, this study used 18S rRNA short amplicon and shotgun metagenomic sequencing approaches to profile protozoan microbial communities as well as their functional pathways in treated and untreated wastewater samples collected from different regions of South Africa. Results demonstrated that protozoan diversity (Shannon index P-value = 0.03) and taxonomic composition (PERMANOVA, P-value = 0.02) was mainly driven by the type of wastewater samples (treated & untreated) and geographic location. However, these WWTPs were also found to contain a core community of protozoan parasites. The untreated wastewater samples revealed a predominant presence of free-living, parasitic, and potentially pathogenic protists typically found in humans and animals, ranging from Alveolata (27 %) phylum (Apicomplexa and Ciliophora) to Excavata (3.88 %) (Discoba and Parasalia) and Amoebozoa (2.84 %) (Entamoeba and Acanthamoeba). Shotgun metagenomics analyses in a subset of the untreated wastewater samples confirmed the presence of public health-importance protozoa, including Cryptosporidium species (3.48 %), Entamoeba hystolitica (6.58 %), Blastocystis hominis (2.91 %), Naegleria gruberi (2.37 %), Toxoplasma gondii (1.98 %), Cyclospora cayetanensis (1.30 %), and Giardia intestinalis (0.31 %). Virulent gene families linked to pathogenic protozoa, such as serine/threonine protein phosphatase and mucin-desulfating sulfatase were identified. Additionally, enriched pathways included thiamine diphosphate biosynthesis III, heme biosynthesis, Methylerythritol 4-Phosphate Pathway, methyl erythritol phosphate (MEP), and pentose phosphate pathways. These findings suggest that protozoan pathogens may possess metabolic and growth potential within WWTPs, posing a severe risk of transmission to humans and animals if inadequately disinfected before release. This study provides a baseline for the future investigation of diverse protozoal communities in wastewater, which are of public health importance.
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Affiliation(s)
- Nonsikelelo P Mthethwa-Hlongwa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - Isaac D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department of Environmental Science, The University of Arizona, Shantz Building Rm 4291177 E 4th St., Tucson, AZ 85721, USA
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Sam Davison
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Poovendhree Reddy
- Department Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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Macharoen P, Mhuantong W, Wannawong T, Leesutthiphonchai W, Tanasupawat S, Suwannarach N, Kuncharoen N. Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01140-9. [PMID: 38315309 DOI: 10.1007/s12223-024-01140-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/20/2024] [Indexed: 02/07/2024]
Abstract
Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.
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Affiliation(s)
- Pipat Macharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Wuttichai Mhuantong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Thippawan Wannawong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10300, Thailand
| | - Nakarin Suwannarach
- Center Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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50
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González A, Fullaondo A, Odriozola A. Techniques, procedures, and applications in microbiome analysis. ADVANCES IN GENETICS 2024; 111:81-115. [PMID: 38908906 DOI: 10.1016/bs.adgen.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microbiota is a complex community of microorganisms living in a defined environment. Until the 20th century, knowledge of microbiota was partial, as the techniques available for their characterization were primarily based on bacteriological culture. In the last twenty years, the development of DNA sequencing technologies, multi-omics, and bioinformatics has expanded our understanding of microorganisms. We have moved from mainly considering them isolated disease-causing agents to recognizing the microbiota as an essential component of host biology. These techniques have shown that the microbiome plays essential roles in various host phenotypes, influencing development, physiology, reproduction, and evolution. This chapter provides researchers with a summary of the primary concepts, sample collection, experimental techniques, and bioinformatics analysis commonly used in microbiome research. The main features, applications in microbiome studies, and their advantages and limitations are included in each section.
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Affiliation(s)
- Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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