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Cao Q, Liu C, Li Y, Qin Y, Wang C, Wang T. The underlying mechanisms of oxytetracycline degradation mediated by gut microbial proteins and metabolites in Hermetia illucens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174224. [PMID: 38914334 DOI: 10.1016/j.scitotenv.2024.174224] [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: 05/10/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Hermetia illucens larvae can enhance the degradation of oxytetracycline (OTC) through its biotransformation. However, the underlying mechanisms mediated by gut metabolites and proteins are unclear. To gain further insights, the kinetics of OTC degradation, the functional structures of gut bacterial communities, proteins, and metabolites were investigated. An availability-adjusted first-order model effectively evaluated OTC degradation kinetics, with degradation half-lives of 4.18 and 21.71 days for OTC degradation with and without larval biotransformation, respectively. Dominant bacteria in the larval guts were Enterococcus, Psychrobacter, Providencia, Myroides, Enterobacteriaceae, and Lactobacillales. OTC exposure led to significant differential expression of proteins, with functional classification revealing involvement in digestion, transformation, and adaptability to environmental stress. Upregulated proteins, such as aromatic ring hydroxylase, acted as oxidoreductases modifying the chemical structure of OTC. Unique metabolites, aclarubicin and sancycline identified were possible OTC metabolic intermediates. Correlation analysis revealed significant interdependence between gut bacteria, metabolites, and proteins. These findings reveal a synergistic mechanism involving gut microbial metabolism and enzyme structure that drives the rapid degradation of OTC and facilitates the engineering applications of bioremediation.
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Affiliation(s)
- 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
| | - 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.
| | - 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
| | - 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
| | - 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.
| | - 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
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2
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Réthi-Nagy Z, Juhász S. Microbiome's Universe: Impact on health, disease and cancer treatment. J Biotechnol 2024; 392:161-179. [PMID: 39009231 DOI: 10.1016/j.jbiotec.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/27/2024] [Accepted: 07/07/2024] [Indexed: 07/17/2024]
Abstract
The human microbiome is a diverse ecosystem of microorganisms that reside in the body and influence various aspects of health and well-being. Recent advances in sequencing technology have brought to light microbial communities in organs and tissues that were previously considered sterile. The gut microbiota plays an important role in host physiology, including metabolic functions and immune modulation. Disruptions in the balance of the microbiome, known as dysbiosis, have been linked to diseases such as cancer, inflammatory bowel disease and metabolic disorders. In addition, the administration of antibiotics can lead to dysbiosis by disrupting the structure and function of the gut microbial community. Targeting strategies are the key to rebalancing the microbiome and fighting disease, including cancer, through interventions such as probiotics, fecal microbiota transplantation (FMT), and bacteria-based therapies. Future research must focus on understanding the complex interactions between diet, the microbiome and cancer in order to optimize personalized interventions. Multidisciplinary collaborations are essential if we are going to translate microbiome research into clinical practice. This will revolutionize approaches to cancer prevention and treatment.
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Affiliation(s)
- Zsuzsánna Réthi-Nagy
- Hungarian Centre of Excellence for Molecular Medicine, Cancer Microbiome Core Group, Budapesti út 9, Szeged H-6728, Hungary
| | - Szilvia Juhász
- Hungarian Centre of Excellence for Molecular Medicine, Cancer Microbiome Core Group, Budapesti út 9, Szeged H-6728, Hungary.
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3
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Meng L, Liang L, Shi Y, Yin H, Li L, Xiao J, Huang N, Zhao A, Xia Y, Hou J. Biofilms in plastisphere from freshwater wetlands: Biofilm formation, bacterial community assembly, and biogeochemical cycles. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134930. [PMID: 38901258 DOI: 10.1016/j.jhazmat.2024.134930] [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: 03/04/2024] [Revised: 05/10/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Microorganisms can colonize to the surface of microplastics (MPs) to form biofilms, termed "plastisphere", which could significantly change their physiochemical properties and ecological roles. However, the biofilm characteristics and the deep mechanisms (interaction, assembly, and biogeochemical cycles) underlying plastisphere in wetlands currently lack a comprehensive perspective. In this study, in situ biofilm formation experiments were performed in a park with different types of wetlands to examine the plastisphere by extrinsic addition of PVC MPs in summer and winter, respectively. Results from the spectroscopic and microscopic analyses revealed that biofilms attached to the MPs in constructed forest wetlands contained the most abundant biomass and extracellular polymeric substances. Meanwhile, data from the high-throughput sequencing showed lower diversity in plastisphere compared with soil bacterial communities. Network analysis suggested a simple and unstable co-occurrence pattern in plastisphere, and the null model indicated increased deterministic process of heterogeneous selection for its community assembly. Based on the quantification of biogeochemical cycling genes by high-throughput qPCR, the relative abundances of genes involving in carbon degradation, carbon fixation, and denitrification were significantly higher in plastisphere than those of soil communities. This study greatly enhanced our understanding of biofilm formation and ecological effects of MPs in freshwater wetlands.
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Affiliation(s)
- Liang Meng
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China; Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Ministry of Education, Hangzhou 310058, China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai 201722, China
| | - Longrui Liang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yansong Shi
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Haitao Yin
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Li Li
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiamu Xiao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nannan Huang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Angang Zhao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yangrongchang Xia
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jingwen Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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4
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Cao L, Wan M, Xian Z, Zhou Y, Dong L, Huang F, Su D. Lacticaseibacillus casei- and Bifidobacterium breve-fermented red pitaya promotes beneficial microbial proliferation in the colon. Food Funct 2024. [PMID: 39189643 DOI: 10.1039/d4fo02352h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Red pitaya has been demonstrated to strongly inhibit α-glucosidase activity; however, the impact of red pitaya fermentation by probiotic bacteria on α-glucosidase inhibition remains unclear. In this study, six strains of lactic acid bacteria (Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, Lactobacillus bulgaricus, Lacticaseibacillus casei, Lactobacillus acidophilus and Streptococcus thermophilus) and one strain of Bifidobacterium breve were utilized for the fermentation of red pitaya pulp. The α-glucosidase and α-amylase inhibition rates of red pitaya pulp were significantly greater after fermentation by Bifidobacterium breve and Lacticaseibacillus casei than by the other abovementioned strains. The LC group exhibited an α-glucosidase inhibition rate of 99%, with an α-amylase inhibition rate of 89.91%. In contrast, the BB group exhibited an α-glucosidase inhibition rate of 95.28%, accompanied by an α-amylase inhibition rate of 95.28%. Moreover, red pitaya pulp fermented with Bifidobacterium breve and Lacticaseibacillus casei produced a notable quantity of oligosaccharides, which was more than three times greater than that in the other groups. Furthermore, 16S rRNA high-throughput sequencing analysis was conducted to assess alterations in the composition of the gut microbiota. This revealed an increase in the abundance of Lactobacillus and Faecalibacterium in the pulp fermented by Bifidobacterium breve and Lacticaseibacillus casei, whereas the abundance of Sutterella decreased. Further analysis at the species level revealed that Bifidobacterium longum, Faecalibacterium prausnitzii, and Lactobacillus zeae were the dominant strains present during colonic fermentation. These results indicate a beneficial health trend associated with probiotic bacterial fermentation of red pitaya pulp, which is highly important for the development of functional products.
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Affiliation(s)
- Li Cao
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Mengxi Wan
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Zhixing Xian
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Yongqiang Zhou
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Lihong Dong
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510006, China.
| | - Fei Huang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510006, China.
| | - Dongxiao Su
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
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5
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Castells-Nobau A, Mayneris-Perxachs J, Fernández-Real JM. Unlocking the mind-gut connection: Impact of human microbiome on cognition. Cell Host Microbe 2024; 32:1248-1263. [PMID: 39146797 DOI: 10.1016/j.chom.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024]
Abstract
This perspective explores the current understanding of the gut microbiota's impact on cognitive function in apparently healthy humans and in individuals with metabolic disease. We discuss how alterations in gut microbiota can influence cognitive processes, focusing not only on bacterial composition but also on often overlooked components of the gut microbiota, such as bacteriophages and eukaryotes, as well as microbial functionality. We examine the mechanisms through which gut microbes might communicate with the central nervous system, highlighting the complexity of these interactions. We provide a comprehensive overview of the emerging field of microbiota-gut-brain interactions and its significance for cognitive health. Additionally, we summarize novel therapeutic strategies designed to promote cognitive resilience and reduce the risk of cognitive disorders, focusing on interventions that target the gut microbiota. An in-depth understanding of the microbiome-brain axis is imperative for developing innovative treatments aimed at improving cognitive health.
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Affiliation(s)
- Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain.
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6
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Zhou Y, Liu D, Li F, Dong Y, Jin Z, Liao Y, Li X, Peng S, Delgado-Baquerizo M, Li X. Superiority of native soil core microbiomes in supporting plant growth. Nat Commun 2024; 15:6599. [PMID: 39097606 PMCID: PMC11297980 DOI: 10.1038/s41467-024-50685-3] [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: 12/13/2023] [Accepted: 07/18/2024] [Indexed: 08/05/2024] Open
Abstract
Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Donghui Liu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Fengqiao Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhili Jin
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Yangwenke Liao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaohui Li
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Shuguang Peng
- Hunan Province Company of China Tobacco Corporation, Changsha, 410004, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China.
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7
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Gong T, Liu X, Wang X, Lu Y, Wang X. Applications of polysaccharides in enzyme-triggered oral colon-specific drug delivery systems: A review. Int J Biol Macromol 2024; 275:133623. [PMID: 38969037 DOI: 10.1016/j.ijbiomac.2024.133623] [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: 01/30/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Enzyme-triggered oral colon-specific drug delivery system (EtOCDDS1) can withstand the harsh stomach and small intestine environments, releasing encapsulated drugs selectively in the colon in response to colonic microflora, exerting local or systematic therapeutic effects. EtOCDDS boasts high colon targetability, enhanced drug bioavailability, and reduced systemic side effects. Polysaccharides are extensively used in enzyme-triggered oral colon-specific drug delivery systems, and its colon targetability has been widely confirmed, as their properties meet the demand of EtOCDDS. Polysaccharides, known for their high safety and excellent biocompatibility, feature modifiable structures. Some remain undigested in the stomach and small intestine, whether in their natural state or after modifications, and are exclusively broken down by colon-resident microbiota. Such characteristics make them ideal materials for EtOCDDS. This article reviews the design principles of EtOCDDS as well as commonly used polysaccharides and their characteristics, modifications, applications and specific mechanism for colon targeting. The article concludes by summarizing the limitations and potential of ETOCDDS to stimulate the development of innovative design approaches.
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Affiliation(s)
- Tingting Gong
- Institute of Medicinal Plant Development, Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Xinxin Liu
- Institute of Medicinal Plant Development, Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Xi Wang
- Institute of Medicinal Plant Development, Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Yunqian Lu
- Institute of Medicinal Plant Development, Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Xiangtao Wang
- Institute of Medicinal Plant Development, Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China.
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8
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Zhu F, Wei Y, Wang F, Xia Z, Gou M, Tang Y. Enrichment of microbial consortia for MEOR in crude oil phase of reservoir-produced liquid and their response to environmental disturbance. Int Microbiol 2024; 27:1049-1062. [PMID: 38010566 DOI: 10.1007/s10123-023-00458-7] [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: 09/14/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Developing microbial consortiums is necessary for microbial enhanced oil recovery (MEOR) in heavy crude oil production. The aqueous phase of produced fluid has long been considered an ideal source of microorganisms for MEOR. However, it is recently found that rich microorganisms (including hydrocarbon-degrading bacteria) are present in the crude oil phase, which is completely different from the aqueous phase of produced fluid. So, in this study, the microbial consortia from the crude oil phase of produced fluids derived from four wells were enriched, respectively. The microbial community structure during passage was dynamically tracked, and the response of enriched consortia to successive disturbance of environmental factors was investigated. The results showed the crude oil phase had high microbial diversity, and the original microbial community structure from four wells was significantly different. After ten generations of consecutive enrichment, different genera were observed in the four enriched microbial consortia, namely, Geobacillus, Bacillus, Brevibacillus, Chelativorans, Ureibacillus, and Ornithinicoccus. In addition, two enriched consortia (eG1614 and eP30) exhibited robustness to temperature and oxygen perturbations. These results further suggested that the crude oil phase of produced fluids can serve as a potential microbial source for MEOR.
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Affiliation(s)
- Fangfang Zhu
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Yanfeng Wei
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Fangzhou Wang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Ziyuan Xia
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China.
| | - Yueqin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
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9
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Xue M, Xie Y, Zang X, Zhong Y, Ma X, Sun H, Liu J. Deciphering functional groups of rumen microbiome and their underlying potentially causal relationships in shaping host traits. IMETA 2024; 3:e225. [PMID: 39135684 PMCID: PMC11316931 DOI: 10.1002/imt2.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 08/15/2024]
Abstract
Over the years, microbiome research has achieved tremendous advancements driven by culture-independent meta-omics approaches. Despite extensive research, our understanding of the functional roles and causal effects of the microbiome on phenotypes remains limited. In this study, we focused on the rumen metaproteome, combining it with metatranscriptome and metabolome data to accurately identify the active functional distributions of rumen microorganisms and specific functional groups that influence feed efficiency. By integrating host genetics data, we established the potentially causal relationships between microbes-proteins/metabolites-phenotype, and identified specific patterns in which functional groups of rumen microorganisms influence host feed efficiency. We found a causal link between Selenomonas bovis and rumen carbohydrate metabolism, potentially mediated by bacterial chemotaxis and a two-component regulatory system, impacting feed utilization efficiency of dairy cows. Our study on the nutrient utilization functional groups in the rumen of high-feed-efficiency dairy cows, along with the identification of key microbiota functional proteins and their potentially causal relationships, will help move from correlation to causation in rumen microbiome research. This will ultimately enable precise regulation of the rumen microbiota for optimized ruminant production.
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Affiliation(s)
- Ming‐Yuan Xue
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Xianghu LaboratoryHangzhouChina
| | - Yun‐Yi Xie
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Xin‐Wei Zang
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Yi‐Fan Zhong
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Xiao‐Jiao Ma
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Hui‐Zeng Sun
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Ministry of Education Key Laboratory of Molecular Animal NutritionZhejiang UniversityHangzhouChina
| | - Jian‐Xin Liu
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Ministry of Education Key Laboratory of Molecular Animal NutritionZhejiang UniversityHangzhouChina
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10
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Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
Abstract
Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.
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Affiliation(s)
- María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
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11
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Liukkonen M, Muriel J, Martínez-Padilla J, Nord A, Pakanen VM, Rosivall B, Tilgar V, van Oers K, Grond K, Ruuskanen S. Seasonal and environmental factors contribute to the variation in the gut microbiome: A large-scale study of a small bird. J Anim Ecol 2024. [PMID: 39041321 DOI: 10.1111/1365-2656.14153] [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: 11/14/2023] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
Environmental variation can shape the gut microbiome, but broad/large-scale data on among and within-population heterogeneity in the gut microbiome and the associated environmental factors of wild populations is lacking. Furthermore, previous studies have limited taxonomical coverage, and knowledge about wild avian gut microbiomes is still scarce. We investigated large-scale environmental variation in the gut microbiome of wild adult great tits across the species' European distribution range. We collected fecal samples to represent the gut microbiome and used the 16S rRNA gene sequencing to characterize the bacterial gut microbiome. Our results show that gut microbiome diversity is higher during winter and that there are compositional differences between winter and summer gut microbiomes. During winter, individuals inhabiting mixed forest habitat show higher gut microbiome diversity, whereas there was no similar association during summer. Also, temperature was found to be a small contributor to compositional differences in the gut microbiome. We did not find significant differences in the gut microbiome among populations, nor any association between latitude, rainfall and the gut microbiome. The results suggest that there is a seasonal change in wild avian gut microbiomes, but that there are still many unknown factors that shape the gut microbiome of wild bird populations.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jaime Muriel
- Department of Biology, University of Turku, Turku, Finland
| | - Jesús Martínez-Padilla
- Department of Biodiversity Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (IPE-CSIC), Jaca, Spain
| | - Andreas Nord
- Department of Biology, Lund University, Lund, Sweden
| | | | - Balázs Rosivall
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Vallo Tilgar
- Department of Zoology, Tartu University, Tartu, Estonia
| | - Kees van Oers
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Biology, University of Turku, Turku, Finland
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12
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Kulecka M, Czarnowski P, Bałabas A, Turkot M, Kruczkowska-Tarantowicz K, Żeber-Lubecka N, Dąbrowska M, Paszkiewicz-Kozik E, Walewski J, Ługowska I, Koseła-Paterczyk H, Rutkowski P, Kluska A, Piątkowska M, Jagiełło-Gruszfeld A, Tenderenda M, Gawiński C, Wyrwicz L, Borucka M, Krzakowski M, Zając L, Kamiński M, Mikula M, Ostrowski J. Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients. Int J Mol Sci 2024; 25:8026. [PMID: 39125593 PMCID: PMC11311272 DOI: 10.3390/ijms25158026] [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: 06/24/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Paweł Czarnowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maryla Turkot
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Kamila Kruczkowska-Tarantowicz
- Department of Internal Medicine and Hematology, Military Institute of Medicine—National Research Institute, 04-141 Warsaw, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Ewa Paszkiewicz-Kozik
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Iwona Ługowska
- Early Phase Clinical Trials Unit, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Hanna Koseła-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Agnieszka Jagiełło-Gruszfeld
- Department of Breast Cancer & Reconstructive Surgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Tenderenda
- Department of Oncological Surgery and Neuroendocrine Tumors, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Cieszymierz Gawiński
- Department of Oncology and Radiotherapy, Maria Sklodowska-Curie National Cancer Research Institute, 02-781 Warsaw, Poland
| | - Lucjan Wyrwicz
- Department of Oncology and Radiotherapy, Maria Sklodowska-Curie National Cancer Research Institute, 02-781 Warsaw, Poland
| | - Magdalena Borucka
- Department of Lung and Chest Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maciej Krzakowski
- Department of Lung and Chest Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Leszek Zając
- Department of Gastrointestinal Surgical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Kamiński
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
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13
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Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [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: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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14
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Song Y, Zhang J, Li Y, Wang Y, Wan Y. Potential Protective Effect of Selenium-Enriched Lactobacillus plantarum on Cadmium-Induced Liver Injury in Mice. J Microbiol Biotechnol 2024; 34:1328-1339. [PMID: 38754999 PMCID: PMC11239402 DOI: 10.4014/jmb.2312.12051] [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: 01/02/2024] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Cadmium (Cd) is a prevalent environmental contaminant that poses a potential hazard to the health of both humans and animals. In this study, biosynthesized selenium-enriched Lactobacillus plantarum and selenium nanoparticles (SeNPs) were developed and evaluated for their protective effects against Cd-induced hepatic injury in mice through oral administration for 4 weeks. Cadmium exposure resulted in severe impairment of liver function, as evidenced by increased levels of serum markers of liver injury and, oxidative stress and significant damage to liver tissue, and a notable decrease in the diversity of the intestinal microbiota. Oral administration of Se-enriched L. plantarum (LS) reduced cadmium accumulation in the liver by 49.5% and, restored other cadmium-induced damage markers to normal levels. A comparison of the effects with those of L. plantarum (L) and SeNPs isolated from LS revealed that LS could more effectively alleviate hepatic oxidative stress and reduce the intrahepatic inflammatory responses of the liver, further protecting against cadmium-induced liver injury. These findings suggest that the development of LS may be effective at protecting the liver and intestinal tract from cadmium-induced damage.
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Affiliation(s)
- Yanyan Song
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Jing Zhang
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Yidan Li
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Yuxuan Wang
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
| | - Yingxin Wan
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, P.R. China
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15
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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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16
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Vinayamohan PG, Poelstra J, Cheng TY, Goetz H, Renaud DL, Gomez DE, Habing G. Exploring the effects of transport duration on the fecal microbial communities of surplus dairy calves. J Dairy Sci 2024; 107:3863-3884. [PMID: 38216047 DOI: 10.3168/jds.2023-24002] [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: 07/23/2023] [Accepted: 12/03/2023] [Indexed: 01/14/2024]
Abstract
Transportation significantly affects the health and welfare of surplus dairy calves, largely due to the various stressors and pathogen exposures encountered during the process. Concurrently, an animal's microbiome is known to correlate with its health status, with stress-induced alterations in the microbiota potentially precipitating various diseases. This study aimed to compare the effects of transportation durations of 6, 12, or 16 h on the fecal microbiota in young surplus dairy calves. We used a randomized controlled design in which surplus dairy calves aged 1 to 19 d from 5 commercial dairy farms in Ontario were allocated into 1 of 3 transportation groups (6, 12, and 16 h of continuous transportation). Health assessments were conducted before, immediately after, and for 2 wk following transportation. Fecal samples were collected before, immediately after, and at 24 and 72 h after transportation and subjected to 16S rRNA sequencing. Alpha diversity metrics showed no significant differences between the 3 transportation groups at any of the sampling time points. Although β diversity metrics revealed no clustering by transportation groups, they indicated significant differences across sampling time points within each group. The overall analysis revealed a total of 22 phyla and 353 genera, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria being the most abundant phyla. Bacteroides, Escherichia/Shigella, Lactobacillus, Collinsella, and Bifidobacterium were the most abundant genera. The reduction in Fusobacteria abundance before and after transport was significantly larger in the 16-h transportation group when compared with the 6-h transportation group. We also identified several genus-level and amplicon sequence variation-level taxa that displayed significant differences in their abundances across various transportation groups, observed at all sampling time points investigated. This research identifies microbiota changes due to varying transportation durations in surplus dairy calves, providing a broad understanding of the microbial shifts in surplus dairy calves after transportation across varying durations. Although these variations may not directly correlate with overall calf health or indicate dysbiosis, these results emphasize the importance of further investigating transportation practices to enhance calf health and well-being. Further studies are warranted to elucidate the relationship between microbiota and calf health.
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Affiliation(s)
| | - Jelmer Poelstra
- Molecular and Cellular Imaging Center (MCIC), The Ohio State University, Wooster, OH 44691
| | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Hanne Goetz
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - David L Renaud
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - Greg Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210.
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17
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Otaru N, Kourouma L, Pugin B, Constancias F, Braegger C, Mansuy IM, Lacroix C. Transgenerational effects of early life stress on the fecal microbiota in mice. Commun Biol 2024; 7:670. [PMID: 38822061 PMCID: PMC11143345 DOI: 10.1038/s42003-024-06279-2] [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: 11/09/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Stress in early life can affect the progeny and increase the risk to develop psychiatric and cardiometabolic diseases across generations. The cross-generational effects of early life stress have been modeled in mice and demonstrated to be associated with epigenetic factors in the germline. While stress is known to affect gut microbial features, whether its effects can persist across life and be passed to the progeny is not well defined. Here we show that early postnatal stress in mice shifts the fecal microbial composition (binary Jaccard index) throughout life, including abundance of eight amplicon sequencing variants (ASVs). Further effects on fecal microbial composition, structure (weighted Jaccard index), and abundance of 16 ASVs are detected in the progeny across two generations. These effects are not accompanied by changes in bacterial metabolites in any generation. These results suggest that changes in the fecal microbial community induced by early life traumatic stress can be perpetuated from exposed parent to the offspring.
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Affiliation(s)
- Nize Otaru
- Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland
| | - Lola Kourouma
- Department of Health Science and Technology of the ETH Zurich, Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich, and Institute for Neuroscience, Zurich, Switzerland
- Center for Neuroscience Zürich, ETH and University Zürich, Zurich, Switzerland
| | - Benoit Pugin
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland
| | - Florentin Constancias
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland
| | - Christian Braegger
- Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
| | - Isabelle M Mansuy
- Department of Health Science and Technology of the ETH Zurich, Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich, and Institute for Neuroscience, Zurich, Switzerland.
- Center for Neuroscience Zürich, ETH and University Zürich, Zurich, Switzerland.
| | - Christophe Lacroix
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland.
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18
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Kondo K, Suzuki M, Amadaira M, Araki C, Watanabe R, Murakami K, Ochiai S, Ogura T, Hayakawa T. Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas. PeerJ 2024; 12:e17385. [PMID: 38818452 PMCID: PMC11138522 DOI: 10.7717/peerj.17385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Background Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection. Methods Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala's gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection. Results and Discussion This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection. Conclusion We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.
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Affiliation(s)
- Kotaro Kondo
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mirei Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mana Amadaira
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Chiharu Araki
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Rie Watanabe
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | | | | | - Tadatoshi Ogura
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
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19
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Kok CR, Rose DJ, Cui J, Whisenhunt L, Hutkins R. Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses. BMC Microbiol 2024; 24:183. [PMID: 38796418 PMCID: PMC11127362 DOI: 10.1186/s12866-024-03344-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: 10/15/2023] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. RESULTS Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. CONCLUSIONS Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.
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Affiliation(s)
- Car Reen Kok
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Devin J Rose
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lisa Whisenhunt
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Robert Hutkins
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 258 Food Innovation Center, Lincoln, NE, 68588-6205, USA.
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20
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Dong WJ, Xu MD, Yang XW, Yang XM, Long XZ, Han XY, Cui LY, Tong Q. Rice straw ash and amphibian health: A deep dive into microbiota changes and potential ecological consequences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171651. [PMID: 38490417 DOI: 10.1016/j.scitotenv.2024.171651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/05/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
Rice straw is burned as a result of agricultural practices and technical limitations, generating significant volumes of ash that might have environmental and ecological consequences; however, the effects on organisms have not been researched. Amphibians depend on their gut and skin microbiomes. Ash exposure may cause inflammation and changes in microbial diversity and function in frogs' skin and gut microbiota due to its chemical composition and physical presence, but the implications remain unclear. Rana dybowskii were exposed to five aqueous extracts of ashes (AEA) concentrations for 30 days to study survival, metal concentrations, and microbial diversity, analyzing the microbiota of the cutaneous and gut microbiota using Illumina sequencing. Dominant elements in ash: K > Ca > Mg > Na > Al > Fe. In AEA, K > Na > Ca > Mg > As > Cu. Increased AEA concentrations significantly reduced frog survival. Skin microbiota alpha diversity varied significantly among all treatment groups, but not gut microbiota. Skin microbiota differed significantly across treatments via Bray-Curtis and weighted UniFrac; gut microbiota was only affected by Bray-Curtis. Skin microbiota varied significantly with AEA levels in Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, while the gut microbiota's dominant phyla, Firmicutes, Bacteroidetes, and Proteobacteria, remained consistent across all groups. Lastly, the functional prediction showed that the skin microbiota had big differences in how it worked and looked, which were linked to different health and environmental adaptation pathways. The gut microbiota, on the other hand, had smaller differences. In conclusion, AEA exposure affects R. dybowskii survival and skin microbiota diversity, indicating potential health and ecological impacts, with less effect on gut microbiota.
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Affiliation(s)
- Wen-Jing Dong
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Ming-da Xu
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Xue-Wen Yang
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Xiu-Mei Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Xin-Zhou Long
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Xiao-Yun Han
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Li-Yong Cui
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Qing Tong
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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21
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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22
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Martínez-López YE, Neri-Rosario D, Esquivel-Hernández DA, Padron-Manrique C, Vázquez-Jiménez A, Sánchez-Castañeda JP, Girón-Villalobos D, Mendoza-Ortíz C, Reyes-Escogido MDL, Evia-Viscarra ML, Aguilar-Garcia A, Resendis-Antonio O, Guardado-Mendoza R. Effect of metformin and metformin/linagliptin on gut microbiota in patients with prediabetes. Sci Rep 2024; 14:9678. [PMID: 38678119 PMCID: PMC11055900 DOI: 10.1038/s41598-024-60081-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: 09/23/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Lifestyle modifications, metformin, and linagliptin reduce the incidence of type 2 diabetes (T2D) in people with prediabetes. The gut microbiota (GM) may enhance such interventions' efficacy. We determined the effect of linagliptin/metformin (LM) vs metformin (M) on GM composition and its relationship to insulin sensitivity (IS) and pancreatic β-cell function (Pβf) in patients with prediabetes. A cross-sectional study was conducted at different times: basal, six, and twelve months in 167 Mexican adults with prediabetes. These treatments increased the abundance of GM SCFA-producing bacteria M (Fusicatenibacter and Blautia) and LM (Roseburia, Bifidobacterium, and [Eubacterium] hallii group). We performed a mediation analysis with structural equation models (SEM). In conclusion, M and LM therapies improve insulin sensitivity and Pβf in prediabetics. GM is partially associated with these improvements since the SEM models suggest a weak association between specific bacterial genera and improvements in IS and Pβf.
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Affiliation(s)
- Yoscelina Estrella Martínez-López
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Doctorado en Ciencias Médicas, Odontológicas y de la Salud, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Metabolic Research Laboratory, Department of Medicine and Nutrition, University of Guanajuato, León, Guanajuato, Mexico
| | - Daniel Neri-Rosario
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | | | - Cristian Padron-Manrique
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Aarón Vázquez-Jiménez
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
| | - Jean Paul Sánchez-Castañeda
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - David Girón-Villalobos
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Cristian Mendoza-Ortíz
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | | | | | | | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico.
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación - Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico.
| | - Rodolfo Guardado-Mendoza
- Metabolic Research Laboratory, Department of Medicine and Nutrition, University of Guanajuato, León, Guanajuato, Mexico.
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23
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Stone JK, von Muhlinen N, Zhang C, Robles AI, Flis AL, Vega-Valle E, Miyanaga A, Matsumoto M, Greathouse KL, Cooks T, Trinchieri G, Harris CC. Acidovorax temperans skews neutrophil maturation and polarizes Th17 cells to promote lung adenocarcinoma development. Oncogenesis 2024; 13:13. [PMID: 38570533 PMCID: PMC10991269 DOI: 10.1038/s41389-024-00513-6] [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: 06/15/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Change within the intratumoral microbiome is a common feature in lung and other cancers and may influence inflammation and immunity in the tumor microenvironment, affecting growth and metastases. We previously characterized the lung cancer microbiome in patients and identified Acidovorax temperans as enriched in tumors. Here, we instilled A. temperans in an animal model driven by mutant K-ras and Tp53. This revealed A. temperans accelerates tumor development and burden through infiltration of proinflammatory cells. Neutrophils exposed to A. temperans displayed a mature, pro-tumorigenic phenotype with increased cytokine signaling, with a global shift away from IL-1β signaling. Neutrophil to monocyte and macrophage signaling upregulated MHC II to activate CD4+ T cells, polarizing them to an IL-17A+ phenotype detectable in CD4+ and γδ populations (T17). These T17 cells shared a common gene expression program predictive of poor survival in human LUAD. These data indicate bacterial exposure promotes tumor growth by modulating inflammation.
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Affiliation(s)
- Joshua K Stone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Natalia von Muhlinen
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Chenran Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Amy L Flis
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Eleazar Vega-Valle
- Laboratory Animal Science Program, Laboratory of Human Carcinogenesis, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Akihiko Miyanaga
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Masaru Matsumoto
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - K Leigh Greathouse
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, TX, 76798, USA
| | - Tomer Cooks
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
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24
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Biada I, Ibáñez-Escriche N, Blasco A, Casto-Rebollo C, Santacreu MA. Microbiome composition as a potential predictor of longevity in rabbits. Genet Sel Evol 2024; 56:25. [PMID: 38565991 PMCID: PMC10986140 DOI: 10.1186/s12711-024-00895-6] [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: 06/30/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Longevity and resilience are two fundamental traits for more sustainable livestock production. These traits are closely related, as resilient animals tend to have longer lifespans. An interesting criterion for increasing longevity in rabbit could be based on the information provided by its gut microbiome. The gut microbiome is essential for regulating health and plays crucial roles in the development of the immune system. The aim of this research was to investigate if animals with different longevities have different microbial profiles. We sequenced the 16S rRNA gene from soft faeces from 95 does. First, we compared two maternal rabbit lines with different longevities; a standard longevity maternal line (A) and a maternal line (LP) that was founded based on longevity criteria: females with a minimum of 25 parities with an average prolificacy per parity of 9 or more. Second, we compared the gut microbiota of two groups of animals from line LP with different longevities: females that died/were culled with two parities or less (LLP) and females with more than 15 parities (HLP). RESULTS Differences in alpha and beta diversity were observed between lines A and LP, and a partial least square discriminant analysis (PLS-DA) showed a high prediction accuracy (> 91%) of classification of animals to line A versus LP (146 amplicon sequence variants (ASV)). The PLS-DA also showed a high prediction accuracy (> 94%) to classify animals to the LLP and HLP groups (53 ASV). Interestingly, some of the most important taxa identified in the PLS-DA were common to both comparisons (Akkermansia, Christensenellaceae R-7, Uncultured Eubacteriaceae, among others) and have been reported to be related to resilience and longevity. CONCLUSIONS Our results indicate that the first parity gut microbiome profile differs between the two rabbit maternal lines (A and LP) and, to a lesser extent, between animals of line LP with different longevities (LLP and HLP). Several genera were able to discriminate animals from the two lines and animals with different longevities, which shows that the gut microbiome could be used as a predictive factor for longevity, or as a selection criterion for these traits.
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Affiliation(s)
- Iliyass Biada
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Maria A Santacreu
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
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25
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Ali A, Wu L, Ali SS. Gut microbiota and acute kidney injury: immunological crosstalk link. Int Urol Nephrol 2024; 56:1345-1358. [PMID: 37749436 DOI: 10.1007/s11255-023-03760-5] [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: 04/14/2023] [Accepted: 08/14/2023] [Indexed: 09/27/2023]
Abstract
The gut microbiota, often called the "forgotten organ," plays a crucial role in bidirectional communication with the host for optimal physiological function. This communication helps regulate the host's immunity and metabolism positively and negatively. Many factors influence microbiota homeostasis and subsequently lead to an immune system imbalance. The correlation between an unbalanced immune system and acute diseases such as acute kidney injury is not fully understood, and the role of gut microbiota in disease pathogenesis is still yet uncovered. This review summarizes our understanding of gut microbiota, focusing on the interactions between the host's immune system and the microbiome and their impact on acute kidney injury.
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Affiliation(s)
- Asmaa Ali
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
- Department of Pulmonary Medicine, Abbassia Chest Hospital, MOH, Cairo, Egypt.
- Department of Respiratory Allergy, A Al-Rashed Allergy Center, Ministry of Health, Kuwait, Kuwait.
| | - Liang Wu
- Yizheng Hospital, Nanjing Drum Tower Hospital Group, Yizheng, 210008, China.
| | - Sameh Samir Ali
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, China
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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26
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Stallmach A, Quickert S, Puta C, Reuken PA. The gastrointestinal microbiota in the development of ME/CFS: a critical view and potential perspectives. Front Immunol 2024; 15:1352744. [PMID: 38605969 PMCID: PMC11007072 DOI: 10.3389/fimmu.2024.1352744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Like other infections, a SARS-CoV-2 infection can also trigger Post-Acute Infection Syndromes (PAIS), which often progress into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). ME/CFS, characterized by post-exercise malaise (PEM), is a severe multisystemic disease for which specific diagnostic markers or therapeutic concepts have not been established. Despite numerous indications of post-infectious neurological, immunological, endocrinal, and metabolic deviations, the exact causes and pathophysiology remain unclear. To date, there is a paucity of data, that changes in the composition and function of the gastrointestinal microbiota have emerged as a potential influencing variable associated with immunological and inflammatory pathways, shifts in ME/CFS. It is postulated that this dysbiosis may lead to intestinal barrier dysfunction, translocation of microbial components with increased oxidative stress, and the development or progression of ME/CFS. In this review, we detailed discuss the findings regarding alterations in the gastrointestinal microbiota and its microbial mediators in ME/CFS. When viewed critically, there is currently no evidence indicating causality between changes in the microbiota and the development of ME/CFS. Most studies describe associations within poorly defined patient populations, often combining various clinical presentations, such as irritable bowel syndrome and fatigue associated with ME/CFS. Nevertheless, drawing on analogies with other gastrointestinal diseases, there is potential to develop strategies aimed at modulating the gut microbiota and/or its metabolites as potential treatments for ME/CFS and other PAIS. These strategies should be further investigated in clinical trials.
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Affiliation(s)
- Andreas Stallmach
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Stefanie Quickert
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Christian Puta
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
- Center for Interdisciplinary Prevention of Diseases Related to Professional Activities, Jena, Germany
| | - Philipp A. Reuken
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
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27
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Bouilloud M, Galan M, Pradel J, Loiseau A, Ferrero J, Gallet R, Roche B, Charbonnel N. Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota. Anim Microbiome 2024; 6:16. [PMID: 38528597 DOI: 10.1186/s42523-024-00301-y] [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: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.
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Affiliation(s)
- Marie Bouilloud
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France.
- Centre de Biologie pour la Gestion des Populations, 750 Avenue Agropolis, 34988, Montferrier sur Lez, France.
| | - Maxime Galan
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Pradel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Ferrero
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Romain Gallet
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Benjamin Roche
- MIVEGEC, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Nathalie Charbonnel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
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28
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Jeong Y, Ahmad S, Irudayaraj J. Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes. ACS Biomater Sci Eng 2024; 10:1461-1472. [PMID: 38315631 PMCID: PMC10936524 DOI: 10.1021/acsbiomaterials.3c01678] [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: 11/12/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
The presence of β-lactamase positive microorganisms imparts a pharmacological effect on a variety of organisms that can impact drug efficacy by influencing the function or composition of bacteria. Although studies to assess dynamic intra- and interspecies communication with bacterial communities exist, the efficacy of drug treatment and quantitative assessment of multiorganism response is not well understood due to the lack of technological advances that can be used to study coculture interactions in a dynamic format. In this study, we investigate how β-lactamase positive microorganisms can neutralize the effect of β-lactam antibiotics in a dynamic format at the inter- and intraspecies level using microbial bead technology. Three interactive models for the biological compartmentalization of organisms were demonstrated to evaluate the effect of β-lactam antibiotics on coculture systems. Our model at the intraspecies level attempts to mimic the biofilm matrix more closely as a community-level feature of microorganisms, which acknowledges the impact of nondrug-resistant species in shaping the dynamic response. In particular, the results of intraspecies studies are highly supportive of the biofilm mode of bacterial growth, which can provide structural support and protect the bacteria from an assault on host or environmental factors. Our findings also indicate that β-lactamase positive bacteria can neutralize the cytotoxic effect of β-lactam antibiotics at the interspecies level when cocultured with cancer cells. Results were validated using β-lactamase positive bacteria isolated from environmental niches, which can trigger phenotypical alteration of β-lactams when cocultured with other organisms. Our compartmentalization strategy acts as an independent ecosystem and provides a new avenue for multiscale studies to assess intra- and interspecies interactions.
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Affiliation(s)
- Yoon Jeong
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Saeed Ahmad
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
- Carle
R. Woese Institute for Genomic Biology, Beckman Institute, Urbana, Illinois 61801, United States
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29
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Jernfors T, Lavrinienko A, Vareniuk I, Landberg R, Fristedt R, Tkachenko O, Taskinen S, Tukalenko E, Mappes T, Watts PC. Association between gut health and gut microbiota in a polluted environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169804. [PMID: 38184263 DOI: 10.1016/j.scitotenv.2023.169804] [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: 04/27/2023] [Revised: 08/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, digestion of otherwise undigestible foodstuffs, and impacts on host behaviour. Exposure to stressors, such as environmental pollution, parasites, and/or predators, can alter the composition of the gut microbiome, potentially affecting host-microbiome interactions that can be manifest in the host as, for example, metabolic dysfunction or inflammation. However, whether a change in gut microbiota in wild animals associates with a change in host condition is seldom examined. Thus, we quantified whether wild bank voles inhabiting a polluted environment, areas where there are environmental radionuclides, exhibited a change in gut microbiota (using 16S amplicon sequencing) and concomitant change in host health using a combined approach of transcriptomics, histological staining analyses of colon tissue, and quantification of short-chain fatty acids in faeces and blood. Concomitant with a change in gut microbiota in animals inhabiting contaminated areas, we found evidence of poor gut health in the host, such as hypotrophy of goblet cells and likely weakened mucus layer and related changes in Clca1 and Agr2 gene expression, but no visible inflammation in colon tissue. Through this case study we show that inhabiting a polluted environment can have wide reaching effects on the gut health of affected animals, and that gut health and other host health parameters should be examined together with gut microbiota in ecotoxicological studies.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland.
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Igor Vareniuk
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Rikard Fristedt
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Olena Tkachenko
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Sara Taskinen
- Department of Mathematics and Statistics, University of Jyväskylä, FI-40014, Finland
| | - Eugene Tukalenko
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, 020000, Ukraine
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
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Tanelian A, Nankova B, Miari M, Sabban EL. Microbial composition, functionality, and stress resilience or susceptibility: unraveling sex-specific patterns. Biol Sex Differ 2024; 15:20. [PMID: 38409102 PMCID: PMC10898170 DOI: 10.1186/s13293-024-00590-7] [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: 09/05/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Following exposure to traumatic stress, women are twice as likely as men to develop mood disorders. Yet, individual responses to such stress vary, with some people developing stress-induced psychopathologies while others exhibit resilience. The factors influencing sex-related disparities in affective disorders as well as variations in resilience remain unclear; however, emerging evidence suggests differences in the gut microbiota play a role. In this study, using the single prolonged stress (SPS) model of post-traumatic stress disorder, we investigated pre- and post-existing differences in microbial composition, functionality, and metabolites that affect stress susceptibility or resilience in each sex. METHODS Male and female Sprague-Dawley rats were randomly assigned to control or SPS groups. Two weeks following SPS, the animals were exposed to a battery of behavioral tests and decapitated a day later. Based on their anxiety index, they were further categorized as SPS-resilient (SPS-R) or SPS-susceptible (SPS-S). On the day of dissection, cecum, and selected brain tissues were isolated. Stool samples were collected before and after SPS, whereas urine samples were taken before and 30 min into the SPS. RESULTS Before SPS exposure, the sympathoadrenal axis exhibited alterations within male subgroups only. Expression of tight junction protein claudin-5 was lower in brain of SPS-S males, but higher in SPS-R females following SPS. Across the study, alpha diversity remained consistently lower in males compared to females. Beta diversity revealed distinct separations between male and female susceptible groups before SPS, with this separation becoming evident in the resilient groups following SPS. At the genus level, Lactobacillus, Lachnospiraceae_Incertae_Sedis, and Barnesiella exhibited sex-specific alterations, displaying opposing abundances in each sex. Additionally, sex-specific changes were observed in microbial predictive functionality and targeted functional modules both before and after SPS. Alterations in the microbial short-chain fatty acids (SCFAs), were also observed, with major and minor SCFAs being lower in SPS-susceptible males whereas branched-chain SCFAs being higher in SPS-susceptible females. CONCLUSION This study highlights distinct pre- and post-trauma differences in microbial composition, functionality, and metabolites, associated with stress resilience in male and female rats. The findings underscore the importance of developing sex-specific therapeutic strategies to effectively address stress-related disorders. Highlights SPS model induces divergent anxiety and social behavioral responses to traumatic stress in both male and female rodents. SPS-resilient females displayed less anxiety-like behavior and initiated more interactions towards a juvenile rat than SPS-resilient males. Sex-specific pre-existing and SPS-induced differences in the gut microbial composition and predictive functionality were observed in susceptible and resilient rats. SPS-resilient males displayed elevated cecal acetate levels, whereas SPS-susceptible females exhibited heightened branched-chain SCFAs.
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Affiliation(s)
- Arax Tanelian
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
| | - Bistra Nankova
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
- Division of Newborn Medicine, Departments of Pediatrics, New York Medical College, Valhalla, NY, 10595, USA
| | - Mariam Miari
- Department of Clinical Sciences in Malmo, Lund University Diabetes Center, Malmo, Sweden
| | - Esther L Sabban
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA.
- Department of Psychiatry and Behavioral Science, New York Medical College, Valhalla, NY, 10595, USA.
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31
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Zhang S, Liu S, Liu H, Li H, Luo J, Zhang A, Ding Y, Ren T, Chen W. Stochastic Assembly Increases the Complexity and Stability of Shrimp Gut Microbiota During Aquaculture Progression. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:92-102. [PMID: 38165637 DOI: 10.1007/s10126-023-10279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Saisai Zhang
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Shuang Liu
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Hongwei Liu
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Hui Li
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Jun Luo
- Dalian Sun Asia Tourism Holding Co. Ltd., Dalian, Liaoning, 116023, China
| | - Aili Zhang
- Dalian Ocean School, Dalian, Liaoning, 116023, China
| | - Yinpeng Ding
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Tongjun Ren
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Wenbo Chen
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China.
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Wang M, Chen X, Fang Y, Zheng X, Huang T, Nie Y, Wu XL. The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities. Cell Syst 2024; 15:63-74.e5. [PMID: 38237552 DOI: 10.1016/j.cels.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/17/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
In microbial systems, a metabolic pathway can be either completed by one autonomous population or distributed among a consortium performing metabolic division of labor (MDOL). MDOL facilitates the system's function by reducing the metabolic burden; however, it may hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the function of a community is influenced by the trade-offs between the metabolic specialization and versatility of individuals. To experimentally test this hypothesis, we deconstructed the naphthalene degradation pathway into four steps and introduced them individually or combinatorically into different strains with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia and found that 74 consortia exhibited higher degradation function than both the autonomous population and rigorous MDOL consortium. Quantitative modeling provides general strategies for identifying the most effective MDOL configuration. Our study provides critical insights into the engineering of high-performance microbial systems.
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Affiliation(s)
- Miaoxiao Wang
- College of Engineering, Peking University, Beijing 100871, China; Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Dübendorf 8600, Switzerland
| | - Xiaoli Chen
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China
| | - Yuan Fang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Xin Zheng
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Ting Huang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China; Institute of Ecology, Peking University, Beijing 100871, China.
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33
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Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [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] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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34
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Mure A, Sugiura Y, Maeda R, Honda K, Sakurai N, Takahashi Y, Watada M, Katoh T, Gotoh A, Gotoh Y, Taniguchi I, Nakamura K, Hayashi T, Katayama T, Uemura T, Hattori Y. Identification of key yeast species and microbe-microbe interactions impacting larval growth of Drosophila in the wild. eLife 2023; 12:RP90148. [PMID: 38150375 PMCID: PMC10752588 DOI: 10.7554/elife.90148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.
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Affiliation(s)
- Ayumi Mure
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Yuki Sugiura
- Center for Cancer Immunotherapy and Immunobiology, Kyoto UniversityKyotoJapan
| | - Rae Maeda
- Center for Cancer Immunotherapy and Immunobiology, Kyoto UniversityKyotoJapan
| | - Kohei Honda
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | | | | | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime UniversityMatsuyamaJapan
| | | | - Aina Gotoh
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Itsuki Taniguchi
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | | | - Tadashi Uemura
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Center for Living Systems Information Science, Kyoto UniversityKyotoJapan
- AMED-CRESTTokyoJapan
| | - Yukako Hattori
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Center for Living Systems Information Science, Kyoto UniversityKyotoJapan
- JST FORESTTokyoJapan
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35
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Cerdó T, Ruiz-Rodríguez A, Acuña I, Torres-Espínola FJ, Menchén-Márquez S, Gámiz F, Gallo M, Jehmlich N, Haange SB, von Bergen M, Campoy C, Suárez A. Infant gut microbiota contributes to cognitive performance in mice. Cell Host Microbe 2023; 31:1974-1988.e4. [PMID: 38052208 DOI: 10.1016/j.chom.2023.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
Gut microbiota has been linked to infant neurodevelopment. Here, an association between infant composite cognition and gut microbiota composition is established as soon as 6 months. Higher diversity and evenness characterize microbial communities of infants with composite cognition above (Inf-aboveCC) versus below (Inf-belowCC) median values. Metaproteomic and metabolomic analyses establish an association between microbial histidine ammonia lyase and infant histidine metabolome with cognition. Fecal transplantation from Inf-aboveCC versus Inf-belowCC donors into germ-free mice shows that memory, assessed by a novel object recognition test, is a transmissible trait. Furthermore, Inf-aboveCC mice are enriched in species belonging to Phocaeicola, as well as Bacteroides and Bifidobacterium, previously linked to cognition. Finally, Inf-aboveCC mice show lower fecal histidine and urocanate:histidine and urocanate:glutamate ratios in the perirhinal cortex compared to Inf-belowCC mice. Overall, these findings reveal a causative role of gut microbiota on infant cognition, pointing at the modulation of histidine metabolite levels as a potential underlying mechanism.
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Affiliation(s)
- Tomás Cerdó
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; Centre for Rheumatology Research, Division of Medicine, University College London, London WC1E 6JF, UK
| | - Alicia Ruiz-Rodríguez
- Department of Biochemistry and Molecular Biology 2, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain; Department of Microbiology, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain.
| | - Inmaculada Acuña
- Department of Biochemistry and Molecular Biology 2, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Francisco José Torres-Espínola
- EURISTIKOS Excellence Centre for Pediatric Research, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Sergio Menchén-Márquez
- Department of Psychobiology, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Fernando Gámiz
- Department of Psychobiology, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Milagros Gallo
- Department of Psychobiology, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain; Instituto de Investigación Biosanitaria (IBS), 18014 Granada, Spain
| | - Nico Jehmlich
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Cristina Campoy
- EURISTIKOS Excellence Centre for Pediatric Research, Institute of Neurosciences, Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain; Instituto de Investigación Biosanitaria (IBS), 18014 Granada, Spain; Department of Pediatrics, School of Medicine, University of Granada, 18016 Granada, Spain
| | - Antonio Suárez
- Department of Biochemistry and Molecular Biology 2, Nutrition and Food Technology Institute "José Mataix" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
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36
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Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [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: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
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Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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37
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Beauvais M, Schatt P, Montiel L, Logares R, Galand PE, Bouget FY. Functional redundancy of seasonal vitamin B 12 biosynthesis pathways in coastal marine microbial communities. Environ Microbiol 2023; 25:3753-3770. [PMID: 38031968 DOI: 10.1111/1462-2920.16545] [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: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.
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Affiliation(s)
- Maxime Beauvais
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Philippe Schatt
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Lidia Montiel
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - François-Yves Bouget
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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38
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Collins HI, Griffin TW, Holohan BA, Ward JE. Nylon microfibers develop a distinct plastisphere but have no apparent effects on the gut microbiome or gut tissue status in the blue mussel, Mytilus edulis. Environ Microbiol 2023; 25:2792-2806. [PMID: 37661930 DOI: 10.1111/1462-2920.16496] [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: 06/25/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Ingestion of microplastics (MP) by suspension-feeding bivalves has been well-documented. However, it is unclear whether exposure to MP could damage the stomach and digestive gland (gut) of these animals, causing ramifications for organism and ecosystem health. Here, we show no apparent effects of nylon microfiber (MF) ingestion on the gut microbiome or digestive tissues of the blue mussel, Mytilus edulis. We exposed mussels to two low concentrations (50 and 100 particles/L) of either nylon MF or Spartina spp. particles (dried, ground marsh grass), ca. 250-500 μm in length, or a no particle control laboratory treatment for 21 days. Results showed that nylon MF, when aged in coarsely filtered seawater, developed a different microbial community than Spartina spp. particles and seawater, however, even after exposure to this different community, mussel gut microbial communities resisted disturbance from nylon MF. The microbial communities of experimental mussels clustered together in ordination and were similar in taxonomic composition and measures of alpha diversity. Additionally, there was no evidence of damage to gut tissues after ingestion of nylon MF or Spartina spp. Post-ingestive particle processing likely mediated a short gut retention time of these relatively large particles, contributing to the negligible treatment effects.
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Affiliation(s)
- Hannah I Collins
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Tyler W Griffin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Bridget A Holohan
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - J Evan Ward
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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39
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Rojas L, van de Wouw M, Wang Y, Vaghef-Mehrabani E, Dewey D, Reimer RA, Letourneau N, Campbell T, Arrieta MC, Giesbrecht GF. Long-term and trimester-specific effects of prenatal stress on the child gut microbiota. Psychoneuroendocrinology 2023; 158:106380. [PMID: 37696229 DOI: 10.1016/j.psyneuen.2023.106380] [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: 06/05/2023] [Revised: 08/25/2023] [Accepted: 09/03/2023] [Indexed: 09/13/2023]
Abstract
OBJECTIVE Stress is common among pregnant individuals and is associated with an altered gut microbiota composition in infants. It is unknown if these compositional changes persist into the preschool years when the gut microbiota reaches an adult-like composition. This study aimed to investigate if indicators of prenatal stress (i.e., psychological distress and stress-related physiology) are associated with children's gut microbiota composition and metabolites at 3-4 years of age. METHODS Maternal-child pairs (n = 131) were from the Alberta Pregnancy Outcomes and Nutrition (APrON) cohort. Each trimester, psychological distress was measured as symptoms of anxiety (Symptom Checklist-90-R) and depressed mood (Edinburgh Postnatal Depression Scale), whereas salivary cortisol was quantified as a measure of stress-related physiology. Child stool samples were collected at 3-4 years to evaluate gut microbiota composition using 16S rRNA gene sequencing and fecal metabolome using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Associations between prenatal distress and cortisol with the gut microbiota were determined using Pearson and Spearman correlations and corrected for multiple testing. Associations between prenatal distress and cortisol with the fecal metabolome were assessed using Metaboanalyst. RESULTS Symptoms of depressed mood during the 2nd and 3rd trimesters and anxiety during the 2nd trimester of pregnancy were associated with increased alpha diversity of the child's gut microbiota. Cortisol levels during the 1st trimester were also associated with increased Faith PD diversity (r = 0.32), whereas cortisol levels during the 2nd trimester were associated with reduced Shannon diversity (r = -0.27). Depression scores during the 2nd and 3rd trimesters were associated with reductions in the relative abundances of Eggerthella, Parasutterella, and increases in Ruminococcaceae (rs = -0.28, rs = -0.32, rs = 0.32, respectively), as well as the fecal metabolome (e.g., branched-chain amino acid metabolism). Cortisol levels during the 2nd trimester correlated with 7 bacterial taxa, whereas 1st-trimester cortisol levels were associated with the child's fecal metabolome. CONCLUSIONS Prenatal distress and cortisol were associated with both child gut microbiota composition and fecal metabolome at preschool age. Understanding these associations may allow for the identification of microbiota-targeted interventions to support child developmental outcomes affected by prenatal stress.
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Affiliation(s)
- Laura Rojas
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Marcel van de Wouw
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Yanan Wang
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; Microbiomes for One Systems Health, Health & Biosecurity, CSIRO, Adelaide, SA, Australia
| | | | - Deborah Dewey
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; Alberta Children's Hospital Research Institute (ACHRI), Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute (HBI), Calgary, Alberta, Canada
| | - Raylene A Reimer
- Alberta Children's Hospital Research Institute (ACHRI), Calgary, Alberta, Canada; Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Nicole Letourneau
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; Alberta Children's Hospital Research Institute (ACHRI), Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta
| | - Tavis Campbell
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; Department of Psychiatry, Cumming School of Medicine, University of Calgary, Alberta, Canada; International Microbiome Centre, Calgary, Alberta, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; Department of Psychology, University of Calgary, Calgary, Alberta, Canada; Alberta Children's Hospital Research Institute (ACHRI), Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.
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Guan X, Zhao Z, Jiang J, Fu L, Liu J, Pan Y, Gao S, Wang B, Chen Z, Wang X, Sun H, Jiang B, Dong Y, Zhou Z. Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:545-556. [PMID: 37537784 PMCID: PMC10667648 DOI: 10.1111/1758-2229.13188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Xiaoyan Guan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Jingwei Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Lei Fu
- Dalian Salt Chemical Group Co., LtdDalianLiaoningPeople's Republic of China
| | - Jiaojiao Liu
- Dalian Salt Chemical Group Co., LtdDalianLiaoningPeople's Republic of China
| | - Yongjia Pan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Shan Gao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Bai Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zhong Chen
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Xuda Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Hongjuan Sun
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Bing Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Ying Dong
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zunchun Zhou
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
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41
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Yun HM, Hyun S. Role of gut commensal bacteria in juvenile developmental growth of the host: insights from Drosophila studies. Anim Cells Syst (Seoul) 2023; 27:329-339. [PMID: 38023592 PMCID: PMC10653766 DOI: 10.1080/19768354.2023.2282726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
The gut microbiome plays a crucial role in maintaining health in a variety of organisms, from insects to humans. Further, beneficial symbiotic microbes are believed to contribute to improving the quality of life of the host. Drosophila is an optimal model for studying host-commensal microbe interactions because it allows for convenient manipulation of intestinal microbial composition. Fly microbiota has a simple taxonomic composition and can be cultivated and genetically tracked. This permits functional studies and analyses of the molecular mechanisms underlying their effects on host physiological processes. In this context, we briefly introduce the principle of juvenile developmental growth in Drosophila. Then, we discuss the current understanding of the molecular mechanisms underlying the effects of gut commensal bacteria, such as Lactiplantibacillus plantarum and Acetobacter pomorum, in the fly gut microbiome on Drosophila juvenile growth, including specific actions of gut hormones and metabolites in conserved cellular signaling systems, such as the insulin/insulin-like (IIS) and the target of rapamycin (TOR) pathways. Given the similarities in tissue function/structure, as well as the high conservation of physiological systems between Drosophila and mammals, findings from the Drosophila model system will have significant implications for understanding the mechanisms underlying the interaction between the host and the gut microbiome in metazoans.
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Affiliation(s)
- Hyun Myoung Yun
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Seogang Hyun
- Department of Life Science, Chung-Ang University, Seoul, South Korea
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42
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Quan J, Xu C, Ruan D, Ye Y, Qiu Y, Wu J, Zhou S, Luan M, Zhao X, Chen Y, Lin D, Sun Y, Yang J, Zheng E, Cai G, Wu Z, Yang J. Composition, function, and timing: exploring the early-life gut microbiota in piglets for probiotic interventions. J Anim Sci Biotechnol 2023; 14:143. [PMID: 37957747 PMCID: PMC10641937 DOI: 10.1186/s40104-023-00943-z] [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: 06/21/2023] [Accepted: 09/20/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND The establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous effects. However, the optimal timeframe for introducing probiotics to achieve this outcome remains uncertain. RESULTS In the context of this investigation, we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time points. Simultaneously, we gathered vaginal and fecal samples from 23 sows. Employing 16S rRNA gene and metagenomic sequencing methodologies, we conducted a comprehensive analysis of the fluctuation patterns in microbial composition, functional capacity, interaction networks, and colonization resistance within the gut microbiota of piglets. As the piglets progressed in age, discernible modifications in intestinal microbial diversity, composition, and function were observed. A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal piglets. By D21, the microbial interaction network displayed a more concise and efficient configuration, accompanied by enhanced colonization resistance relative to the other two time points. Moreover, we identified three strains of Ruminococcus sp. at D10 as potential candidates for improving piglets' weight gain during the weaning phase. CONCLUSIONS The findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet development. This investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.
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Affiliation(s)
- Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
- National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, Guangdong, People's Republic of China
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Menghao Luan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Xiang Zhao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Yue Chen
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Danyang Lin
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Ying Sun
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Jifei Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China.
- National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, Guangdong, People's Republic of China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
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Mancilla VJ, Braden-Kuhle PN, Brice KN, Mann AE, Williams MT, Zhang Y, Chumley MJ, Barber RC, White SN, Boehm GW, Allen MS. A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice. Microorganisms 2023; 11:2694. [PMID: 38004705 PMCID: PMC10673175 DOI: 10.3390/microorganisms11112694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.
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Affiliation(s)
- Viviana J. Mancilla
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Paige N. Braden-Kuhle
- Department of Psychology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA
| | - Kelly N. Brice
- Department of Psychology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA
| | - Allison E. Mann
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634, USA
| | - Megan T. Williams
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Yan Zhang
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Michael J. Chumley
- Department of Biology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA;
| | - Robert C. Barber
- Department of Pharmacology and Neuroscience, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Sabrina N. White
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Gary W. Boehm
- Department of Psychology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA
| | - Michael S. Allen
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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Koziol A, Odriozola I, Leonard A, Eisenhofer R, San José C, Aizpurua O, Alberdi A. Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors. mBio 2023; 14:e0160623. [PMID: 37650630 PMCID: PMC10653949 DOI: 10.1128/mbio.01606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.
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Affiliation(s)
- Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Aoife Leonard
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carlos San José
- Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Marcelino VR, Welsh C, Diener C, Gulliver EL, Rutten EL, Young RB, Giles EM, Gibbons SM, Greening C, Forster SC. Disease-specific loss of microbial cross-feeding interactions in the human gut. Nat Commun 2023; 14:6546. [PMID: 37863966 PMCID: PMC10589287 DOI: 10.1038/s41467-023-42112-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/27/2023] [Indexed: 10/22/2023] Open
Abstract
Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us to identify and rank metabolic interactions that are significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn's disease case-control study, our approach identifies a lack of species with the ability to consume hydrogen sulfide as the main distinguishing microbiome feature of disease. We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem.
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Affiliation(s)
- Vanessa R Marcelino
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia.
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.
- Melbourne Integrative Genomics, School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Caitlin Welsh
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, 3800, Australia
| | | | - Emily L Gulliver
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Emily L Rutten
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Remy B Young
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Edward M Giles
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- eScience Institute, University of Washington, Seattle, WA, 98195, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, 3800, Australia
| | - Samuel C Forster
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia.
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.
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46
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Sun X, Sanchez A. Synthesizing microbial biodiversity. Curr Opin Microbiol 2023; 75:102348. [PMID: 37352679 DOI: 10.1016/j.mib.2023.102348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/20/2023] [Accepted: 05/25/2023] [Indexed: 06/25/2023]
Abstract
The diversity of microbial ecosystems is linked to crucial ecological processes and functions. Despite its significance, the ecological mechanisms responsible for the initiation and maintenance of microbiome diversity are still not fully understood. The primary challenge lies in the difficulty of isolating, monitoring, and manipulating the complex and interrelated ecological processes that modulate the diversity of microbial communities in their natural habitats. Synthetic ecology experiments provide a suitable alternative for investigating the mechanisms behind microbial biodiversity in controlled laboratory settings, as the environment can be systematically and modularly manipulated by adding and removing components. This enables the testing of hypotheses and the advancement of predictive theories. In this review, we present an overview of recent progress toward achieving this goal.
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Affiliation(s)
- Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Alvaro Sanchez
- Department of Microbial Biotechnology, National Center for Biotechnology CNB-CSIC, Madrid, Spain.
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47
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Magnuson JT, Monticelli G, Schlenk D, Bisesi JH, Pampanin DM. Connecting gut microbiome changes with fish health conditions in juvenile Atlantic cod (Gadus morhua) exposed to dispersed crude oil. ENVIRONMENTAL RESEARCH 2023; 234:116516. [PMID: 37399986 DOI: 10.1016/j.envres.2023.116516] [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: 05/04/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Polycyclic aromatic hydrocarbons found in crude oil can impair fish health following sublethal exposure. However, the dysbiosis of microbial communities within the fish host and influence it has on the toxic response of fish following exposure has been less characterized, particularly in marine species. To better understand the effect of dispersed crude oil (DCO) on juvenile Atlantic cod (Gadus morhua) microbiota composition and potential targets of exposure within the gut, fish were exposed to 0.05 ppm DCO for 1, 3, 7, or 28 days and 16 S metagenomic and metatranscriptomic sequencing on the gut and RNA sequencing on intestinal content were conducted. In addition to assessing species composition, richness, and diversity from microbial gut community analysis and transcriptomic profiling, the functional capacity of the microbiome was determined. Mycoplasma and Aliivibrio were the two most abundant genera after DCO exposure and Photobacterium the most abundant genus in controls, after 28 days. Metagenomic profiles were only significantly different between treatments after a 28-day exposure. The top identified pathways were involved in energy and the biosynthesis of carbohydrates, fatty acids, amino acids, and cellular structure. Biological processes following fish transcriptomic profiling shared common pathways with microbial functional annotations such as energy, translation, amide biosynthetic process, and proteolysis. There were 58 differently expressed genes determined from metatranscriptomic profiling after 7 days of exposure. Predicted pathways that were altered included those involved in translation, signal transduction, and Wnt signaling. EIF2 signaling was consistently dysregulated following exposure to DCO, regardless of exposure duration, with impairments in IL-22 signaling and spermine and spermidine biosynthesis in fish after 28 days. Data were consistent with predictions of a potentially reduced immune response related to gastrointestinal disease. Herein, transcriptomic-level responses helped explain the relevance of differences in gut microbial communities in fish following DCO exposure.
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Affiliation(s)
- Jason T Magnuson
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway.
| | - Giovanna Monticelli
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, Riverside, CA, USA
| | - Joseph H Bisesi
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Daniela M Pampanin
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
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48
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Hellal J, Barthelmebs L, Bérard A, Cébron A, Cheloni G, Colas S, Cravo-Laureau C, De Clerck C, Gallois N, Hery M, Martin-Laurent F, Martins J, Morin S, Palacios C, Pesce S, Richaume A, Vuilleumier S. Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol 2023; 99:fiad102. [PMID: 37669892 PMCID: PMC10516372 DOI: 10.1093/femsec/fiad102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.
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Affiliation(s)
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs – Analyse-Environnement, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Annette Bérard
- UMR EMMAH INRAE/AU – équipe SWIFT, 228, route de l'Aérodrome, 84914 Avignon Cedex 9, France
| | | | - Giulia Cheloni
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Simon Colas
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech (Liege University), Passage des Déportés 2, 5030 Gembloux, Belgium
| | | | - Marina Hery
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Fabrice Martin-Laurent
- Institut Agro Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, 21065 Dijon, France
| | - Jean Martins
- IGE, UMR 5001, Université Grenoble Alpes, CNRS, G-INP, INRAE, IRD Grenoble, France
| | | | - Carmen Palacios
- Université de Perpignan Via Domitia, CEFREM, F-66860 Perpignan, France
- CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | | | - Agnès Richaume
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
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49
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Chen J, Zhu J, Lu W, Wang H, Pan M, Tian P, Zhao J, Zhang H, Chen W. Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance. Nutrients 2023; 15:3925. [PMID: 37764709 PMCID: PMC10536327 DOI: 10.3390/nu15183925] [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: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic treatment can lead to a loss of diversity of gut microbiota and may adversely affect gut microbiota composition and host health. Previous studies have indicated that the recovery of gut microbes from antibiotic-induced disruption may be guided by specific microbial species. We expect to predict recovery or non-recovery using these crucial species or other indices after antibiotic treatment only when the gut microbiota changes. This study focused on this prediction problem using a novel ensemble learning framework to identify a set of common and reasonably predictive recovery-associated bacterial species (p-RABs), enabling us to predict the host microbiome recovery status under broad-spectrum antibiotic treatment. Our findings also propose other predictive indicators, suggesting that higher taxonomic and functional diversity may correlate with an increased likelihood of successful recovery. Furthermore, to explore the validity of p-RABs, we performed a metabolic support analysis and identified Akkermansia muciniphila and Bacteroides uniformis as potential key supporting species for reconstruction interventions. Experimental results from a C57BL/6J male mouse model demonstrated the effectiveness of p-RABs in facilitating intestinal microbial reconstitution. Thus, we proved the reliability of the new p-RABs and validated a practical intervention scheme for gut microbiota reconstruction under antibiotic disturbance.
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Affiliation(s)
- Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingluo Pan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Peijun Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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50
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Kononova S, Kashparov M, Xue W, Bobkova N, Leonov S, Zagorodny N. Gut Microbiome Dysbiosis as a Potential Risk Factor for Idiopathic Toe-Walking in Children: A Review. Int J Mol Sci 2023; 24:13204. [PMID: 37686011 PMCID: PMC10488280 DOI: 10.3390/ijms241713204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Idiopathic toe walking (ITW) occurs in about 5% of children. Orthopedic treatment of ITW is complicated by the lack of a known etiology. Only half of the conservative and surgical methods of treatment give a stable positive result of normalizing gait. Available data indicate that the disease is heterogeneous and multifactorial. Recently, some children with ITW have been found to have genetic variants of mutations that can lead to the development of toe walking. At the same time, some children show sensorimotor impairment, but these studies are very limited. Sensorimotor dysfunction could potentially arise from an imbalanced production of neurotransmitters that play a crucial role in motor control. Using the data obtained in the studies of several pathologies manifested by the association of sensory-motor dysfunction and intestinal dysbiosis, we attempt to substantiate the notion that malfunction of neurotransmitter production is caused by the imbalance of gut microbiota metabolites as a result of dysbiosis. This review delves into the exciting possibility of a connection between variations in the microbiome and ITW. The purpose of this review is to establish a strong theoretical foundation and highlight the benefits of further exploring the possible connection between alterations in the microbiome and TW for further studies of ITW etiology.
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Affiliation(s)
- Svetlana Kononova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Mikhail Kashparov
- Department of Traumatology and Orthopedics, Peoples’ Friendship University of Russia, 117198 Moscow, Russia; (M.K.); (N.Z.)
- Scientific and Practical Center for Child Psychoneurology, 119602 Moscow, Russia
| | - Wenyu Xue
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (W.X.); (S.L.)
| | - Natalia Bobkova
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Sergey Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (W.X.); (S.L.)
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Nikolaj Zagorodny
- Department of Traumatology and Orthopedics, Peoples’ Friendship University of Russia, 117198 Moscow, Russia; (M.K.); (N.Z.)
- N.N. Priorov Central Research Institute of Traumatology and Orthopedics, 127299 Moscow, Russia
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