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Van Le V, Kang M, Ko SR, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Response of particle-attached and free-living bacterial communities to Microcystis blooms. Appl Microbiol Biotechnol 2024; 108:42. [PMID: 38183480 DOI: 10.1007/s00253-023-12828-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/29/2023] [Accepted: 11/13/2023] [Indexed: 01/08/2024]
Abstract
The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Deng F, Xie H, Zheng T, Yang Y, Bao X, He H, Zhang X, Liang C. Dynamic responses of soil microbial communities to seasonal freeze-thaw cycles in a temperate agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175228. [PMID: 39102954 DOI: 10.1016/j.scitotenv.2024.175228] [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: 03/05/2024] [Revised: 06/22/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Soil freeze-thaw cycles (FTCs) are common in temperate agricultural ecosystems during the non-growing season and are progressively influenced by climate change. The impact of these cycles on soil microbial communities, crucial for ecosystem functioning, varies under different agricultural management practices. Here, we investigated the dynamic changes in soil microbial communities in a Mollisol during seasonal FTCs and examined the effects of stover mulching and nitrogen fertilization. We revealed distinct responses between bacterial and fungal communities. The dominant bacterial phyla reacted differently to FTCs: for example, Proteobacteria responded opportunistically, Actinobacteria, Acidobacteria, Choroflexi and Gemmatimonadetes responded sensitively, and Saccharibacteria exhibited a tolerance response. In contrast, the fungal community composition remained relatively stable during FTCs, except for a decline in Glomeromycota. Certain bacterial OTUs acted as sensitive indicators of FTCs, forming keystone modules in the network that are closely linked to soil carbon, nitrogen content and potential functions. Additionally, neither stover mulching nor nitrogen fertilization significantly influenced microbial richness, diversity and potential functions. However, over time, more indicator species specific to these agricultural practices began to emerge within the networks and gradually occupied the central positions. Furthermore, our findings suggest that farming practices, by introducing keystone microbes and changing interspecies interactions (even without changing microbial richness and diversity), can enhance microbial community stability against FTC disturbances. Specifically, higher nitrogen input with stover removal promotes fungal stability during soil freezing, while lower nitrogen levels increase bacterial stability during soil thawing. Considering the fungal tolerance to FTCs, we recommend reducing nitrogen input for manipulating bacterial interactions, thereby enhancing overall microbial resilience to seasonal FTCs. In summary, our research reveals that microbial responses to seasonal FTCs are reshaped through land management to support ecosystem functions under environmental stress amid climate change.
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Affiliation(s)
- Fangbo Deng
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongtu Xie
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Tiantian Zheng
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yali Yang
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xuelian Bao
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongbo He
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xudong Zhang
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chao Liang
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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Cui S, Zhou L, Fang Q, Xiao H, Jin D, Liu Y. Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175334. [PMID: 39117232 DOI: 10.1016/j.scitotenv.2024.175334] [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: 06/01/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.
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Affiliation(s)
- Shaowei Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Lianzhu Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiandong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haijun Xiao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Moreira VA, Cravo-Laureau C, de Carvalho ACB, Baldy A, Bidone ED, Sabadini-Santos E, Duran R. Greenhouse gas emission potential of tropical coastal sediments in densely urbanized area inferred from metabarcoding microbial community data. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174341. [PMID: 38960166 DOI: 10.1016/j.scitotenv.2024.174341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/17/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
Although benthic microbial community offers crucial insights into ecosystem services, they are underestimated for coastal sediment monitoring. Sepetiba Bay (SB) in Rio de Janeiro, Brazil, holds long-term metal pollution. Currently, SB pollution is majorly driven by domestic effluents discharge. Here, functional prediction analysis inferred from 16S rRNA gene metabarcoding data reveals the energy metabolism profiles of benthic microbial assemblages along the metal pollution gradient. Methanogenesis, denitrification, and N2 fixation emerge as dominant pathways in the eutrophic/polluted internal sector (Spearman; p < 0.05). These metabolisms act in the natural attenuation of sedimentary pollutants. The methane (CH4) emission (mcr genes) potential was found more abundant in the internal sector, while the external sector exhibited higher CH4 consumption (pmo + mmo genes) potential. Methanofastidiosales and Exiguobacterium, possibly involved in CH4 emission and associated with CH4 consumers respectively, are the main taxa detected in SB. Furthermore, SB exhibits higher nitrous oxide (N2O) emission potential since the norB/C gene proportions surpass nosZ up to 4 times. Blastopirellula was identified as the main responsible for N2O emissions. This study reveals fundamental contributions of the prokaryotic community to functions involved in greenhouse gas emissions, unveiling their possible use as sentinels for ecosystem monitoring.
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Affiliation(s)
- Vanessa Almeida Moreira
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Angelo Cezar Borges de Carvalho
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Alice Baldy
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Edison Dausacker Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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Fu X, Ma Y, Yang T, He S, Wang D, Jin L, Zhan L, Guo Z, Fan K, Li J, Chu H. Bacterial community composition of wheat aboveground compartments correlates with yield during the reproductive phase. Appl Environ Microbiol 2024:e0107824. [PMID: 39212378 DOI: 10.1128/aem.01078-24] [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: 05/31/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Plant-associated microbial communities play important roles in agricultural productivity, and their composition has been shown to vary across plant compartments and developmental stages. However, the response of microbial communities within different plant compartments and at different developmental stages to diverse long-term fertilization treatments, as well as their linkages with crop yields, remains underexplored. This study analyzed wheat-associated bacterial communities within various soil and plant compartments under three fertilization treatments throughout the vegetative and reproductive phases. The variance in bacterial community was primarily attributed to compartments, followed by fertilization treatments and developmental stages. The composition of belowground bacterial communities (bulk soil, rhizosphere soil, and root) exhibited stronger responses to fertilization treatments than aboveground compartments (stem and leaf). The composition of belowground bacterial communities responded to fertilization treatments at all developmental stages, and it was significantly correlated with crop yields during the vegetative phase, whereas the aboveground community composition only showed a response to fertilization during the reproductive phase, at which point it was significantly correlated with crop yields. Moreover, during this reproductive phase, the co-occurrence network of aboveground bacterial communities exhibited enhanced complexity, and it contained an increased number of keystone species associated with crop yields, such as Sphingomonas spp., Massilia spp., and Frigoribacterium spp. Structural equation modeling indicated that augmenting total phosphorus levels in aboveground compartments could enhance crop yields by increasing the relative abundance of these keystone species during the reproductive phase. These findings highlight the pivotal role of aboveground bacterial communities in wheat production during the reproductive phase. IMPORTANCE The developmental stage significantly influences crop-associated bacterial communities, but the relative importance of bacterial communities in different compartments to crop yields across various stages is still not well understood. This study reveals that belowground bacterial communities during the vegetative phase are significantly correlated with crop yields. Notably, during the reproductive phase, the composition of aboveground bacterial communities was significantly correlated with crop yields. During this phase, the complexity and enriched keystone species within the aboveground co-occurrence network underscore their role in boosting crop production. These results provide a foundation for developing microbiome-based products that are phase-specific and promote sustainable agricultural practices.
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Affiliation(s)
- Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuobing He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Daozhong Wang
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lin Jin
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Linchuan Zhan
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Zhibin Guo
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiasui Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Xing C, Zhang X, Wang D, Chen H, Gao X, Sun C, Guo W, Roshan S, Li Y, Hang Z, Cai S, Lei T, Bi W, Hou L, Li L, Wu Y, Li L, Zeng Z, Du H. Neuroprotective effects of mesenchymal stromal cells in mouse models of Alzheimer's Disease: The Mediating role of gut microbes and their metabolites via the Microbiome-Gut-Brain axis. Brain Behav Immun 2024; 122:510-526. [PMID: 39191350 DOI: 10.1016/j.bbi.2024.08.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 08/03/2024] [Accepted: 08/24/2024] [Indexed: 08/29/2024] Open
Abstract
The intricacy and multifaceted nature of Alzheimer's disease (AD) necessitate therapies that target multiple aspects of the disease. Mesenchymal stromal cells (MSCs) emerge as potential agents to mitigate AD symptoms; however, whether their therapeutic efficacy involves modulation of gut microbiota and the microbiome-gut-brain axis (MGBA) remains unexplored. In this study, we evaluated the effects of three distinct MSCs types-derived from the umbilical cord (UCMSC), dental pulp (SHED), and adipose tissue (ADSC)-in an APP/PS1 mouse model of AD. In comparison to saline control, MSCs administration resulted in a significant reduction of behavioral disturbances, amyloid plaques, and phosphorylated tau in the hippocampus and frontal cortex, accompanied by an increase in neuronal count and Nissl body density across AD-afflicted brain regions. Through 16S rRNA gene sequencing, we identified partial restoration of gut microbial balance in AD mice post-MSCs treatment, evidenced by the elevation of neuroprotective Akkermansia and reduction of the AD-associated Sphingomonas. To examine whether gut microbiota involved in MSCs efficacy in treating AD, SHED with better anti-inflammatory and gut microbiota recovery effects among three MSCs, and another AD model 5 × FAD mice with earlier and more pathological proteins in brain than APP/PS1, were selected for further studies. Antibiotic-mediated gut microbial inactivation attenuated MSCs efficacy in 5 × FAD mice, implicating the involvement of gut microbiota in the therapeutic mechanism. Functional analysis of altered gut microbiota and targeted bile acid metabolism profiling revealed a significant enhancement in bile acid variety following MSCs therapy. A chief bile acid constituent, taurocholic acid (TCA), was orally administered to AD mice and similarly abated AD symptoms. Nonetheless, the disruption of intestinal neuronal integrity with enterotoxin abrogated the ameliorative impact of both MSCs and TCA treatments. Collectively, our findings substantiate that MSCs confer therapeutic benefits in AD within a paradigm that primarily involves regulation of gut microbiota and their metabolites through the MGBA.
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Affiliation(s)
- Cencan Xing
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Xiaoshuang Zhang
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Donghui Wang
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Hongyu Chen
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Xiaoyu Gao
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Chunbin Sun
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Wenhua Guo
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China; Reproductive Center, Peking University Third Hospital, Beijing, China
| | - Shah Roshan
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Yingxian Li
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Zhongci Hang
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Shanglin Cai
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Tong Lei
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Wangyu Bi
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Liangxuan Hou
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Luping Li
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Yawen Wu
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Liang Li
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China
| | - Zehua Zeng
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China.
| | - Hongwu Du
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, No. 30 XueYuan Road, Haidian District, Beijing 100083, China.
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Wang X, Wang G, Cen P, Lan H, Guo L, Yisha Z, Gu A, Liu G, Wang Z, Liu T, Yu Q. Lactobacillus-Polydopamine System for Targeted Drug Delivery in Overactive Bladder: Evidence from Bladder Cell Spheroids, Rat Models, and Urinary Microbiome Profiling. Int J Nanomedicine 2024; 19:8353-8371. [PMID: 39161357 PMCID: PMC11332418 DOI: 10.2147/ijn.s465745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
Introduction Overactive bladder (OAB) is a highly prevalent condition with limited treatment options due to poor efficacy, side effects, and patient compliance. Novel drug delivery systems that can target the bladder wall may improve OAB therapy. Methods We explored a polydopamine (PDA)-coated lactobacillus platform as a potential carrier for localized OAB treatment. Urinary microbiome profiling was performed to identify the presence of lactobacillus in healthy and OAB groups. Lactobacillus-PDA nanoparticles were synthesized and characterized by electron microscopy and spectrophotometry. A rat bladder perfusion model and human bladder smooth muscle cell spheroids were used to assess the distribution and penetration of the nanoparticles. The efficacy of the Lactobacillus-PDA system (LPS) for delivering the antimuscarinic drug solifenacin was evaluated in an OAB rat model. Results Urinary microbiome profiling revealed lactobacillus as a dominant genus in both healthy and OAB groups. The synthesized Lactobacillus-PDA nanoparticles exhibited uniform size and optical properties. In the rat bladder perfusion model, the nanoparticles distributed throughout the bladder wall and smooth muscle without toxicity. The nanoparticles also penetrated human bladder smooth muscle cell spheroids. In the OAB rat model, LPS facilitated the delivery of solifenacin and improved treatment efficacy. Discussion The results highlight LPS as a promising drug carrier for targeted OAB therapy via penetration into bladder tissues. This bacteriotherapy approach may overcome limitations of current systemic OAB medications. Lactobacillus, a probiotic bacterium present in the urinary tract microbiome, was hypothesized to adhere to and penetrate the bladder wall when coated with PDA nanoparticles, making it a suitable candidate for localized drug delivery.
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Affiliation(s)
- Xiaolong Wang
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Guanyi Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Peibin Cen
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Hongyu Lan
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linfa Guo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Zuhaer Yisha
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Aodun Gu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Guiyong Liu
- Department of Urology, Qianjiang Central Hospital of Hubei Province, Qianjiang, People’s Republic of China
| | - Zijian Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Tongzu Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Hubei Key Laboratory of Urological Diseases, Wuhan University, Wuhan, People’s Republic of China
- Hubei Clinical Research Center for Laparoscopic/Endoscopic Urologic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Institute of Urology, Wuhan University, Wuhan, People’s Republic of China
- Hubei Medical Quality Control Center for Laparoscopic/Endoscopic Urologic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Wuhan Clinical Research Center for Urogenital Tumors, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Qingfeng Yu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Urological Diseases, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Institute of Urology, Guangzhou Medical University, Guangzhou, People’s Republic of China
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Shi Y, Gahagan AC, Morrison MJ, Gregorich E, Lapen DR, Chen W. Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation. Microorganisms 2024; 12:1635. [PMID: 39203479 PMCID: PMC11356494 DOI: 10.3390/microorganisms12081635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.
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Affiliation(s)
- Yichao Shi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Alison Claire Gahagan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Malcolm J. Morrison
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Edward Gregorich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - David R. Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; (Y.S.); (A.C.G.); (M.J.M.); (E.G.); (D.R.L.)
- Department of Biology, University of Ottawa, 60 Marie Curie Prv., Ottawa, ON K1N 6N5, Canada
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9
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Liu Y, Chen Y, Chen J, Zhang J, Teng HH. Combined toxicity of Cd and aniline to soil bacteria varying with exposure sequence. ENVIRONMENT INTERNATIONAL 2024; 190:108916. [PMID: 39094404 DOI: 10.1016/j.envint.2024.108916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/16/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Joint toxicity of organic-metal co-contamination can vary depending on organisms, toxicants, and even the sequence of exposure. This study examines how the combined toxicity of aniline (An) and cadmium (Cd) to soil bacteria in microcosms changes when the order of contaminant introduction is altered. Through analyzing biodiversity, molecular ecological network, functional redundancy, functional genes and pathways, we find the treatment of Cd followed by An brings about the strongest adverse impact to the bacterial consortium, followed by the reverse-ordered exposure and the simple mixture of the two chemicals. On the level of individual organisms, exposure sequence also affects the bacteria that are otherwise resistant to the standalone toxicity of both An and Cd. The dynamic behavior of aniline-cadmium composite is interpreted by considering the tolerance of organisms to individual chemicals, the interactions of the two toxicants, the recovery time, as well as the priority effect. The overall effect of the composite contamination is conceptualized by treating the chemicals as environmental filters screening the growth of the community.
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Affiliation(s)
- Yanjiao Liu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Yuxuan Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Jiubin Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China
| | - Jianchao Zhang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China.
| | - H Henry Teng
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, China.
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10
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Peddle SD, Hodgson RJ, Borrett RJ, Brachmann S, Davies TC, Erickson TE, Liddicoat C, Muñoz-Rojas M, Robinson JM, Watson CD, Krauss SL, Breed MF. Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions. Biol Rev Camb Philos Soc 2024. [PMID: 39075839 DOI: 10.1111/brv.13124] [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: 03/16/2023] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024]
Abstract
Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil microbiota into (i) restoration planning, (ii) direct interventions for shaping soil biodiversity, and (iii) strategies for monitoring and predicting restoration trajectories. We show how better planning of restoration activities to account for soil microbiota can help improve progress towards restoration targets. We show how planning to embed soil microbiota experiments into restoration projects will permit a more rigorous assessment of the effectiveness of different restoration methods, especially when complemented by statistical modelling approaches that capitalise on existing data sets to improve causal understandings and prioritise research strategies where appropriate. In addition to recovering belowground microbiota, restoration strategies that include soil microbiota can improve the resilience of whole ecosystems. Fundamentally, restoration planning should identify appropriate reference target ecosystem attributes and - from the perspective of soil microbiota - comprehensibly consider potential physical, chemical and biological influences on recovery. We identify that inoculating ecologically appropriate soil microbiota into degraded environments can support a range of restoration interventions (e.g. targeted, broad-spectrum and cultured inoculations) with promising results. Such inoculations however are currently underutilised and knowledge gaps persist surrounding successful establishment in light of community dynamics, including priority effects and community coalescence. We show how the ecological trajectories of restoration sites can be assessed by characterising microbial diversity, composition, and functions in the soil. Ultimately, we highlight practical ways to apply the soil microbiota toolbox across the planning, intervention, and monitoring stages of ecosystem restoration and address persistent open questions at each stage. With continued collaborations between researchers and practitioners to address knowledge gaps, these approaches can improve current restoration practices and ecological outcomes.
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Affiliation(s)
- Shawn D Peddle
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Riley J Hodgson
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Ryan J Borrett
- SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - Stella Brachmann
- University of Waikato Te Whare Wananga o Waikato Gate 1, Knighton Road, Hamilton, 3240, New Zealand
| | - Tarryn C Davies
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Todd E Erickson
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, Kattidj Close, Kings Park, Western Australia, 6005, Australia
- Centre for Engineering Innovation, School of Agriculture and Environment, The University of Western Australia, Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Miriam Muñoz-Rojas
- Department of Plant Biology and Ecology, University of Seville, C. San Fernando, Sevilla, Spain
- School of Biological, Earth and Environmental Sciences, Centre for Ecosystem Science, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Jake M Robinson
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Carl D Watson
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Siegfried L Krauss
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, Kattidj Close, Kings Park, Western Australia, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
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11
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Qiu Z, He S, Lian CA, Qiao X, Zhang Q, Yao C, Mu R, Wang L, Cao XA, Yan Y, Yu K. Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments. NPJ Biofilms Microbiomes 2024; 10:62. [PMID: 39069527 DOI: 10.1038/s41522-024-00537-1] [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: 01/03/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Shuhang He
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Qing Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Ciqin Yao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Li Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xiao-Ai Cao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China.
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12
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Williams SE, Varliero G, Lurgi M, Stach JEM, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073401 DOI: 10.1099/mic.0.001478] [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: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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13
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You HS, Park JY, Seo H, Kim BJ, Kim JG. Increasing correlation between oral and gastric microbiota during gastric carcinogenesis. Korean J Intern Med 2024; 39:590-602. [PMID: 38910513 PMCID: PMC11236816 DOI: 10.3904/kjim.2023.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND/AIMS Recent research has increasingly focused on the role of the gastric microbiome in the development of gastric cancer. We aimed to investigate the changes in the microbiome during gastric carcinogenesis in structural and functional aspects, with a specific focus on the association between oral and gastric microbiomes. METHODS We collected saliva, gastric juice, and gastric tissue samples from 141 patients at different stages of gastric carcinogenesis and processed them for microbiome analysis using 16S rRNA gene profiling. The alpha and beta diversities were analyzed, and the differences in microbiome composition and function profiles were analyzed among the groups, as well as the correlation between changes in the oral and gastric microbiomes during carcinogenesis. RESULTS We observed significant differences in microbial diversity and composition between the disease and control groups, primarily in the gastric juice. Specific bacterial strains, including Schaalia odontolytica, Streptococcus cristatus, and Peptostreptococcus stomatis, showed a significant increase in abundance in the gastric juice in the low-grade dysplasia and gastric cancer groups. Notably, the correlation between the oral and gastric microbiota compositions, increased as the disease progressed. Predictive analysis of the metagenomic functional profiles revealed changes in functional pathways that may be associated with carcinogenesis (ABC transport and two-component systems). CONCLUSION During gastric carcinogenesis, the abundance of oral commensals associated with cancer increased in the stomach. The similarity in microbial composition between the stomach and oral cavity also increased, implying a potential role of oral-gastric bacterial interactions in gastric cancer development.
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Affiliation(s)
- Hee Sang You
- Laboratory of Gastrointestinal Mucosal Immunology, Chung-Ang University College of Medicine, Seoul,
Korea
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul,
Korea
| | - Jae Yong Park
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul,
Korea
| | - Hochan Seo
- Laboratory of Gastrointestinal Mucosal Immunology, Chung-Ang University College of Medicine, Seoul,
Korea
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul,
Korea
| | - Beom Jin Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul,
Korea
| | - Jae Gyu Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul,
Korea
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14
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Oliero M, Cuisiniere T, Ajayi AS, Gerkins C, Hajjar R, Fragoso G, Calvé A, Vennin Rendos H, Mathieu-Denoncourt A, Dagbert F, De Broux É, Loungnarath R, Schwenter F, Sebajang H, Ratelle R, Wassef R, Richard C, Duperthuy M, Gravel AE, Vincent AT, Santos MM. Putrescine Supplementation Limits the Expansion of pks+ Escherichia coli and Tumor Development in the Colon. CANCER RESEARCH COMMUNICATIONS 2024; 4:1777-1792. [PMID: 38934090 PMCID: PMC11261243 DOI: 10.1158/2767-9764.crc-23-0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/11/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024]
Abstract
Escherichia coli that harbor the polyketide synthase (pks) genomic island produce colibactin and are associated with sporadic colorectal cancer development. Given the considerable prevalence of pks+ bacteria in healthy individuals, we sought to identify strategies to limit the growth and expansion of pks+ E. coli. We found that culture supernatants of the probiotic strain E. coli Nissle 1917 were able to inhibit the growth of the murine pathogenic strain pks+ E. coli NC101 (EcNC101). We performed a nontargeted analysis of the metabolome in supernatants from several E. coli strains and identified putrescine as a potential postbiotic capable of suppressing EcNC101 growth in vitro. The effect of putrescine supplementation was then evaluated in the azoxymethane/dextran sulfate sodium mouse model of colorectal cancer in mice colonized with EcNC101. Putrescine supplementation inhibited the growth of pks+ E. coli, reduced the number and size of colonic tumors, and downmodulated the release of inflammatory cytokines in the colonic lumen. Additionally, putrescine supplementation led to shifts in the composition and function of gut microbiota, characterized by an increase in the Firmicutes/Bacteroidetes ratio and enhanced acetate production. The effect of putrescine was further confirmed in vitro using a pks+ E. coli strain isolated from a patient with colorectal cancer. These results suggest that probiotic-derived metabolites can be used as an alternative to live bacteria in individuals at risk of developing colorectal cancer due to the presence of pks+ bacteria in their colon. SIGNIFICANCE Putrescine supplementation inhibits the growth of cancer-promoting bacteria in the gut, lowers inflammation, and reduces colon cancer development. The consumption of healthy foods rich in putrescine may be a potential prophylactic approach for individuals at risk of developing colorectal cancer due to the presence of pks+ bacteria in their colon.
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Affiliation(s)
- Manon Oliero
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Thibault Cuisiniere
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Ayodeji S. Ajayi
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Claire Gerkins
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Roy Hajjar
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
- Department of Surgery, Faculty of Medicine, Université de Montréal, Montréal, Canada.
| | - Gabriela Fragoso
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Annie Calvé
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Hervé Vennin Rendos
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
| | - Annabelle Mathieu-Denoncourt
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Canada.
| | - François Dagbert
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Éric De Broux
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Rasmy Loungnarath
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Frank Schwenter
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Herawaty Sebajang
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Richard Ratelle
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Ramses Wassef
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Carole Richard
- Department of Surgery, Faculty of Medicine, Université de Montréal, Montréal, Canada.
- Digestive Surgery Service, Department of Surgery, Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Canada.
| | - Marylise Duperthuy
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Canada.
| | - Andrée E. Gravel
- Drug Discovery Platform, Research Institute McGill University Health Centre, Montreal, Canada.
| | - Antony T. Vincent
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, Canada.
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Canada.
| | - Manuela M. Santos
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada.
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada.
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15
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Zhu W, Chang L, Zhang M, Chen Q, Sui L, Shen C, Jiang J. Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors. iScience 2024; 27:109907. [PMID: 38812552 PMCID: PMC11135016 DOI: 10.1016/j.isci.2024.109907] [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: 07/12/2023] [Revised: 11/30/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, the links between climatic factors and variations in host-associated microbiota necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated microbial samples (64 gut and 62 skin) and 101 environmental microbial samples (51 soil and 50 water) from the eastern Tibetan Plateau, revealed host factors as primary drivers of the variations in host-associated microbiota. However, climatic factors contributed to additional variations in gut microbial beta-diversity and skin microbial function. Water microbiota were identified as a significant contributor to the amphibian-associated microbiomes, with their climate-driven variations mediating an indirect association between the variations in climatic factors and host-associated microbiota. These findings extend our understanding of the assembly of host-associated microbiota in amphibians, emphasizing the significance of microbiota in evaluating the impact of climate change on animals.
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Affiliation(s)
- Wei Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Liming Chang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meihua Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Qiheng Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Sui
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Shen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Carneiro RB, Gomes GM, Camargo FP, Zaiat M, Santos-Neto ÁJ. Anaerobic co-metabolic biodegradation of pharmaceuticals and personal care products driven by glycerol fermentation. CHEMOSPHERE 2024; 357:142006. [PMID: 38621493 DOI: 10.1016/j.chemosphere.2024.142006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Anaerobic digestion in two sequential phases, acidogenesis and methanogenesis, has been shown to be beneficial for enhancing the biomethane generation from wastewater. In this work, the application of glycerol (GOH) as a fermentation co-substrate during the wastewater treatment was evaluated on the biodegradation of different pharmaceuticals and personal care products (PPCPs). GOH co-digestion during acidogenesis led to a significant increase in the biodegradation of acetaminophen (from 78 to 89%), ciprofloxacin (from 25 to 46%), naproxen (from 73 to 86%), diclofenac (from 36 to 48%), ibuprofen (from 65 to 88%), metoprolol (from 45 to 59%), methylparaben (from 64 to 78%) and propylparaben (from 68 to 74%). The heterotrophic co-metabolism of PPCPs driven by glycerol was confirmed by the biodegradation kinetics, in which kbio (biodegradation kinetics constant) values increased from 0.18 to 2.11 to 0.27-3.60 L g-1-VSS d-1, for the operational phases without and with GOH, respectively. The assessment of metabolic pathways in each phase revealed that the prevalence of aromatic compounds degradation, metabolism of xenobiotics by cytochrome P450, and benzoate degradation routes during acidogenesis are key factors for the enzymatic mechanisms linked to the PPCPs co-metabolism. The phase separation of anaerobic digestion was effective in the PPCPs biodegradation, and the co-fermentation of glycerol provided an increase in the generation potential of biomethane in the system (energetic potential of 5.0 and 6.3 kJ g-1-CODremoved, without and with GOH, respectively). This study showed evidence that glycerol co-fermentation can exert a synergistic effect on the PPCPs removal during anaerobic digestion mediated by heterotrophic co-metabolism.
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Affiliation(s)
- Rodrigo B Carneiro
- São Carlos Institute of Chemistry, University of São Paulo (USP), 400, Trabalhador São-Carlense Ave., São Carlos, São Paulo, 13566-590, Brazil; Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Severo Ochoa Excellence Center, Spanish Council of Scientific Research (CSIC), Jordi Girona 18-26, E-08034, Barcelona, Spain.
| | - Gisele M Gomes
- São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, 13563-120, São Carlos, São Paulo, Brazil.
| | - Franciele P Camargo
- Bioenergy Research Institute (IPBEN), UNESP- São Paulo State University, Rio Claro, SP, 13500-230, Brazil.
| | - Marcelo Zaiat
- São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, 13563-120, São Carlos, São Paulo, Brazil.
| | - Álvaro J Santos-Neto
- São Carlos Institute of Chemistry, University of São Paulo (USP), 400, Trabalhador São-Carlense Ave., São Carlos, São Paulo, 13566-590, Brazil.
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17
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Geng J, Zhang W, Liang S, Xue N, Song W, Yang Y. Diversity and biogeography of bacterial community in the Ili River network varies locally and regionally. WATER RESEARCH 2024; 256:121561. [PMID: 38581986 DOI: 10.1016/j.watres.2024.121561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Microorganisms in rivers indeed play a crucial role in nutrient cycling within aquatic ecosystems. Understanding the assembly mechanisms of bacterial communities in river networks is essential for predicting their special composition and functional characteristics in natural rivers. This study employed 16S rRNA gene amplicon sequence variation (ASVs) to scrutinize the bacterial community within the uniquely topographical Ili River network. The bacterial community composition varied across the three tributaries with distinct sources and the mainstream. The confluence of various sources diminished the diversity of the bacterial community and altered the functionality of within mainstream. We suggest that strong dispersal limitation predominantly shaped the community at the regional scale (46.6 %), underscoring the significant contribution of headwater sites to bacterial community composition. Contrary to expectation, the bacterial resources in the mainstream were not enriched by the higher diversity in three tributaries. Instead, confluence disturbance potentially increased the undominated processes (36.7 %) and alter the bacterial community composition at the local scale of the mainstream. The intricate coalescence at the confluence could potentially be an intriguing causative factor. Our research indicates that the composition of bacterial communities within intricate river networks exhibits biogeographic patterns, simultaneously influenced by river confluence and geographical features, necessitating multi-scale analysis.
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Affiliation(s)
- Jun Geng
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, China
| | - Weihong Zhang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, China
| | - Shuxin Liang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Nana Xue
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wenjuan Song
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, China; Xinjiang Laboratory of Environmental Pollution and Ecological Remediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, China.
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18
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Pirete LDM, Camargo FP, Grosseli GM, Sakamoto IK, Fadini PS, Silva EL, Varesche MBA. Microbial diversity and metabolic inference of diclofenac removal in optimised batch heterotrophic-denitrifying conditions by means of factorial design. ENVIRONMENTAL TECHNOLOGY 2024; 45:2847-2866. [PMID: 36927407 DOI: 10.1080/09593330.2023.2192365] [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: 09/26/2022] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Using the Response Surface Methodology (RSM) and Rotational Central Composite Design (RCCD), this study evaluated the removal of DCF under denitrifying conditions, with ethanol as cosubstrate, in batch reactors, being 1 L Erlenmeyer flasks (330 mL of reactional volume) containing Dofing medium and kept under agitation at 130 rpm and incubated at mesophilic temperature (30 °C). It considered the individual and multiple effects of the variables: nitrate (130 - 230 mg NO3- L-1), DCF (60-100 µg DCF L-1) and ethanol (130 - 230 mg EtOH L-1). The highest drug removal efficiency (17.5%) and total nitrate removal were obtained at 176.6 ± 4.3 mg NO3 -L-1, 76.8 ± 3.7 µg DCF L-1, and 180.0 ± 2.5 mg EtOH L-1. Under such conditions, the addition of ethanol and nitrate was significant for the additional removal of diclofenac (p > 0.05). The prevalence of Rhodanobacter, Haliangium and Terrimonas in the inoculum biomass (activated sludge systems) was identified through the 16S rRNA gene sequencing. The potential of these genera to remove nitrate and degrade diclofenac was inferred, and the main enzymes potentially involved in this process were α-methylacyl-CoA racemase, long-chain fatty acid-CoA ligase, catalases and pseudoperoxidases.
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Affiliation(s)
- Luciana de Melo Pirete
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, Brazil
| | - Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, Brazil
| | | | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, Brazil
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19
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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [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: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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20
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Wang Y, Zou Q. Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences. MICROBIAL ECOLOGY 2024; 87:74. [PMID: 38771320 PMCID: PMC11108897 DOI: 10.1007/s00248-024-02390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.
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Affiliation(s)
- Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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21
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Nath AR, Natarajan J. Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers. Genomics Inform 2024; 22:1. [PMID: 38907281 PMCID: PMC11184957 DOI: 10.1186/s44342-024-00001-8] [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: 06/12/2023] [Accepted: 03/07/2024] [Indexed: 06/23/2024] Open
Abstract
The goal of the study was to investigate the changes in the gut microbiota during the advancement of gastric cancer (GC) and identify pertinent taxa associated with the disease. We used a public fecal amplicon gastric cancer dataset from the Sequence Retrieval Archive (SRA), of patients with GC, gastritis, and healthy individuals. We did sequence pre-processing, including quality filtering of the sequences. Then, we performed a diversity analysis, evaluating α- and β-diversity. Next, taxonomic composition analysis was performed and the relative abundances of different taxa at the phylum and genus levels were compared between GC, gastritis, and healthy controls. The obtained results were subsequently subjected to statistical validation. To conclude, metagenomic function prediction was carried out, followed by correlation analysis between the microbiota and KEGG pathways. α analysis revealed a significant difference between male and female categories, while β analysis demonstrated significant distinctions between GC, gastritis, and healthy controls, as well as between sexes within the GC and gastritis groups. The statistically confirmed taxonomic composition analysis highlighted the presence of the microbes Bacteroides and Veillonella. Furthermore, through metagenomic prediction analysis and correlation analysis with pathways, three taxa, namely Akkermansia, Gammaproteobacteria, and Veillonella, were identified as potential biomarkers for GC. Additionally, this study reports, for the first time, the presence of two bacteria, Desulfobacteriota and Synergistota, in GC, necessitating further investigation. Overall, this research sheds light on the potential involvement of gut microbiota in GC pathophysiology; however, additional studies are warranted to explore its functional significance.
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Affiliation(s)
- Anju R Nath
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046, India.
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22
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Wang J, Liu C, Cao Q, Li Y, Chen L, Qin Y, Wang T, Wang C. Enhanced biodegradation of microplastic and phthalic acid ester plasticizer: The role of gut microorganisms in black soldier fly larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171674. [PMID: 38479533 DOI: 10.1016/j.scitotenv.2024.171674] [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: 01/04/2024] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Hermetia illucens larvae are recognized for their ability to mitigate or eliminate contaminants by biodegradation. However, the biodegradation characteristics of microplastics and phthalic acid esters plasticizers, as well as the role of larval gut microorganisms, have remained largely unrevealed. Here, the degradation kinetics of plasticizers, and biodegradation characteristics of microplastics were examined. The role of larval gut microorganisms was investigated. For larval development, microplastics slowed larval growth significantly (P < 0.01), but the effect of plasticizer was not significant. The degradation kinetics of plasticizers were enhanced, resulting in an 8.11 to 20.41-fold decrease in degradation half-life and a 3.34 to 3.82-fold increase in final degradation efficiencies, compared to degradation without larval participation. The depolymerization and biodeterioration of microplastics were conspicuously evident, primarily through a weight loss of 17.63 %-25.52 %, variation of chemical composition and structure, bio-oxidation and bioerosion of microplastic surface. The synergistic effect driven by larval gut microorganisms, each with various functions, facilitated the biodegradation. Specifically, Ignatzschineria, Paenalcaligenes, Moheibacter, Morganella, Dysgonomonas, Stenotrophomonas, Bacteroides, Sphingobacterium, etc., appeared to be the key contributors, owing to their xenobiotic biodegradation and metabolism functions. These findings offered a new perspective on the potential for microplastics and plasticizers biodegradation, assisted by larval gut microbiota.
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Affiliation(s)
- Jiaqing Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Cuncheng Liu
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China; Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China.
| | - Qingcheng Cao
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Yun Li
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Li Chen
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Yuanhang Qin
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Tielin Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Cunwen Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China.
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23
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Li H, Wang M, Chen P, Zhu M, Chen L. A high-dose of ursodeoxycholic acid treatment alleviates liver inflammation by remodeling gut microbiota and bile acid profile in a mouse model of non-alcoholic steatohepatitis. Biomed Pharmacother 2024; 174:116617. [PMID: 38643542 DOI: 10.1016/j.biopha.2024.116617] [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: 01/04/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024] Open
Abstract
Ursodeoxycholic acid (UDCA) is a hydrophilic bile acid commonly used for treating cholestatic liver disease. However, its efficacy on non-alcoholic steatohepatitis (NASH) was controversial. This study aimed to investigate the impact of a high dosage of UDCA on a mouse model of NASH. Forty 6-week-old mice were fed a high-fat high-cholesterol (HFHC) diet for 12 weeks to establish a mouse model of NASH, and then divided into four groups: two groups transitioned to a normal diet, and the other two groups maintained the HFHC diet. Each group was administered a daily dosage of 300 mg/kg of UDCA or saline for a period of 8 weeks. The 16 s ribosomal RNA genes extracted from mice fecal pellets were sequenced using next-generation sequencing techniques. Serum bile acid profiles were quantified using liquid chromatography electrospray ionization tandem mass spectrometry method. The results showed that UDCA treatment ameliorated liver inflammation, without affecting liver fibrosis. UDCA treatment reduced the relative abundance of the genera Bacteroides, Parabacteroides, and Intestinimonas, whereas increased the relative abundance of the genera norank_f_Muribaculaceae and Parasutterella in the HFHC-maintaining groups. The serum levels of total bile acids and total primary bile acids increased, whereas those of endogenous primary bile acids decreased after UDCA treatment. Correlation analysis showed that primary bile acids were negatively correlated with the genera norank_f_Christensenellaceae and unclassified_f_Ruminococcaceae. In conclusion, a high dosage of UDCA can alleviate liver inflammation, probably by modifying the composition of gut microbiota and serum bile acid profiles in NASH mice.
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Affiliation(s)
- Hu Li
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 201821, China; Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People`s Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200235, China
| | - Mingjie Wang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 201821, China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 201821, China
| | - Mingyu Zhu
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 201821, China
| | - Li Chen
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 201821, China.
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24
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Osadchiy V, Belarmino A, Kianian R, Sigalos JT, Furtado TP, Ancira JS, Kanie T, Mangum SF, Tipton CD, Hsieh TCM, Mills JN, Eleswarapu SV. Urine microbes and predictive metagenomic profiles associate with abnormalities in sperm parameters: implications for male subfertility. F&S SCIENCE 2024; 5:163-173. [PMID: 38336233 DOI: 10.1016/j.xfss.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
OBJECTIVE To explore the taxonomic and predicted functional relationship between the urine microbiome and alterations of semen analysis (SA) parameters. DESIGN Cross-sectional study. SETTING Academic medical center. PATIENT(S) Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited and stratified on the basis of alterations, or lack thereof, in SA parameters. MAIN OUTCOME MEASURE Changes in the functional and taxonomic urine microbiome profiles of participants with or without alterations in SA parameters. RESULTS Seventy-three participants were included in our study. Men with abnormal sperm motility (N = 27) showed a nearly 50-fold higher abundance of Dialister micraerophilus compared with those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.439). Men with abnormal sperm concentration (N = 20) showed a lower abundance of Enterococcus faecalis and Staphylococcus aureus, compared with those with normal sperm concentration (N = 53). The urine of participants with impaired sperm motility demonstrated dramatic differences in predictive functional profiles in pathways involved in oxidation-reduction balance and cell longevity. CONCLUSIONS Our findings underscore differences in the urinary microbiome and abnormalities in semen parameters, especially sperm motility. By incorporating predictive functional profiling, we also highlight possible mechanisms that may drive the observed differences in sperm parameters.
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Affiliation(s)
- Vadim Osadchiy
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Andre Belarmino
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Reza Kianian
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - John T Sigalos
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Thiago P Furtado
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Jacob S Ancira
- RTL Genomics, MicroGen DX, Lubbock, Texas; Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | - Trisha Kanie
- Department of Urology, University of California, San Diego, California
| | | | | | - Tung-Chin M Hsieh
- Department of Urology, University of California, San Diego, California
| | - Jesse N Mills
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sriram V Eleswarapu
- Division of Andrology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.
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25
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Zhang L, Yuan L, Wen Y, Zhang M, Huang S, Wang S, Zhao Y, Hao X, Li L, Gao Q, Wang Y, Zhang S, Huang S, Liu K, Yu X, Li D, Xu J, Zhao B, Zhang L, Zhang H, Zhou W, Ai C. Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices. THE NEW PHYTOLOGIST 2024; 242:1275-1288. [PMID: 38426620 DOI: 10.1111/nph.19653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.
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Affiliation(s)
- Liyu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Liang Yuan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanchen Wen
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Meiling Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shuyu Huang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shiyu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yuanzheng Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Xiangxiang Hao
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Lujun Li
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Qiang Gao
- Jilin Agricultural University, Changchun, 130118, China
| | - Yin Wang
- Jilin Agricultural University, Changchun, 130118, China
| | - Shuiqing Zhang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Shaomin Huang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Kailou Liu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Xichu Yu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Dongchu Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiukai Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Bingqiang Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Lu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huimin Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Chao Ai
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
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Zeng JY, Li W, Su JQ, Wang YZ, Li Y, Yao H. Manure application amplified the co-selection of quaternary ammonium disinfectant and antibiotic on soil antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133792. [PMID: 38368685 DOI: 10.1016/j.jhazmat.2024.133792] [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: 10/13/2023] [Revised: 01/17/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Disinfectants and antibiotics are widely used for the prevention and control of bacterial infectious diseases. Frequent disinfection is thought to exacerbate antibiotic resistance. However, little is known about how disinfectants and antibiotics co-induce changes in the soil antibiotic resistance genes (ARGs). This study determined the ARG profiles and bacterial community dynamics between unamended soil and manure-amended soil exposed to benzalkonium chloride (C12) (BC, 10 mg kg-1) disinfectant and sulfamethazine (SMZ, 1 mg kg-1), using high-throughput quantitative PCR and 16 S rRNA gene sequencing. Manure application enriched the soil in terms of ARGs abundance and diversity, which synergistically amplified the co-selection effect of BC and SMZ on soil antibiotic resistome. Compared with the control treatment, BC and SMZ exposure had a smaller impact on the bacterial infectious diseases and antimicrobial resistance-related functions in manure-amended soil, in which bacterial communities with greater tolerance to antimicrobial substances were constructed. Manure application increased the proportion of rank I ARGs and potential human pathogenic bacteria, while BC and SMZ exposure increased the drug-resistant pathogens transmission risk. This study validated that BC and SMZ aggravated the antimicrobial resistance under manure application, providing a reference for managing the spread risk of antimicrobial resistance in agricultural activities.
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Affiliation(s)
- Jie-Yi Zeng
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Wei Li
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
| | - Yan-Zi Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China.
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27
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Isokpehi RD, Kim Y, Krejci SE, Trivedi VD. Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential. Microorganisms 2024; 12:791. [PMID: 38674735 PMCID: PMC11052009 DOI: 10.3390/microorganisms12040791] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.
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Affiliation(s)
| | - Yungkul Kim
- Oyster Microbiome Project, College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (S.E.K.); (V.D.T.)
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Chen See JR, Leister J, Wright JR, Kruse PI, Khedekar MV, Besch CE, Kumamoto CA, Madden GR, Stewart DB, Lamendella R. Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities. Front Microbiol 2024; 15:1398018. [PMID: 38680911 PMCID: PMC11045941 DOI: 10.3389/fmicb.2024.1398018] [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: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Clostridioides difficile infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ (n = 20) and CDI- (n = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, p > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, p ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens Enterocloster bolteae and Ruminococcus gnavus in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by C. difficile. This provides evidence of another possible contributor to C. difficile's resistance to antibiotics and frequent recurrence in vivo. Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if C. difficile is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.
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Affiliation(s)
| | | | - Justin R. Wright
- Juniata College, Huntingdon, PA, United States
- Wright Labs LLC, Huntingdon, PA, United States
| | | | | | | | - Carol A. Kumamoto
- Molecular Biology and Microbiology, Tufts University, Boston, MA, United States
| | - Gregory R. Madden
- University of Virginia School of Medicine, Charlottesville, VA, United States
| | - David B. Stewart
- Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL, United States
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Sarpong N, Seifert J, Bennewitz J, Rodehutscord M, Camarinha-Silva A. Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency. Front Microbiol 2024; 15:1354537. [PMID: 38659980 PMCID: PMC11040106 DOI: 10.3389/fmicb.2024.1354537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome's role in NUE, paving the way for future strategies to enhance sustainable pig production.
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Affiliation(s)
- Naomi Sarpong
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Markus Rodehutscord
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
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Hara M, Suzuki H, Hayashi D, Morii W, Nakamura T, Kiyoki K, Hara H, Ishii R, Noguchi E, Takada H. Gut microbiota of one-and-a-half-year-old food-allergic and healthy children. Allergol Int 2024:S1323-8930(24)00042-X. [PMID: 38600019 DOI: 10.1016/j.alit.2024.03.004] [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: 06/28/2023] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Intestinal bacteria may play a role in the development of food allergies. This study aimed to analyze and compare the gut microbiota of food-allergic children with that of healthy children of the same age. METHODS Stool samples were collected from one-and-a-half-year-old food-allergic (FA group, n = 29) and healthy controls (HC group, n = 19). A questionnaire was provided to examine the children's birth, dietary, medical, and social histories. The gut microbiota was profiled by 16S rRNA sequencing. Differences in taxonomic composition were assessed using linear discriminant analysis effect size (LEfSe), and microbial functional profiles were predicted with Tax4Fun2. RESULTS No significant difference in the alpha diversity index between the two groups; however, a negative correlation was observed between the Shannon diversity index and the relative abundance of Bacteroides. A significant difference was observed in beta diversity (permutational multivariate analysis of variance) in the bacterial composition between the FA and HC groups (P < 0.05). The FA group had a higher abundance of Escherichia and Anaeromassilibacillus and a lower abundance of Bacteroides, Oscillibacter, Ruminococcus, Hungateiclostridium and Anaerotaenia than the HC group (LEfSe: linear discriminant analysis score >2). The FA group showed a predicted increase in the expression levels of genes associated with intestinal pathogenicity compared with that in the HC group. CONCLUSIONS The gut microbiota of food-allergic children has a higher abundance of bacteria involved in intestinal inflammation and a lower abundance of bacteria involved in immune tolerance than that of healthy children. This dysbiosis may also be associated with food allergies.
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Affiliation(s)
- Monami Hara
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan; Department of Child Health, Institute of Medicine, University of Tsukuba, Ibaraki, Japan; Department of Medical Genetics, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Hisato Suzuki
- Department of Child Health, Institute of Medicine, University of Tsukuba, Ibaraki, Japan; Department of Medical Genetics, Institute of Medicine, University of Tsukuba, Ibaraki, Japan; Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Hayashi
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan; Department of Pediatrics, Tsukuba Medical Center Hospital, Ibaraki, Japan
| | - Wataru Morii
- Department of Medical Genetics, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takako Nakamura
- Department of Medical Genetics, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Kaori Kiyoki
- Department of Pediatrics, Tsukuba Medical Center Hospital, Ibaraki, Japan
| | - Hideki Hara
- Department of Pediatrics, Tsukuba Medical Center Hospital, Ibaraki, Japan
| | - Ryota Ishii
- Department of Biostatistics, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Emiko Noguchi
- Department of Medical Genetics, Institute of Medicine, University of Tsukuba, Ibaraki, Japan.
| | - Hidetoshi Takada
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan; Department of Child Health, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
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Saba E, Farhat M, Daoud A, Khashan A, Forkush E, Menahem NH, Makkawi H, Pandi K, Angabo S, Kawasaki H, Plaschkes I, Parnas O, Zamir G, Atlan K, Elkin M, Katz L, Nussbaum G. Oral bacteria accelerate pancreatic cancer development in mice. Gut 2024; 73:770-786. [PMID: 38233197 DOI: 10.1136/gutjnl-2023-330941] [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: 08/17/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
OBJECTIVE Epidemiological studies highlight an association between pancreatic ductal adenocarcinoma (PDAC) and oral carriage of the anaerobic bacterium Porphyromonas gingivalis, a species highly linked to periodontal disease. We analysed the potential for P. gingivalis to promote pancreatic cancer development in an animal model and probed underlying mechanisms. DESIGN We tracked P. gingivalis bacterial translocation from the oral cavity to the pancreas following administration to mice. To dissect the role of P. gingivalis in PDAC development, we administered bacteria to a genetically engineered mouse PDAC model consisting of inducible acinar cell expression of mutant Kras (Kras +/LSL-G12D; Ptf1a-CreER, iKC mice). These mice were used to study the cooperative effects of Kras mutation and P. gingivalis on the progression of pancreatic intraepithelial neoplasia (PanIN) to PDAC. The direct effects of P. gingivalis on acinar cells and PDAC cell lines were studied in vitro. RESULTS P. gingivalis migrated from the oral cavity to the pancreas in mice and can be detected in human PanIN lesions. Repetitive P. gingivalis administration to wild-type mice induced pancreatic acinar-to-ductal metaplasia (ADM), and altered the composition of the intrapancreatic microbiome. In iKC mice, P. gingivalis accelerated PanIN to PDAC progression. In vitro, P. gingivalis infection induced acinar cell ADM markers SOX9 and CK19, and intracellular bacteria protected PDAC cells from reactive oxygen species-mediated cell death resulting from nutrient stress. CONCLUSION Taken together, our findings demonstrate a causal role for P. gingivalis in pancreatic cancer development in mice.
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Affiliation(s)
- Elias Saba
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Maria Farhat
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Alaa Daoud
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Arin Khashan
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Esther Forkush
- Gastroenterology, Hadassah Medical Center, Jerusalem, Israel
| | - Noam Hallel Menahem
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Hasnaa Makkawi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Karthikeyan Pandi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Sarah Angabo
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Hiromichi Kawasaki
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
- Central Research Institute, Wakunaga Pharmaceutical Co Ltd, Koda-cho, Akitakata-shi, Hiroshima, Japan
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Parnas
- Immunology and Cancer Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gideon Zamir
- Experimental Surgery, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | | | - Michael Elkin
- Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Lior Katz
- Department of Gastroenterology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gabriel Nussbaum
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
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Zhang D, Wu C, Liu Y, Li W, Li S, Peng L, Kang L, Ullah S, Gong Z, Li Z, Ding D, Jin Z, Huang H. Microplastics are detected in human gallstones and have the ability to form large cholesterol-microplastic heteroaggregates. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133631. [PMID: 38335610 DOI: 10.1016/j.jhazmat.2024.133631] [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: 10/12/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Ubiquitous pollution due to microplastics through the food chain is a major cause of various deleterious effects on the human health. The aim of this study was to determine the existence of microplastics and the internal mechanism of microplastics as accelerators of cholelithiasis. Gallstones were collected from 16 patients after cholecystectomy, and microplastics in the gallstones were detected through laser direct infrared and pyrolysis gas chromatographymass spectrometry examinations. Mice model of gallstone were constructed with or without different diameters of microplastic (0.5, 5 and 50 µm). The affinity between microplastic and cholesterol or bilirubin was tested by co-culturing and qualified using molecular dynamics simulations. Finally, altered gut microbiota among the groups were identified using 16 s rRNA sequencing. The presence of microplastics in the gallstones of all the patients were confirmed. Microplastic content was significantly higher in younger chololithiasis patients (age<50 years). Mice fed a high-cholesterol diet with microplastic drinks showed more severe chololithiasis. In terms of the mechanism, microplastics showed a higher affinity for cholesterol than for bilirubin. Significant alterations in the gut microbiota have also been identified after microplastic intake in mice. Our study revealed the presence of microplastics in human gallstones, showcasing their potential to aggravate chololithiasis by forming large cholesterol-microplastic heteroaggregates and altering the gut microbiota.
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Affiliation(s)
- Deyu Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chang Wu
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yue Liu
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Wanshun Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Shiyu Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Lisi Peng
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Le Kang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Saif Ullah
- Department of Gastroenterology, First affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Zijun Gong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Dan Ding
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Zhendong Jin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Haojie Huang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China.
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Yang Y, Wang H, Tu J, Li Y, Guan H. Comprehensive genomic analysis of Burkholderia arboris PN-1 reveals its biocontrol potential against Fusarium solani-induced root rot in Panax notoginseng. Curr Genet 2024; 70:4. [PMID: 38555312 DOI: 10.1007/s00294-024-01288-4] [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: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Panax notoginseng (Burkill) F.H. Chen, a valuable traditional Chinese medicine, faces significant yield and quality challenges stemming from root rot primarily caused by Fusarium solani. Burkholderia arboris PN-1, isolated from the rhizosphere soil of P. notoginseng, demonstrated a remarkable ability to inhibit the growth of F. solani. This study integrates phenotypic, phylogenetic, and genomic analyses to enhance our understanding of the biocontrol mechanisms employed by B. arboris PN-1. Phenotype analysis reveals that B. arboris PN-1 effectively suppresses P. notoginseng root rot both in vitro and in vivo. The genome of B. arboris PN-1 comprises three circular chromosomes (contig 1: 3,651,544 bp, contig 2: 1,355,460 bp, and contig 3: 3,471,056 bp), with a 66.81% GC content, housing 7,550 protein-coding genes. Notably, no plasmids were detected. Phylogenetic analysis places PN-1 in close relation to B. arboris AU14372, B. arboris LMG24066, and B. arboris MEC_B345. Average nucleotide identity (ANI) values confirm the PN-1 classification as B. arboris. Comparative analysis with seven other B. arboris strains identified 4,628 core genes in B. arboris PN-1. The pan-genome of B. arboris appears open but may approach closure. Whole-genome sequencing revealed 265 carbohydrate-active enzymes and identified 9 gene clusters encoding secondary metabolites. This comprehensive investigation enhances our understanding of B. arboris genomes, paving the way for their potential as effective biocontrol agents against fungal plant pathogens in the future.
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Affiliation(s)
- Yun Yang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan, China
| | - Haoji Wang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Jielei Tu
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Yan Li
- Yunnan Provincial Rural Energy Management Station, Kunming, 650233, Yunnan, China
| | - Huilin Guan
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China.
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China.
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Calderon RB, Dangi SR. Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions. Microorganisms 2024; 12:667. [PMID: 38674611 PMCID: PMC11052256 DOI: 10.3390/microorganisms12040667] [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: 03/08/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) and rhizobium play a significant role in plant symbiosis. However, their influence on the rhizosphere soil microbiome associated with nutrient acquisition and soil health is not well defined in the drylands of Montana (MT), USA. This study investigated the effect of microbial inoculants as seed treatment on pea yield, nutrient uptake, potential microbial functions, and rhizosphere soil microbial communities using high-throughput sequencing of 16S and ITS rRNA genes. The experiment was conducted under two contrasting dryland conditions with four treatments: control, single inoculation with AMF or Rhizobium, and dual inoculations of AMF and Rhizobium (AMF+Rhizobium). Our findings revealed that microbial inoculation efficacy was site-specific. AMF+Rhizobium synergistically increased grain yield at Sidney dryland field site (DFS) 2, while at Froid site, DFS 1, AMF improved plant resilience to acidic soil but contributed a marginal yield under non-nutrient limiting conditions. Across dryland sites, the plants' microbial dependency on AMF+Rhizobium (12%) was higher than single inoculations of AMF (8%) or Rhizobium (4%) alone. Variations in microbial community structure and composition indicate a site-specific response to AMF and AMF+Rhizobium inoculants. Overall, site-specific factors significantly influenced plant nutrient uptake, microbial community dynamics, and functional potential. It underscores the need for tailored management strategies that consider site-specific characteristics to optimize benefits from microbial inoculation.
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Affiliation(s)
- Rosalie B. Calderon
- Agricultural Research Service, Northern Plains Agricultural Research Laboratory, USDA, 1500 N Central Avenue, Sidney, MT 59270, USA
| | - Sadikshya R. Dangi
- Correspondence: (R.B.C.); (S.R.D.); Tel.: +1-(406)-433-9479 (R.B.C.); +1-(406)-433-9490 (S.R.D.); Fax: +1-(406)-433-5038 (R.B.C. & S.R.D.)
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35
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He C, An Y, Shi L, Huang Y, Zhang H, Fu W, Wang M, Shan Z, Du Y, Xie J, Huang Z, Sun W, Zhao Y, Zhao B. Xiasangju alleviate metabolic syndrome by enhancing noradrenaline biosynthesis and activating brown adipose tissue. Front Pharmacol 2024; 15:1371929. [PMID: 38576483 PMCID: PMC10993144 DOI: 10.3389/fphar.2024.1371929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/06/2024] [Indexed: 04/06/2024] Open
Abstract
Metabolic syndrome (MetS) is a clinical condition associated with multiple metabolic risk factors leading to type 2 diabetes mellitus and other metabolic diseases. Recent evidence suggests that modulating adipose tissue to adaptive thermogenesis may offer therapeutic potential for MetS. Xiasangju (XSJ) is a marketed drug and dietary supplement used for the treatment of metabolic disease with anti-inflammatory activity. This study investigated the therapeutic effects of XSJ and the underlying mechanisms affecting the activation of brown adipose tissue (BAT) in MetS. The results revealed that XSJ ameliorated MetS by enhancing glucose and lipid metabolism, leading to reduced body weight and abdominal circumference, decreased adipose tissue and liver index, and improved blood glucose tolerance. XSJ administration stimulated catecholamine biosynthesis, increasing noradrenaline (NA) levels and activating NA-mediated proteins in BAT. Thus, BAT enhanced thermogenesis and oxidative phosphorylation (OXPHOS). Moreover, XSJ induced changes in gut microbiota composition, with an increase in Oscillibacter abundance and a decrease in Bilophila, Candidatus Stoquefichus, Holdemania, Parasutterella and Rothia. XSJ upregulated the proteins associated with intestinal tight junctions corresponding with lower serum lipopolysaccharide (LPS), tumor necrosis factor α (TNF-α) monocyte chemoattractant protein-1 (MCP-1) and interleukin-6 (IL-6) levels to maintain NA signaling transport. In summary, XSJ may alleviate MetS by promoting thermogenesis in BAT to ultimately boost energy metabolism through increasing NA biosynthesis, strengthening intestinal barrier integrity and reducing low-grade inflammation. These findings suggest XSJ has potential as a natural therapeutic agent for the treatment of MetS.
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Affiliation(s)
- Changhao He
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yongcheng An
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Lu Shi
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
- Central Laboratories, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Yan Huang
- College of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Huilin Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wanxin Fu
- College of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Menglu Wang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Ziyi Shan
- College of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuhang Du
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiamei Xie
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhiyun Huang
- Guangzhou Baiyunshan Xingqun Pharmaceutical Co., Ltd, Guangzhou, China
| | - Weiguang Sun
- Guangzhou Baiyunshan Xingqun Pharmaceutical Co., Ltd, Guangzhou, China
| | - Yonghua Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Baosheng Zhao
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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36
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Louvado A, Coelho FJRC, Palma M, Magnoni LJ, Silva-Brito F, Ozório ROA, Cleary DFR, Viegas I, Gomes NCM. Study of the influence of tributyrin-supplemented diets on the gut bacterial communities of rainbow trout (Oncorhynchus mykiss). Sci Rep 2024; 14:5645. [PMID: 38454011 PMCID: PMC10920674 DOI: 10.1038/s41598-024-55660-y] [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: 01/23/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Dietary supplementation with triglyceride tributyrin (TBT), a butyrate precursor, has been associated with beneficial effects on fish health and improvements in the ability of carnivorous fish to tolerate higher levels of plant-based protein. In this study, we aimed to investigate the effects of a plant-based diet supplemented with TBT on the structural diversity and putative function of the digesta-associated bacterial communities of rainbow trout (Oncorhynchus mykiss). In addition to this, we also assessed the response of fish gut digestive enzyme activities and chyme metabolic profile in response to TBT supplementation. Our results indicated that TBT had no significant effects on the overall fish gut bacterial communities, digestive enzyme activities or metabolic profile when compared with non-supplemented controls. However, a more in-depth analysis into the most abundant taxa showed that diets at the highest TBT concentrations (0.2% and 0.4%) selectively inhibited members of the Enterobacterales order and reduced the relative abundance of a bacterial population related to Klebsiella pneumoniae, a potential fish pathogen. Furthermore, the predicted functional analysis of the bacterial communities indicated that increased levels of TBT were associated with depleted KEGG pathways related to pathogenesis. The specific effects of TBT on gut bacterial communities observed here are intriguing and encourage further studies to investigate the potential of this triglyceride to promote pathogen suppression in the fish gut environment, namely in the context of aquaculture.
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Affiliation(s)
- A Louvado
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - M Palma
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - L J Magnoni
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
| | - F Silva-Brito
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - R O A Ozório
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - D F R Cleary
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - I Viegas
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - N C M Gomes
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
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37
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Ni Z, Gong Z, Song L, Jia C, Zhang X. Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances. CHEMOSPHERE 2024; 351:141139. [PMID: 38185422 DOI: 10.1016/j.chemosphere.2024.141139] [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: 07/18/2023] [Revised: 12/25/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.
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Affiliation(s)
- Zijun Ni
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zongqiang Gong
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Lei Song
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chunyun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Xiaorong Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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38
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Kuo J, Liu D, Wen WH, Chiu CY, Chen W, Wu YW, Lai FT, Lin CH. Different microbial communities in paddy soils under organic and nonorganic farming. Braz J Microbiol 2024; 55:777-788. [PMID: 38147271 PMCID: PMC10920611 DOI: 10.1007/s42770-023-01218-5] [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] [Received: 10/04/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023] Open
Abstract
Organic agriculture is a farming method that provides healthy food and is friendly to the environment, and it is developing rapidly worldwide. This study compared microbial communities in organic farming (Or) paddy fields to those in nonorganic farming (Nr) paddy fields based on 16S rDNA sequencing and analysis. The predominant microorganisms in both soils were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, and Nitrospirota. The alpha diversity of the paddy soil microbial communities was not different between the nonorganic and organic farming systems. The beta diversity of nonmetric multidimensional scaling (NMDS) revealed that the two groups were significantly separated. Distance-based redundancy analysis (db-RDA) suggested that soil pH and electrical conductivity (EC) had a positive relationship with the microbes in organic paddy soils. There were 23 amplicon sequence variants (ASVs) that showed differential abundance. Among them, g_B1-7BS (Proteobacteria), s_Sulfuricaulis limicola (Proteobacteria), g_GAL15 (p_GAL15), c_Thermodesulfovibrionia (Nitrospirota), two of f_Anaerolineaceae (Chloroflexi), and two of g_S085 (Chloroflexi) showed that they were more abundant in organic soils, whereas g_11-24 (Acidobacteriota), g__Subgroup_7 (Acidobacteriota), and g_Bacillus (Firmicutes) showed differential abundance in nonorganic paddy soils. Functional prediction of microbial communities in paddy soils showed that functions related to carbohydrate metabolism could be the major metabolic activities. Our work indicates that organic farming differs from nonorganic farming in terms of microbial composition in paddy soils and provides specific microbes that might be helpful for understanding soil fertility.
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Affiliation(s)
- Jimmy Kuo
- Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 94450, Taiwan
| | - Daniel Liu
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Wei Hao Wen
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Ching Yuan Chiu
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Wanyu Chen
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Yun Wen Wu
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Fang-Ting Lai
- Department of Medicinal Botanicals and Foods On Health Applications, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Chorng-Horng Lin
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan.
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39
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Dash SP, Manu S, Kim JY, Rastogi G. Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon. MARINE POLLUTION BULLETIN 2024; 200:116138. [PMID: 38359478 DOI: 10.1016/j.marpolbul.2024.116138] [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: 10/14/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.
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Affiliation(s)
- Stiti Prangya Dash
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India; KIIT School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India
| | - Shivakumara Manu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500048, India
| | - Ji Yoon Kim
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India.
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40
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Xia M, Hua Z, Zhao Y, Zhang G, Hou X, Yang G, Liu S, Fang Y. Improvement of Urolithin A Yield by In Vitro Cofermentation of Streptococcus thermophilus FUA329 with Human Gut Microbiota from Different Urolithin Metabotypes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3008-3016. [PMID: 38301119 DOI: 10.1021/acs.jafc.3c09734] [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: 02/03/2024]
Abstract
Streptococcus thermophilus FUA329 converts ellagic acid (EA) to urolithin A (Uro-A), which is not autonomously converted by the gut microbiota to produce highly bioavailable and multibiologically active Uro-A in urolithin metabotype 0 (UM-0) populations. We consider that Streptococcus thermophilus FUA329 has the potential to be developed as a probiotic. Therefore, we utilized S. thermophilus FUA329 for in vitro cofermentation with gut microbiota. The results revealed that strain FUA329 increased the production of EA-converted Uro-A during in vitro cofermentation with the human gut microbiota of different urolithin metabotypes (UMs), with a significant increase in the production of Uro-A in the experimental group of UM-0. In addition, changes in the in vitro cofermentation microbial community were determined using high-throughput sequencing. Strain FUA329 modulated the structure and composition of the gut microbiota in different UMs, thereby significantly increasing the abundance of beneficial microbiota in the gut microbiota while decreasing the abundance of harmful microbiota. Of greatest interest was the significant increase in the abundance of Actinobacteria phylum after the cofermentation of strain FUA329 with UM-0 gut microbiota, which might be related to the significant increase in the production of Uro-A.
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Affiliation(s)
- Mengjie Xia
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Ziyan Hua
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yaling Zhao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Gewen Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaoyue Hou
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Guang Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shu Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yaowei Fang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- China Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- College of Ocean Food and Biochemical Engineering, Jiangsu Ocean University, Lianyungang 222005, China
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Delanote J, Correa Rojo A, Wells PM, Steves CJ, Ertaylan G. Systematic identification of the role of gut microbiota in mental disorders: a TwinsUK cohort study. Sci Rep 2024; 14:3626. [PMID: 38351227 PMCID: PMC10864280 DOI: 10.1038/s41598-024-53929-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Mental disorders are complex disorders influenced by multiple genetic, environmental, and biological factors. Specific microbiota imbalances seem to affect mental health status. However, the mechanisms by which microbiota disturbances impact the presence of depression, stress, anxiety, and eating disorders remain poorly understood. Currently, there are no robust biomarkers identified. We proposed a novel pyramid-layer design to accurately identify microbial/metabolomic signatures underlying mental disorders in the TwinsUK registry. Monozygotic and dizygotic twins discordant for mental disorders were screened, in a pairwise manner, for differentially abundant bacterial genera and circulating metabolites. In addition, multivariate analyses were performed, accounting for individual-level confounders. Our pyramid-layer study design allowed us to overcome the limitations of cross-sectional study designs with significant confounder effects and resulted in an association of the abundance of genus Parabacteroides with the diagnosis of mental disorders. Future research should explore the potential role of Parabacteroides as a mediator of mental health status. Our results indicate the potential role of the microbiome as a modifier in mental disorders that might contribute to the development of novel methodologies to assess personal risk and intervention strategies.
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Affiliation(s)
- Julie Delanote
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Alejandro Correa Rojo
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
- Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London, SE1 7EH, UK
| | - Gökhan Ertaylan
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium.
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Kumar B, Lorusso E, Fosso B, Pesole G. A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions. Front Microbiol 2024; 15:1343572. [PMID: 38419630 PMCID: PMC10900530 DOI: 10.3389/fmicb.2024.1343572] [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: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of implementation of Machine Learning (ML) in metadata retrieval, offering promising avenues for a deeper understanding of microbial communities and their ecological roles. Leveraging these tools will enhance our insights into microbial functional capabilities and ecological dynamics in diverse ecosystems. Finally, we emphasize the crucial metadata role in ML models development.
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Affiliation(s)
- Bablu Kumar
- Università degli Studi di Milano, Milan, Italy
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
| | - Erika Lorusso
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
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43
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [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: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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Soldan R, Fusi M, Cardinale M, Homma F, Santos LG, Wenzl P, Bach-Pages M, Bitocchi E, Chacon Sanchez MI, Daffonchio D, Preston GM. Consistent effects of independent domestication events on the plant microbiota. Curr Biol 2024; 34:557-567.e4. [PMID: 38232731 DOI: 10.1016/j.cub.2023.12.056] [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: 08/23/2022] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence of a domestication effect on the composition and abundance of the plant microbiota. We focused on the genus Phaseolus, which underwent four independent domestication events within two species (P. vulgaris and P. lunatus), providing multiple replicates of a process spanning thousands of years. We targeted Phaseolus seeds to identify a link between domesticated traits and bacterial community composition as Phaseolus seeds have been subject to large and consistent phenotypic changes during these independent domestication events. The seed bacterial communities of representative plant accessions from subpopulations descended from each domestication event were analyzed under controlled and field conditions. The results showed that independent domestication events led to similar seed bacterial community signatures in independently domesticated plant populations, which could be partially explained by selection for common domesticated plant phenotypes. Our results therefore provide evidence of a consistent effect of plant domestication on seed microbial community composition and abundance and offer avenues for applying knowledge of the impact of plant domestication on the plant microbiota to improve microbial applications in agriculture.
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Affiliation(s)
| | - Marco Fusi
- Center for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
| | - Massimiliano Cardinale
- University of Salento, Department of Biological and Environmental Sciences and Technologies, Lecce, Italy
| | - Felix Homma
- University of Oxford, Department of Biology, Oxford, UK
| | - Luis Guillermo Santos
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | - Peter Wenzl
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Isabel Chacon Sanchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gail M Preston
- University of Oxford, Department of Biology, Oxford, UK.
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45
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Matchado MS, Rühlemann M, Reitmeier S, Kacprowski T, Frost F, Haller D, Baumbach J, List M. On the limits of 16S rRNA gene-based metagenome prediction and functional profiling. Microb Genom 2024; 10:001203. [PMID: 38421266 PMCID: PMC10926695 DOI: 10.1099/mgen.0.001203] [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: 11/24/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type two diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.
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Affiliation(s)
- Monica Steffi Matchado
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Sandra Reitmeier
- ZIEL - Institute for Food & Health, Core Facility Microbiome, Technical University of Munich, Freising, Germany
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Core Facility Microbiome, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Guo K, Figueroa-Romero C, Noureldein MH, Murdock BJ, Savelieff MG, Hur J, Goutman SA, Feldman EL. Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis. Brain 2024; 147:665-679. [PMID: 37721161 PMCID: PMC10834248 DOI: 10.1093/brain/awad306] [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: 05/16/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex, fatal neurodegenerative disease. Disease pathophysiology is incompletely understood but evidence suggests gut dysbiosis occurs in ALS, linked to impaired gastrointestinal integrity, immune system dysregulation and altered metabolism. Gut microbiome and plasma metabolome have been separately investigated in ALS, but little is known about gut microbe-plasma metabolite correlations, which could identify robust disease biomarkers and potentially shed mechanistic insight. Here, gut microbiome changes were longitudinally profiled in ALS and correlated to plasma metabolome. Gut microbial structure at the phylum level differed in ALS versus control participants, with differential abundance of several distinct genera. Unsupervised clustering of microbe and metabolite levels identified modules, which differed significantly in ALS versus control participants. Network analysis found several prominent amplicon sequence variants strongly linked to a group of metabolites, primarily lipids. Similarly, identifying the features that contributed most to case versus control separation pinpointed several bacteria correlated to metabolites, predominantly lipids. Mendelian randomization indicated possible causality from specific lipids related to fatty acid and acylcarnitine metabolism. Overall, the results suggest ALS cases and controls differ in their gut microbiome, which correlates with plasma metabolites, particularly lipids, through specific genera. These findings have the potential to identify robust disease biomarkers and shed mechanistic insight into ALS.
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Affiliation(s)
- Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Figueroa-Romero
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mohamed H Noureldein
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin J Murdock
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masha G Savelieff
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Stephen A Goutman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eva L Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
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47
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Liu M, Wang T, Wang L, Xiao H, Li J, Duan C, Gao L, Liu Y, Yan H, Zhang Y, Ji S. Core microbiota for nutrient digestion remained and ammonia utilization increased after continuous batch culture of rumen microbiota in vitro. Front Microbiol 2024; 15:1331977. [PMID: 38328430 PMCID: PMC10848171 DOI: 10.3389/fmicb.2024.1331977] [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: 11/02/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction This study aimed to investigate the digestive function, urea utilization ability, and bacterial composition changes in rumen microbiota under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro. Methods The gas production, dry matter digestibility, and bacterial counts were determined for the continuously batch-cultured rumen fluid (CRF). The changes in fermentation parameters, NH3-N utilization efficiency, and microbial taxa were analyzed in CRF and were compared with that of fresh rumen fluid (RF), frozen rumen fluid (FRF, frozen rumen fluid at -80°C for 1 month), and the mixed rumen fluid (MRF, 3/4 RF mixed with 1/4 CRF) with in vitro rumen fermentation. Results The results showed that the dry matter digestibility remained stable while both the microbial counts and diversity significantly decreased over the 23 days of continuous batch culture. However, the NH3-N utilization efficiency of the CRF group was significantly higher than that of RF, FRF, and MRF groups (p < 0.05), while five core genera including Succinivibrio, Prevotella, Streptococcus, F082, and Megasphaera were retained after 23 days of continuous batch culture. The NH3-N utilization efficiency was effectively improved after continuous batch culture in vitro, and Streptococcus, Succinivibrio, Clostridium_sensu_stricto_1, p.251.o5, Oxalobacter, Bacteroidales_UCG.001, and p.1088.a5_gut_group were identified to explain 75.72% of the variation in NH3-N utilization efficiency with the RandomForest model. Conclusion Thus, core bacterial composition and function retained under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro, and bacterial biomarkers for ammonia utilization were illustrated in this study. These findings might provide potential applications in improving the efficiency and safety of non-protein nitrogen utilization in ruminants.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hui Yan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Yingjie Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Shoukun Ji
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
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48
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Sun C, Zhang S, Yang J, Zhou H, Cheng H, Chen Z, Yu L, Wang Y, Chen X. Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench. ENVIRONMENTAL RESEARCH 2024; 241:117602. [PMID: 37951379 DOI: 10.1016/j.envres.2023.117602] [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: 08/05/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.
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Affiliation(s)
- Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Libo Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China.
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Liang S, Zhang W, Grossart HP, Gadd GM, Liu W, Yang Y. The unique climate shapes distinct life-history traits of abundant bacteria in Tibetan Plateau grassland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168353. [PMID: 37935266 DOI: 10.1016/j.scitotenv.2023.168353] [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: 08/05/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023]
Abstract
The unique geographical patterns of the Qinghai-Tibet Plateau have shaped the different climatic characteristics of the Lhasa and Nyang River watersheds. However, our understanding of climate-dependent life history strategies in riparian grasslands is very limited. In this research, we have compared the causes and consequences of variations in the composition of soil abundant and rare bacterial taxa in the Nyang and Lhasa River watersheds. The results showed that the abundant bacteria, rather than the rare bacteria, exhibited distinct life history strategies between the Lhasa and Nyang watersheds that were a consequence of climate patterns. The wetter climate of the Nyang watershed led to a high ratio of r-strategists among the abundant bacteria (Abundant K:r = 0.323), while in the less favourable climate of the Lhasa watershed, K-strategists were more common among the soil abundant bacteria (Abundant K:r = 0.542). The assembly processes of abundant and rare bacteria in the Lhasa region under relatively harsh climatic conditions seemed to be more affected by variable selection than those in the Nyang region. Moreover, abundant bacteria in the Lhasa region developed stronger potentially cooperative relationships and exhibited a stronger metabolic capacity than those in the Nyang region. The 26 different functional genes identified in LS were highly associated with 38 abundant bacterial species. In contrast, the 16 identified functional genes in NY were highly correlated with 16 abundant bacterial species. These results provide new insights into climate-dependent life history strategies of soil bacterial communities with different abundances in riparian grasslands of the Tibetan Plateau. Contrasting the life history strategies of bacterial taxa with different abundances contributes to a better mechanistic knowledge of their impact on ecosystem functioning under current and future effects of global climate change.
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Affiliation(s)
- Shuxin Liang
- School of Ecology and Environment, Tibet University, Lhasa 850000, China; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan 430074, China
| | - Hans-Peter Grossart
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries (IGB), Neuglobsow 16775, Germany; Institute for Biochemistry and Biology, Potsdam University, Potsdam 14469, Germany
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK; State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing 102249, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan 430074, China.
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan 430074, China.
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50
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Richards SC, King WL, Sutherland JL, Bell TH. Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists. FEMS Microbiol Lett 2024; 371:fnae025. [PMID: 38553956 DOI: 10.1093/femsle/fnae025] [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: 08/20/2023] [Revised: 02/03/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.
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Affiliation(s)
- Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
| | - William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- School of Biological Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Jeremy L Sutherland
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, United States
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C1A4, Canada
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