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Balasundaram D, Veerasamy V, Sylvia Singarayar M, Neethirajan V, Ananth Devanesan A, Thilagar S. Therapeutic potential of probiotics in gut microbial homeostasis and Rheumatoid arthritis. Int Immunopharmacol 2024; 137:112501. [PMID: 38885604 DOI: 10.1016/j.intimp.2024.112501] [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: 02/29/2024] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by inflammation and joint damage. Existing treatment options primarily focus on managing symptoms and slowing disease progression, often with side effects and limitations. The gut microbiome, a vast community of microorganisms present in the gastrointestinal tract, plays a crucial role in health and disease. Recent research suggests a bidirectional relationship between the gut microbiome and RA, highlighting its potential as a therapeutic option. This review focuses on the interaction between the gut microbiome and RA development, by discussing how dysbiosis, an imbalance in gut bacteria, can contribute to RA through multiple mechanisms such as molecular mimicry, leaky gut, and metabolic dysregulation. Probiotics, live microorganisms with health benefits, are emerging as promising tools for managing RA. They can prevent the negative effects of dysbiosis by displacing harmful bacteria, producing anti-inflammatory metabolites like short-chain fatty acids (SCFA), Directly influencing immune cells, and modifying host metabolism. animal and clinical studies demonstrate the potential of probiotics in improving RA symptoms and disease outcomes. However, further research is needed to optimize probiotic strains, dosages, and treatment protocols for personalized and effective management of RA. This review summarizes the current understanding of the gut microbiome and its role in RA and discusses future research directions. In addition to the established role of gut dysbiosis in RA, emerging strategies like fecal microbiota transplantation, prebiotics, and postbiotics offer exciting possibilities. However, individual variations in gut composition necessitate personalized treatment plans. Long-term effects and clear regulations need to be established. Future research focusing on metagenomic analysis, combination therapies, and mechanistic understanding will unlock the full potential of gut microbiome modulation for effective RA management.
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Affiliation(s)
| | - Veeramurugan Veerasamy
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India
| | - Magdalin Sylvia Singarayar
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India
| | - Vivek Neethirajan
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India
| | | | - Sivasudha Thilagar
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India.
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2
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Fang X, Liu H, Du Y, Jiang L, Gao F, Wang Z, Chi Z, Shi B, Zhao X. Bacillus siamensis Targeted Screening from Highly Colitis-Resistant Pigs Can Alleviate Ulcerative Colitis in Mice. RESEARCH (WASHINGTON, D.C.) 2024; 7:0415. [PMID: 39015206 PMCID: PMC11249912 DOI: 10.34133/research.0415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Ulcerative colitis (UC) is often accompanied by intestinal inflammation and disruption of intestinal epithelial structures, which are closely associated with changes in the intestinal microbiota. We previously revealed that Min pigs, a native Chinese breed, are more resistant to dextran sulfate sodium (DSS)-induced colitis than commercial Yorkshire pigs. Characterizing the microbiota in Min pigs would allow identification of the core microbes that confer colitis resistance. By analyzing the microbiota linked to the disease course in Min and Yorkshire pigs, we observed that Bacillus spp. were enriched in Min pigs and positively correlated with pathogen resistance. Using targeted screening, we identified and validated Bacillus siamensis MZ16 from Min pigs as a bacterial species with biofilm formation ability, superior salt and pH tolerance, and antimicrobial characteristics. Subsequently, we administered B. siamensis MZ16 to conventional or microbiota-deficient BALB/c mice with DSS-induced colitis to assess its efficacy in alleviating colitis. B. siamensis MZ16 partially counteracted DSS-induced colitis in conventional mice, but it did not mitigate DSS-induced colitis in microbiota-deficient mice. Further analysis revealed that B. siamensis MZ16 administration improved intestinal ecology and integrity and immunological barrier function in mice. Compared to the DSS-treated mice, mice preadministered B. siamensis MZ16 exhibited improved relative abundance of potentially beneficial microbes (Lactobacillus, Bacillus, Christensenellaceae R7, Ruminococcus, Clostridium, and Eubacterium), reduced relative abundance of pathogenic microbes (Escherichia-Shigella), and maintained colonic OCLN and ZO-1 levels and IgA and SIgA levels. Furthermore, B. siamensis MZ16 reduced proinflammatory cytokine levels by reversing NF-κB and MAPK pathway activation in the DSS group. Overall, B. siamensis MZ16 from Min pigs had beneficial effects on a colitis mouse model by enhancing intestinal barrier functions and reducing inflammation in a gut microbiota-dependent manner.
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Affiliation(s)
- Xiuyu Fang
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Haiyang Liu
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Yongqing Du
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Lin Jiang
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Feng Gao
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Zhengyi Wang
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Zihan Chi
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Baoming Shi
- College of Animal Science and Technology,
Northeast Agricultural University, Harbin 150030, People’s Republic of China
| | - Xuan Zhao
- College of Animal Science and Technology,
Southwest University, Chongqing 400715, People’s Republic of China
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3
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Jin Q, Feng Y, Cabana-Puig X, Chau TN, Difulvio R, Yu D, Hu A, Li S, Luo XM, Ogejo J, Lin F, Huang H. Combined dilute alkali and milling process enhances the functionality and gut microbiota fermentability of insoluble corn fiber. Food Chem 2024; 446:138815. [PMID: 38428087 DOI: 10.1016/j.foodchem.2024.138815] [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: 09/25/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
In this study, we developed a process combining dilute alkali (NaOH or NaHCO3) and physical (disk milling and/or ball milling) treatments to improve the functionality and fermentability of corn fiber. The results showed that combining chemical with physical processes greatly improved the functionality and fermentability of corn fiber. Corn fiber treated with NaOH followed by disk milling (NaOH-DM-CF) had the highest water retention (19.5 g/g), water swelling (38.8 mL/g), and oil holding (15.5 g/g) capacities. Moreover, NaOH-DM-CF produced the largest amount (42.9 mM) of short-chain fatty acid (SCFA) during the 24-hr in vitro fermentation using porcine fecal inoculum. In addition, in vitro fermentation of NaOH-DM-CF led to a targeted microbial shifting to Prevotella (genus level), aligning with a higher fraction of propionic acid. The outstanding functionality and fermentability of NaOH-DM-CF were attributed to its thin and loose structure, decreased ester linkages and acetyl groups, and enriched structural carbohydrate exposure.
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Affiliation(s)
- Qing Jin
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States; School of Food and Agriculture, University of Maine, Orono, ME 04469, United States
| | - Yiming Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Xavier Cabana-Puig
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Tran N Chau
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Ronnie Difulvio
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Dajun Yu
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Anyang Hu
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Xin M Luo
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Jactone Ogejo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Feng Lin
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Haibo Huang
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States.
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4
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Wunderlich M, Miller M, Ritter B, Le Gleut R, Marchi H, Majzoub-Altweck M, Knerr PJ, Douros JD, Müller TD, Brielmeier M. Experimental colonization with H. hepaticus, S. aureus and R. pneumotropicus does not influence the metabolic response to high-fat diet or incretin-analogues in wildtype SOPF mice. Mol Metab 2024; 87:101992. [PMID: 39019114 DOI: 10.1016/j.molmet.2024.101992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
OBJECTIVES We here assessed whether typical pathogens of laboratory mice affect the development of diet-induced obesity and glucose intolerance, and whether colonization affects the efficacy of the GLP-1R agonist liraglutide and of the GLP-1/GIP co-agonist MAR709 to treat obesity and diabetes. METHODS Male C57BL/6J mice were experimentally infected with Helicobacter hepaticus, Rodentibacter pneumotropicus and Staphylococcus aureus and compared to a group of uninfected specific and opportunistic pathogen free (SOPF) mice. The development of diet-induced obesity and glucose intolerance was monitored over a period of 26 weeks. To study the influence of pathogens on drug treatment, mice were then subjected for 6 days daily treatment with either the GLP-1 receptor agonist liraglutide or the GLP-1/GIP co-agonist MAR709. RESULTS Colonized mice did not differ from SOPF controls regarding HFD-induced body weight gain, food intake, body composition, glycemic control, or responsiveness to treatment with liraglutide or the GLP-1/GIP co-agonist MAR709. CONCLUSIONS We conclude that the occurrence of H. hepaticus, R. pneumotropicus and S. aureus does neither affect the development of diet-induced obesity or type 2 diabetes, nor the efficacy of GLP-1-based drugs to decrease body weight and to improve glucose control in mice.
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Affiliation(s)
| | - Manuel Miller
- Core Facility Laboratory Animal Services, Helmholtz Munich, Germany.
| | - Bärbel Ritter
- Core Facility Laboratory Animal Services, Helmholtz Munich, Germany
| | - Ronan Le Gleut
- Core Facility Statistical Consulting, Helmholtz Munich, Germany
| | - Hannah Marchi
- Core Facility Statistical Consulting, Helmholtz Munich, Germany; Faculty of Business Administration and Economics, Bielefeld University, Germany
| | - Monir Majzoub-Altweck
- Institute of Veterinary Pathology, Ludwig-Maximilians-University Munich (LMU), Germany
| | - Patrick J Knerr
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | | | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Munich, Germany, and German Center for Diabetes Research, DZD, and Walther-Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University Munich (LMU), Germany
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5
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Seethalakshmi PS, Kumaresan TN, Vishnu Prasad Nair RU, Prathiviraj R, Seghal Kiran G, Selvin J. Comparative analysis of commercially available kits for optimal DNA extraction from bovine fecal samples. Arch Microbiol 2024; 206:314. [PMID: 38900289 DOI: 10.1007/s00203-024-04047-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/19/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
In the field of metagenomic research, the choice of DNA extraction methods plays a pivotal yet often underestimated role in shaping the reliability and interpretability of microbial community data. This study delves into the impact of five commercially available DNA extraction kits on the analysis of bovine fecal microbiota. Recognizing the importance of accurate DNA extraction in elucidating microbial community dynamics, we systematically assessed DNA yield, quality, and microbial composition across these kits using 16S rRNA gene sequencing. Notably, the FastDNA spin soil kit yielded the highest DNA concentration, while significant variations in quality were observed across kits. Furthermore, differential abundance analysis revealed kit-specific biases that impacted taxa representation. Microbial richness and diversity were significantly influenced by the choice of extraction kit, with QIAamp DNA stool minikit, QIAamp Power Pro, and DNeasy PowerSoil outperforming the Stool DNA Kit. Principal-coordinate analysis revealed distinct clustering based on DNA isolation procedures, particularly highlighting the unique microbial community composition derived from the Stool DNA Kit. This study also addressed practical implications, demonstrating how kit selection influences the concentration of Gram-positive and Gram-negative bacterial taxa in samples. This research highlights the need for consideration of DNA extraction kits in metagenomic studies, offering valuable insights for researchers striving to advance the precision and depth of microbiota analyses in ruminants.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - T N Kumaresan
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | | | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India.
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Hou J, Zhang L, Xu W, Liu Z, Yu J, Yu R, Chen L. Glycometabolic disorder induced by chronic exposure to low-concentration imidacloprid in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173421. [PMID: 38788955 DOI: 10.1016/j.scitotenv.2024.173421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
The health risks induced by chronic exposure to low concentrations of imidacloprid (IMI) to zebrafish were investigated in this study. The results indicated that the growth of zebrafish was inhibited after being exposed to 10, 100, and 500 μg/L of IMI for 90 days. Moreover, the blood glucose levels in the IMI-exposed groups were significantly higher compared to the control group. Investigation into the development of zebrafish larvae revealed that IMI exposure hindered the development of the liver and pancreatic islets, organs crucial for glucose metabolism. In addition, the IMI-exposed groups exhibited reduced liver glycogen and plasma insulin levels, along with changes in the activity of enzymes and the transcription levels of genes associated with liver glucose metabolism. These findings suggest that IMI induces glycometabolic disorders in zebrafish. The analysis of intestinal flora revealed that several key bacteria associated with an elevated risk of diabetes were significantly altered in IMI-exposed fish. Specifically, a remarkable decrease was found in the abundance of the genera Aeromonas and Shewanella, which have been found closely related to the development of pancreatic islets. This implies that the alteration of key bacteria in the fish gut by IMI, which in turn affects the development of organs such as the pancreatic islets, may be the initial trigger for abnormalities in glucose metabolism. Our results revealed that chronic exposure to low concentrations of IMI led to glycometabolic disorder in fish. Therefore, considering the pervasive existence of IMI residues in the environment, the health hazards posed by low-concentration IMI to fish cannot be overlooked.
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Affiliation(s)
- Jiayin Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Lulu Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; Ningbo Univ, Coll Food & Pharmaceut Sci, Ningbo 315832, Zhejiang, China
| | - Wanghui Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; Zhejiang Univ Technol, Catalyt Hydrogenat Res Ctr, Zhejiang Green Pesticide Collaborat Innovat Ctr, Zhejiang Key Lab Green Pesticides & Cleaner Prod, Hangzhou 310014, Zhejiang, China
| | - Zhiyu Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; Ningbo Univ, Coll Food & Pharmaceut Sci, Ningbo 315832, Zhejiang, China
| | - Jianzhong Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Ruixian Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Liezhong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China.
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7
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Hu J, Bi R, Luo Y, Wu K, Jin S, Liu Z, Jia Y, Mao CX. The gut microbiome promotes locomotion of Drosophila larvae via octopamine signaling. INSECT SCIENCE 2024. [PMID: 38643372 DOI: 10.1111/1744-7917.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/10/2024] [Accepted: 03/24/2024] [Indexed: 04/22/2024]
Abstract
The gut microbiome is a key partner of animals, influencing various aspects of their physiology and behaviors. Among the diverse behaviors regulated by the gut microbiome, locomotion is vital for survival and reproduction, although the underlying mechanisms remain unclear. Here, we reveal that the gut microbiome modulates the locomotor behavior of Drosophila larvae via a specific neuronal type in the brain. The crawling speed of germ-free (GF) larvae was significantly reduced compared to the conventionally reared larvae, while feeding and excretion behaviors were unaffected. Recolonization with Acetobacter and Lactobacillus can fully and partially rescue the locomotor defects in GF larvae, respectively, probably due to the highest abundance of Acetobacter as a symbiotic bacterium in the larval gut, followed by Lactobacillus. Moreover, the gut microbiome promoted larval locomotion, not by nutrition, but rather by enhancing the brain levels of tyrosine decarboxylase 2 (Tdc2), which is an enzyme that synthesizes octopamine (OA). Overexpression of Tdc2 rescued locomotion ability in GF larvae. These findings together demonstrate that the gut microbiome specifically modulates larval locomotor behavior through the OA signaling pathway, revealing a new mechanism underlying larval locomotion regulated by the gut microbiome.
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Affiliation(s)
- Juncheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Ran Bi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yuxuan Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Kaihong Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Shan Jin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhihua Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yicong Jia
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Chuan-Xi Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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Siva Venkatesh IP, Majumdar A, Basu A. Prophylactic Administration of Gut Microbiome Metabolites Abrogated Microglial Activation and Subsequent Neuroinflammation in an Experimental Model of Japanese Encephalitis. ACS Chem Neurosci 2024; 15:1712-1727. [PMID: 38581382 DOI: 10.1021/acschemneuro.4c00028] [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: 04/08/2024] Open
Abstract
Short-chain fatty acids (SCFAs) are gut microbial metabolic derivatives produced during the fermentation of ingested complex carbohydrates. SCFAs have been widely regarded to have a potent anti-inflammatory and neuro-protective role and have implications in several disease conditions, such as, inflammatory bowel disease, type-2 diabetes, and neurodegenerative disorders. Japanese encephalitis virus (JEV), a neurotropic flavivirus, is associated with life threatening neuro-inflammation and neurological sequelae in infected hosts. In this study, we hypothesize that SCFAs have potential in mitigating JEV pathogenesis. Postnatal day 10 BALB/c mice were intraperitoneally injected with either a SCFA mixture (acetate, propionate, and butyrate) or PBS for a period of 7 days, followed by JEV infection. All mice were observed for onset and progression of symptoms. The brain tissue was collected upon reaching terminal illness for further analysis. SCFA-supplemented JEV-infected mice (SCFA + JEV) showed a delayed onset of symptoms, lower hindlimb clasping score, and decreased weight loss and increased survival by 3 days (p < 0.0001) upon infection as opposed to the PBS-treated JEV-infected animals (JEV). Significant downregulation of inflammatory cytokines TNF-α, MCP-1, IL-6, and IFN-Υ in the SCFA + JEV group relative to the JEV-infected control group was observed. Inflammatory mediators, phospho-NF-kB (P-NF-kB) and iba1, showed 2.08 ± 0.1 and 3.132 ± 0.43-fold upregulation in JEV versus 1.19 ± 0.11 and 1.31 ± 0.11-fold in the SCFA + JEV group, respectively. Tissue section analysis exhibited reduced glial activation (JEV group─42 ± 2.15 microglia/ROI; SCFA + JEV group─27.07 ± 1.8 microglia/ROI) in animals that received SCFA supplementation prior to infection as seen from the astrocytic and microglial morphometric analysis. Caspase-3 immunoblotting showed 4.08 ± 1.3-fold upregulation in JEV as compared to 1.03 ± 0.14-fold in the SCFA + JEV group and TUNEL assay showed a reduced cellular death post-JEV infection (JEV-6.4 ± 1.5 cells/ROI and SCFA + JEV-3.7 ± 0.73 cells/ROI). Our study critically contributes to the increasing evidence in support of SCFAs as an anti-inflammatory and neuro-protective agent, we further expand its scope as a potential supplementary intervention in JEV-mediated neuroinflammation.
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MESH Headings
- Gastrointestinal Microbiome/physiology
- Neuroinflammatory Diseases/drug therapy
- Neuroinflammatory Diseases/immunology
- Neuroinflammatory Diseases/metabolism
- Neuroinflammatory Diseases/microbiology
- Microglia/drug effects
- Microglia/immunology
- Encephalitis, Japanese/drug therapy
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/microbiology
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/virology
- Fatty Acids, Volatile/pharmacology
- Fatty Acids, Volatile/therapeutic use
- Encephalitis Viruses, Japanese/drug effects
- Encephalitis Viruses, Japanese/immunology
- Encephalitis Viruses, Japanese/pathogenicity
- Survival Analysis
- Chemokines/immunology
- Chemokines/metabolism
- Inflammation Mediators/immunology
- Inflammation Mediators/metabolism
- Cytokine Release Syndrome/immunology
- Cytokine Release Syndrome/metabolism
- Cytokine Release Syndrome/prevention & control
- Humans
- Female
- Animals
- Mice
- Apoptosis/drug effects
- Brain/drug effects
- Brain/metabolism
- Brain/virology
- Viral Load/drug effects
- Time Factors
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Affiliation(s)
| | - Atreye Majumdar
- National Brain Research Centre, Manesar, Haryana 122052, India
| | - Anirban Basu
- National Brain Research Centre, Manesar, Haryana 122052, India
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Sha H, Lu J, Chen J, Xiong J. Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis. NPJ Biofilms Microbiomes 2024; 10:40. [PMID: 38605016 PMCID: PMC11009345 DOI: 10.1038/s41522-024-00509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Whiley L, Lawler NG, Zeng AX, Lee A, Chin ST, Bizkarguenaga M, Bruzzone C, Embade N, Wist J, Holmes E, Millet O, Nicholson JK, Gray N. Cross-Validation of Metabolic Phenotypes in SARS-CoV-2 Infected Subpopulations Using Targeted Liquid Chromatography-Mass Spectrometry (LC-MS). J Proteome Res 2024; 23:1313-1327. [PMID: 38484742 PMCID: PMC11002931 DOI: 10.1021/acs.jproteome.3c00797] [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: 11/17/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
To ensure biological validity in metabolic phenotyping, findings must be replicated in independent sample sets. Targeted workflows have long been heralded as ideal platforms for such validation due to their robust quantitative capability. We evaluated the capability of liquid chromatography-mass spectrometry (LC-MS) assays targeting organic acids and bile acids to validate metabolic phenotypes of SARS-CoV-2 infection. Two independent sample sets were collected: (1) Australia: plasma, SARS-CoV-2 positive (n = 20), noninfected healthy controls (n = 22) and COVID-19 disease-like symptoms but negative for SARS-CoV-2 infection (n = 22). (2) Spain: serum, SARS-CoV-2 positive (n = 33) and noninfected healthy controls (n = 39). Multivariate modeling using orthogonal projections to latent structures discriminant analyses (OPLS-DA) classified healthy controls from SARS-CoV-2 positive (Australia; R2 = 0.17, ROC-AUC = 1; Spain R2 = 0.20, ROC-AUC = 1). Univariate analyses revealed 23 significantly different (p < 0.05) metabolites between healthy controls and SARS-CoV-2 positive individuals across both cohorts. Significant metabolites revealed consistent perturbations in cellular energy metabolism (pyruvic acid, and 2-oxoglutaric acid), oxidative stress (lactic acid, 2-hydroxybutyric acid), hypoxia (2-hydroxyglutaric acid, 5-aminolevulinic acid), liver activity (primary bile acids), and host-gut microbial cometabolism (hippuric acid, phenylpropionic acid, indole-3-propionic acid). These data support targeted LC-MS metabolic phenotyping workflows for biological validation in independent sample sets.
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Affiliation(s)
- Luke Whiley
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Centre
for Computational and Systems Medicine, Health Futures Institute Harry
Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Nathan G. Lawler
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Centre
for Computational and Systems Medicine, Health Futures Institute Harry
Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Annie Xu Zeng
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Alex Lee
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Sung-Tong Chin
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Maider Bizkarguenaga
- Centro
de Investigación Cooperativa en Biociencias—CIC bioGUNE,
Precision Medicine and Metabolism Laboratory, Basque Research and
Technology Alliance, Bizkaia Science and
Technology Park, Building
800, 48160 Derio, Spain
| | - Chiara Bruzzone
- Centro
de Investigación Cooperativa en Biociencias—CIC bioGUNE,
Precision Medicine and Metabolism Laboratory, Basque Research and
Technology Alliance, Bizkaia Science and
Technology Park, Building
800, 48160 Derio, Spain
| | - Nieves Embade
- Centro
de Investigación Cooperativa en Biociencias—CIC bioGUNE,
Precision Medicine and Metabolism Laboratory, Basque Research and
Technology Alliance, Bizkaia Science and
Technology Park, Building
800, 48160 Derio, Spain
| | - Julien Wist
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Centre
for Computational and Systems Medicine, Health Futures Institute Harry
Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
| | - Elaine Holmes
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Centre
for Computational and Systems Medicine, Health Futures Institute Harry
Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Department
of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial
College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, U.K.
| | - Oscar Millet
- Centro
de Investigación Cooperativa en Biociencias—CIC bioGUNE,
Precision Medicine and Metabolism Laboratory, Basque Research and
Technology Alliance, Bizkaia Science and
Technology Park, Building
800, 48160 Derio, Spain
| | - Jeremy K. Nicholson
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Centre
for Computational and Systems Medicine, Health Futures Institute Harry
Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Institute
of Global Health Innovation, Faculty Building South Kensington Campus, Imperial College London, London SW7 2AZ, U.K.
| | - Nicola Gray
- Australian
National Phenome Centre, Health Futures Institute Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Centre
for Computational and Systems Medicine, Health Futures Institute Harry
Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
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11
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Bhardwaj G, Riadi Y, Afzal M, Bansal P, Kaur H, Deorari M, Tonk RK, Almalki WH, Kazmi I, Alzarea SI, Kukreti N, Thangavelu L, Saleem S. The hidden threat: Environmental toxins and their effects on gut microbiota. Pathol Res Pract 2024; 255:155173. [PMID: 38364649 DOI: 10.1016/j.prp.2024.155173] [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: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota (GM), which consists of a complex and diverse ecosystem of bacteria, plays a vital role in overall wellness. However, the delicate balance of this intricate system is being compromised by the widespread presence of environmental toxins. The intricate connection between contaminants in the environment and human well-being has garnered significant attention in recent times. Although many environmental pollutants and their toxicity have been identified and studied in laboratory settings and animal models, there is insufficient data concerning their relevance to human physiology. Consequently, research on the toxicity of environmental toxins in GM has gained prominence in recent years. Various factors, such as air pollution, chemicals, heavy metals, and pesticides, have a detrimental impact on the composition and functioning of the GM. This comprehensive review aims to comprehend the toxic effects of numerous environmental pollutants, including antibiotics, endocrine-disrupting chemicals, heavy metals, and pesticides, on GM by examining recent research findings. The current analysis concludes that different types of environmental toxins can lead to GM dysbiosis and have various potential adverse effects on the well-being of animals. We investigate the alterations to the GM composition induced by contaminants and their impact on overall well-being, providing a fresh perspective on research related to pollutant exposure.
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Affiliation(s)
- Gautam Bhardwaj
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar sector-3, M-B Road, New Delhi 110017, India
| | - Yassine Riadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh 247341, India; Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand 831001, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Rajiv Kumar Tonk
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar sector-3, M-B Road, New Delhi 110017, India.
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341 Sakaka, Aljouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Lakshmi Thangavelu
- Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Shakir Saleem
- Department of Public Health. College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia.
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12
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Ishizawa H, Tashiro Y, Inoue D, Ike M, Futamata H. Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure. Proc Natl Acad Sci U S A 2024; 121:e2312396121. [PMID: 38315845 PMCID: PMC10873592 DOI: 10.1073/pnas.2312396121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024] Open
Abstract
Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agriculture, wastewater treatment, and human healthcare domains. Traditionally, studies on the microbial community assembly focused on analyzing pairwise relationships among species; however, neglecting higher-order interactions, i.e., the change of pairwise relationships in the community context, may lead to substantial deviation from reality. Herein, we have proposed a simple framework that incorporates higher-order interactions into a bottom-up prediction of the microbial community assembly and examined its accuracy using a seven-member synthetic bacterial community on a host plant, duckweed. Although the synthetic community exhibited emergent properties that cannot be predicted from pairwise coculturing results, our results demonstrated that incorporating information from three-member combinations allows the acceptable prediction of the community structure and actual interaction forces within it. This reflects that the occurrence of higher-order effects follows consistent patterns, which can be predicted even from trio combinations, the smallest unit of higher-order interactions. These results highlight the possibility of predicting, explaining, and understanding the microbial community structure from the bottom-up by learning interspecies interactions from simple beyond-pairwise combinations.
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Affiliation(s)
- Hidehiro Ishizawa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji671-2280, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita565-0821, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita565-0821, Japan
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu432-8561, Japan
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13
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Antoine D, Chupikova I, Jalodia R, Singh PK, Roy S. Chronic Morphine Treatment and Antiretroviral Therapy Exacerbate HIV-Distal Sensory Peripheral Neuropathy and Induce Distinct Microbial Alterations in the HIV Tg26 Mouse Model. Int J Mol Sci 2024; 25:1569. [PMID: 38338849 PMCID: PMC10855564 DOI: 10.3390/ijms25031569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
Distal Sensory Peripheral Neuropathy (DSP) is a common complication in HIV-infected individuals, leading to chronic pain and reduced quality of life. Even with antiretroviral therapy (ART), DSP persists, often prompting the use of opioid analgesics, which can paradoxically worsen symptoms through opioid-induced microbial dysbiosis. This study employs the HIV Tg26 mouse model to investigate HIV-DSP development and assess gut microbiome changes in response to chronic morphine treatment and ART using 16S rRNA sequencing. Our results reveal that chronic morphine and ART exacerbate HIV-DSP in Tg26 mice, primarily through mechanical pain pathways. As the gut microbiome may be involved in chronic pain persistence, microbiome analysis indicated distinct bacterial community changes between WT and Tg26 mice as well as morphine- and ART-induced microbial changes in the Tg26 mice. This study reveals the Tg26 mouse model to be a relevant system that can help elucidate the pathogenic mechanisms of the opioid- and ART-induced exacerbation of HIV-associated pain. Our results shed light on the intricate interplay between HIV infection, ART, opioid use, and the gut microbiome in chronic pain development. They hold implications for understanding the mechanisms underlying HIV-associated pain and microbial dysbiosis, with potential for future research focused on prevention and treatment strategies.
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Affiliation(s)
- Danielle Antoine
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Neuroscience, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Irina Chupikova
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Richa Jalodia
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Praveen Kumar Singh
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sabita Roy
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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14
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Yang JL, Chen S, Xi JF, Lin XY, Xue RY, Ma LQ, Zhou D, Li HB. Sex-dependent effects of rice cadmium exposure on body weight, gut microflora, and kidney metabolomics based on a mouse model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168498. [PMID: 37952668 DOI: 10.1016/j.scitotenv.2023.168498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/24/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Consumption of cadmium (Cd) contaminated rice is the main dietary source of Cd exposure and toxicity. To protect humans from Cd toxicity, it is pivotal to fully understand the sex-dependent toxicity of subchronic rice-Cd exposure. However, the sex-dependent effects of subchronic rice-Cd exposure on body weight gain, gut microflora, and kidney metabolomics are still unclear. In this study, a Cd-free and a Cd-contaminated rice (0.005 and 0.74 mg Cd kg-1) were fed to both female and male mice for one month, with changes in body weight gain, Cd accumulation in tissue, bone mineral concentration, expression of intestinal channels involving in Cd and calcium (Ca) absorption, gut microbiota, and kidney metabolites assessed for both genders. Results showed that female mice had normal body weight gain after rice-Cd exposure, while body weight of male mice was decreased from 19.8 to 17.5 g over the one-month consumption of the Cd-contaminated rice (0.74 mg kg-1), suggesting specific toxicity on growth of male mice. Rice-Cd exposure had limited effects on gut microbiota for both genders. However, higher Cd accumulation in liver and femur was observed in male mice than in females, which may be due to higher intestinal expression of Ca channels involving in intestinal Cd absorption in male mice with rice-Cd exposure. Greater risk of osteoporosis was also observed in male mice. In addition, kidney metabolomic profiling showed special disruption of adrenocortical hormone homeostasis for male mice with rice-Cd exposure. Particularly, expression of cortisol in kidneys of male mice was elevated 37.1-fold with rice-Cd exposure, likely resulting in Cushing's syndrome and contributing to growth retardation. This study advances our understanding of the sex-dependent toxicity of rice-Cd exposure, and highlights the priority of protecting males from the adrenocortical hormone disrupting effects of rice-Cd exposure.
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Affiliation(s)
- Jin-Lei Yang
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jin-Feng Xi
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xin-Ying Lin
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Rong-Yue Xue
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lena Q Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongmei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Hong-Bo Li
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China.
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15
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Wu N, Liu J, Sun Y, Fan X, Zang T, Richardson BN, Bai J, Xianyu Y, Liu Y. Alterations of the gut microbiota and fecal short-chain fatty acids in women undergoing assisted reproduction. Reprod Fertil Dev 2024; 36:RD23096. [PMID: 38252939 DOI: 10.1071/rd23096] [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: 06/06/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
CONTEXT The community structure of gut microbiota changes during pregnancy, which also affects the synthesis of short-chain fatty acids (SCFAs). However, the distribution of gut microbiota composition and metabolite SCFA levels are poorly understood in women undergoing assisted reproductive technology (ART). AIMS To evaluate the changes in gut microbiota composition and metabolic SCFAs in women who received assisted reproduction treatment. METHODS Sixty-three pregnant women with spontaneous pregnancy (SP) and nine with ART pregnancy were recruited to provide fecal samples. Gut microbiota abundance and SCFA levels were determined by 16S ribosomal RNA (rRNA) gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS). KEY RESULTS The ART group showed decreased alpha diversity (the species richness or evenness in a sample). The principal coordinates analysis (a method of analysing beta diversity) showed significant difference in gut microbiota between the ART group versus the SP group (unweighted UniFrac distance, R 2 =0.04, P =0.003). Proteobacteria , Blautia and Escherichia-Shigella were enriched in the ART group, whereas the relative abundance of beneficial intestinal bacteria Faecalibacterium was lower than in the SP group. Different modes of conception were associated with several SCFAs (valeric acid (r =-0.280; P =0.017); isocaproic acid (r =-0.330; P =0.005); caproic acid (r =-0.336; P =0.004)). Significantly different SCFAs between the two groups were synchronously associated with the differential gut microbiota. CONCLUSIONS The diversity and abundance of gut microbiota and the levels of SCFAs in women undergoing ART decreased. IMPLICATIONS The application of ART shaped the microbial composition and metabolism, which may provide critical information for understanding the biological changes that occur in women with assisted reproduction.
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Affiliation(s)
- Ni Wu
- Center for Women's and Children's Health, Wuhan University, Wuhan, China
| | - Jun Liu
- Center for Women's and Children's Health, Wuhan University, Wuhan, China
| | - Yu Sun
- Center for Women's and Children's Health, Wuhan University, Wuhan, China
| | - Xiaoxiao Fan
- Center for Women's and Children's Health, Wuhan University, Wuhan, China
| | - Tianzi Zang
- Center for Women's and Children's Health, Wuhan University, Wuhan, China
| | | | - Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | | | - Yanqun Liu
- Center for Women's and Children's Health, Wuhan University, Wuhan, China
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16
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Zhang J, Shu Z, Lv S, Zhou Q, Huang Y, Peng Y, Zheng J, Zhou Y, Hu C, Lan S. Fermented Chinese Herbs Improve the Growth and Immunity of Growing Pigs through Regulating Colon Microbiota and Metabolites. Animals (Basel) 2023; 13:3867. [PMID: 38136904 PMCID: PMC10740985 DOI: 10.3390/ani13243867] [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: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: the development of new antibiotic substitutes to promote pig growth and health has become an important way to solve the current dilemma and promote the pig industry. (2) Methods: to assess the effects of a fermented Chinese herbal (FCH) formula on the growth and immunity of growing pigs, 100 Duroc × Landrace × Yorshire three-way crossed growing pigs were randomly divided into control and treatment groups that were fed a basal diet, and a basal diet with 1% (group A), 2% (group B), and 3% (group C) FCH formulas, respectively. A sixty-day formal experiment was conducted, and their growth and serum indices, colonic microbiota, and metabolites were analyzed. (3) Results: the daily gain of growing pigs in groups A, B, and C increased by 7.93%, 17.68%, and 19.61%, respectively, and the feed-to-gain ratios decreased by 8.33%, 15.00%, and 14.58%, respectively. Serum immunity and antioxidant activities were significantly increased in all treatment groups. Particularly, adding a 2% FCH formula significantly changed the colon's microbial structure; the Proteobacteria significantly increased and Firmicutes significantly decreased, and the metabolite composition in the colon's contents significantly changed. (4) Conclusions: these results indicate that the FCH formula is a good feed additive for growing pigs, and the recommended addition ratio was 3%.
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Affiliation(s)
- Junhao Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Zhiheng Shu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Sixiao Lv
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Qingwen Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yuanhao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yingjie Peng
- Guangdong Chuangzhan Bona Agricultural Technology Co., Ltd., Guangning 526339, China;
| | - Jun Zheng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yi Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Chao Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Shile Lan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
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17
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Kivistik C, Tammert H, Kisand V, Käiro K, Herlemann DPR. Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system. Mol Ecol 2023; 32:6631-6643. [PMID: 35876211 DOI: 10.1111/mec.16628] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022]
Abstract
The gut microbiome is one of the most important sites of host-microbe interactions, however, mechanisms governing the responses of host-associated microbes to changing environmental conditions are poorly understood. To address this, we investigated individual and combined effects of dietary changes and increase in salinity (from freshwater to salinity 3) or antibiotic concentration on the gastrointestinal bacterial community of the aquatic snail Ampullaceana balthica. In parallel, the energy reserves of the host were quantified. A change of natural food source to biofilm forming green algae Scenedesmus obliquus as well as the combined treatment of salinity and S. obliquus decreased the richness and changed the composition of the A. balthica gastrointestinal bacterial community. In these treatments Pseudomonas became the dominant bacterium. However, energy reserves of the host were higher in these treatments compared to the reference aquaria specimens and the combined treatment of antibiotics with S. obliquus. The presence of antibiotics inhibited the dominance of Pseudomonas and resulted in lower energy reserves despite S. obliquus feeding. Therefore the host seems to be able to adapt and replace its bacterial community composition to respond to mild changes in salinity and food source. Antibiotics in the water can disturb this self-regulating mechanism. Our study underlines the ability of aquatic macroinvertebrates to respond to sudden changes in food source and mild shifts in salinity. Moreover, it emphasizes the strong impact of the food source on the gastrointestinal microbiome and the importance of generalists during disturbance.
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Affiliation(s)
- Carmen Kivistik
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Helen Tammert
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Veljo Kisand
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kairi Käiro
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
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18
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Mu K, Kitts DD. Intestinal polyphenol antioxidant activity involves redox signaling mechanisms facilitated by aquaporin activity. Redox Biol 2023; 68:102948. [PMID: 37922763 PMCID: PMC10643476 DOI: 10.1016/j.redox.2023.102948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
Ascertaining whether dietary polyphenols evoke an antioxidant or prooxidant activity, which translates to a functional role required to maintain intestinal cell homeostasis continues to be an active and controversial area of research for food chemists and biochemists alike. We have proposed that the paradoxical function of polyphenols to autoxidize to generate H2O2 is a required first step in the capacity of some plant phenolics to function as intracellular antioxidants. This is based on the fact that cell redox homeostasis is achieved by a balance between H2O2 formation and subsequent outcomes of antioxidant systems function. Maintaining optimal extracellular and intracellular H2O2 concentrations is required for cell survival, since low levels are important to upregulate endogenous antioxidant capacity; whereas, concentrations that go beyond homeostatic control typically result in an inflammatory response, growth arrest, or eventual cell death. Aquaporins (AQPs) are a family of water channel membrane proteins that facilitate cellular transportation of water and other small molecule-derived solutes, such as H2O2, in all organisms. In the intestine, AQPs act as gatekeepers to regulate intracellular uptake of H2O2, generated from extracellular polyphenol autoxidation, thus enabling an intracellular cell signaling responses to mitigate onset of oxidative stress and intestinal inflammation. In this review, we highlight the potential role of AQPs to control important underlying mechanisms that define downstream regulation of intestinal redox homeostasis, specifically. It has been established that polyphenols that undergo oxidation to the quinone form, resulting in subsequent adduction to a thiol group on Keap1-Nrf2 complex, trigger Nrf2 activation and a cascade of indirect intracellular antioxidant effects. Here, we propose a similar mechanism that involves H2O2 generated from specific dietary polyphenols with a predisposition to undergo autoxidation. The ultimate bioactivity is regulated and expressed by AQP membrane function and thus, by extension, represents expression of an intracellular antioxidant chemoprotection mechanism.
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Affiliation(s)
- Kaiwen Mu
- Food Science, Food Nutrition and Health Program. Faculty of Land and Food System, The University of British Columbia, 2205 East Mall, Vancouver, B.C, V6T 1Z4, Canada
| | - David D Kitts
- Food Science, Food Nutrition and Health Program. Faculty of Land and Food System, The University of British Columbia, 2205 East Mall, Vancouver, B.C, V6T 1Z4, Canada.
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Farooqi T, Bhuyan DJ, Low M, Sinclair J, Leonardi M, Armour M. Cannabis and Endometriosis: The Roles of the Gut Microbiota and the Endocannabinoid System. J Clin Med 2023; 12:7071. [PMID: 38002684 PMCID: PMC10671947 DOI: 10.3390/jcm12227071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Endometriosis, a chronic condition affecting around 10-14% of women, is challenging to manage, due to its complex pathogenesis and limited treatment options. Research has suggested a potential role of the gut microbiota and the endocannabinoid system in the development and progression of endometriosis. This narrative review aims to explore the role of, and any potential interactions between, the endocannabinoid system (ECS) and the gut microbiota in endometriosis. This review found that both the ECS and microbiota influence endometriosis, with the former regulating inflammation and pain perception and the latter influencing immune responses and hormonal balance. There is evidence that a dysregulation of the endocannabinoid system and the gut microbiota influence endometriosis symptoms and progression via changes in CB1 receptor expression and increased circulating levels of endocannabinoids. Microbial imbalances in the gut, such as increases in Prevotella, have been directly correlated to increased bloating, a common endometriosis symptom, while increases in E. coli have supported the bacterial contamination hypothesis as a potential pathway for endometriosis pathogenesis. These microbial imbalances have been correlated with increases in inflammatory markers such as TNF-α and IL-6, both often raised in those with endometriosis. Protective effects of the ECS on the gut were observed by increases in endocannabinoids, including 2-AG, resulting in decreased inflammation and improved gut permeability. Given these findings, both the ECS and the gut microbiota may be targets for therapeutic interventions for endometriosis; however, clinical studies are required to determine effectiveness.
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Affiliation(s)
- Toobah Farooqi
- NICM Health Research Institute, Western Sydney University, Sydney 2751, Australia; (T.F.); (D.J.B.); (M.L.); (J.S.)
| | - Deep Jyoti Bhuyan
- NICM Health Research Institute, Western Sydney University, Sydney 2751, Australia; (T.F.); (D.J.B.); (M.L.); (J.S.)
- School of Science, Western Sydney University, Sydney 2751, Australia
| | - Mitchell Low
- NICM Health Research Institute, Western Sydney University, Sydney 2751, Australia; (T.F.); (D.J.B.); (M.L.); (J.S.)
| | - Justin Sinclair
- NICM Health Research Institute, Western Sydney University, Sydney 2751, Australia; (T.F.); (D.J.B.); (M.L.); (J.S.)
| | - Mathew Leonardi
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON L8V 5C2, Canada;
- Robinson Research Institute, University of Adelaide, Adelaide 5006, Australia
| | - Mike Armour
- NICM Health Research Institute, Western Sydney University, Sydney 2751, Australia; (T.F.); (D.J.B.); (M.L.); (J.S.)
- Translational Health Research Institute, Western Sydney University, Sydney 2751, Australia
- Medical Research Institute of New Zealand, P.O. Box 7902, Wellington 6242, New Zealand
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20
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Jang B, Chung MG, Lee DS. Association between gut microbial change and acute gastrointestinal toxicity in patients with prostate cancer receiving definitive radiation therapy. Cancer Med 2023; 12:20727-20735. [PMID: 37921267 PMCID: PMC10709749 DOI: 10.1002/cam4.6636] [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: 07/28/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND This prospective study investigated the association between gut microbial changes and acute gastrointestinal toxicities in prostate cancer patients receiving definitive radiation therapy (RT). METHODS Seventy-nine fecal samples were analyzed. Stool samples were collected at the following timepoints: pre-RT (prRT), 2 weeks after the start of RT (RT-2w), 5 weeks after the start of RT (RT-5w), 1 month after completion of RT (poRT-1 m), and 3 months after completion of RT (poRT-3 m). We computed the microbial community polarization index (MCPI) as an indicator of RT-induced dysbiosis. RESULTS Patients experiencing toxicity had lower alpha diversity, especially at RT-2w (p = 0.037) and RT-5w (p = 0.003). Compared to patients without toxicity, the MCPI in those experiencing toxicities was significantly elevated (p = 0.019). In terms of predicted metabolic pathways, we found linearly decreasing pathways, including carbon fixation pathways in prokaryotes (p = 0.035) and the bacterial secretion system (p = 0.005), in patients who experienced toxicities. CONCLUSIONS We showed RT-induced dysbiosis among patients who experienced toxicities. Reduced diversity and elevated RT-related MCPI could be helpfully used for developing individualized RT approaches.
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Affiliation(s)
- Bum‐Sup Jang
- Department of Radiation OncologyCollege of MedicineSeoul National UniversitySeoulKorea
| | - Moon Gyu Chung
- Microbiome centerKorea Research Institute of Bio‐medical ScienceDaejeonKorea
| | - Dong Soo Lee
- Department of Radiation Oncology, College of MedicineThe Catholic University of KoreaSeoulKorea
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21
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Fu Y, Zhang K, Shan F, Li J, Wang Y, Li X, Xu H, Qin Z, Zhang L. Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective. BMC Genomics 2023; 24:635. [PMID: 37875797 PMCID: PMC10594901 DOI: 10.1186/s12864-023-09742-2] [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: 12/07/2022] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND With the promotion of "One Health," the health of animals and their impact on the environment have become major concerns recently. Widely distributed in China, the whooper swans (Cygnus cygnus) and black swans (Cygnus atratus) are not only important to the ecological environment, but they may also potentially influence public health security. The metagenomic approach was adopted to uncover the impacts of the gut microbiota of swans on host and public health. RESULTS In this study, the intestinal microbiome and resistome of migratory whooper swans and captive-bred black swans were identified. The results revealed similar gut microbes and functional compositions in whooper and black swans. Interestingly, different bacteria and probiotics were enriched by overwintering whooper swans. We also found that Acinetobacter and Escherichia were significantly enriched in early wintering period swans and that clinically important pathogens were more abundant in black swans. Whooper swans and black swans are potential reservoirs of antibiotic resistance genes (ARGs) and novel ARGs, and the abundance of novel ARGs in whooper swans was significantly higher than that in black swans. Metagenomic assembly-based host tracking revealed that most ARG-carrying contigs originated from Proteobacteria (mainly Gammaproteobacteria). CONCLUSIONS The results revealed spatiotemporal changes in microbiome and resistome in swans, providing a reference for safeguarding public health security and preventing animal epidemics.
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Affiliation(s)
- Yin Fu
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Kaihui Zhang
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Fa Shan
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Yilin Wang
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Huiyan Xu
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Ziyang Qin
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450046, China.
- International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China.
- Ministry of Agriculture and Rural Areas Key Laboratory for Quality and Safety Control of Poultry Products, Zhengzhou, 450046, China.
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22
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Feng J, Yang K, Liu X, Song M, Zhan P, Zhang M, Chen J, Liu J. Machine learning: a powerful tool for identifying key microbial agents associated with specific cancer types. PeerJ 2023; 11:e16304. [PMID: 37901464 PMCID: PMC10601900 DOI: 10.7717/peerj.16304] [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: 02/08/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Machine learning (ML) includes a broad class of computer programs that improve with experience and shows unique strengths in performing tasks such as clustering, classification and regression. Over the past decade, microbial communities have been implicated in influencing the onset, progression, metastasis, and therapeutic response of multiple cancers. Host-microbe interaction may be a physiological pathway contributing to cancer development. With the accumulation of a large number of high-throughput data, ML has been successfully applied to the study of human cancer microbiomics in an attempt to reveal the complex mechanism behind cancer. In this review, we begin with a brief overview of the data sources included in cancer microbiomics studies. Then, the characteristics of the ML algorithm are briefly introduced. Secondly, the application progress of ML in cancer microbiomics is also reviewed. Finally, we highlight the challenges and future prospects facing ML in cancer microbiomics. On this basis, we conclude that the development of cancer microbiomics can not be achieved without ML, and that ML can be used to develop tumor-targeting microbial therapies, ultimately contributing to personalized and precision medicine.
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Affiliation(s)
- Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Kailan Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Min Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Ping Zhan
- Department of Obstetrics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mi Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Jinsong Chen
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
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23
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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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24
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Deck CA, Salger SA, Reynolds HM, Tada MD, Severance ME, Ferket P, Egna HS, Fatema MK, Haque SM, Borski RJ. Nutritional programming in Nile tilapia (Oreochromis niloticus): Effect of low dietary protein on growth and the intestinal microbiome and transcriptome. PLoS One 2023; 18:e0292431. [PMID: 37792787 PMCID: PMC10550151 DOI: 10.1371/journal.pone.0292431] [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: 06/26/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
Nutritional programming is the idea that early nutrient contributions can influence organismal structure or function and is documented in a variety of vertebrates, yet studies in fish are largely lacking. Tilapia are an important foodfish, with global production having increased rapidly since the 1990s. They exhibit high disease-resistance and grow well on formulated feeds which makes them an ideal aquaculture species, however incorporating high quality proteins into feeds can be costly. As feed constitutes 50-70% of total production costs in aquaculture, reducing protein content could curb these costs and increase revenue. Thus, we examined the effects of feeding Nile tilapia (O. niloticus) fry a restricted protein diet for the first 7-21 days on growth, gut microbial flora, and the intestinal transcriptome. Fish were fed either a 25% restricted or 48% control crude protein starter (ST) diet for up to 21 days and then switched to a 25% or 38% control crude protein growout (GO) diet. Fish fed a 25% ST diet for 14 days followed by a 38% GO diet had significantly higher lengths and weights and better feed efficiency than fish fed the control 48% ST and 38% GO diet after 56 days of culture. Growth of fry on the 25% ST, 7-day/38% GO and the 25% ST,7-day/25% GO diets did not differ from the those fed the control protein diets, while fish fed the 25% ST diet for 21 days had significantly lower growth and survival rates. We observed no significant differences in either alpha or beta diversity of the gut microbial flora between diets, however species richness (Shannon Index) was higher in fry fed the 25% protein ST diet regardless of the GO diet. Similarly, fish fed the 25% ST diet for 14 days followed by the 38% GO diet had minimal changes to the intestinal transcriptome relative to fish fed the control 48% ST and 38% GO diet. However, those fed 25% ST and GO diets for the entire 56 days exhibited substantial differences in the gut transcriptome from other groups showing gene expression profiles characteristic of detrimental changes to gut physiology, protein metabolism and immune function. Results suggest protein restriction for up to 14 days early in development leads to enhanced growth and feed efficiency with minimal effects on gut microbes or intestinal function. Protein restriction beyond this period appears detrimental to fish growth and health as underscored by expression of disease related genes and higher mortality rates.
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Affiliation(s)
- Courtney A. Deck
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Scott A. Salger
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- School of Sciences, Barton College, Wilson, NC, United States of America
| | - Hannah M. Reynolds
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Michael D. Tada
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Madeline E. Severance
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Peter Ferket
- Department of Poultry Science, North Carolina State University, Raleigh, NC, United States of America
| | - Hillary S. Egna
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Mst. Kaniz Fatema
- Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Shahroz M. Haque
- Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Russell J. Borski
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
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25
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Yaghjyan L, Mai V, Darville LNF, Cline J, Wang X, Ukhanova M, Tagliamonte MS, Martinez YC, Rich SN, Koomen JM, Egan KM. Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women. Cancer Causes Control 2023; 34:873-881. [PMID: 37286847 DOI: 10.1007/s10552-023-01728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE The gut microbiome is a potentially important contributor to endogenous estrogen levels after menopause. In healthy postmenopausal women, we examined associations of fecal microbiome composition with levels of urinary estrogens, their metabolites, and relevant metabolic pathway ratios implicated in breast cancer risk. METHODS Eligible postmenopausal women (n = 164) had a body mass index (BMI) ≤ 35 kg/m2 and no history of hormone use (previous 6 months) or cancer/metabolic disorders. Estrogens were quantified in spot urine samples with liquid chromatography-high resolution mass spectrometry (corrected for creatinine). Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of gut microbiome's indices of within-sample (alpha) diversity (i.e., Shannon, Chao1, and Inverse Simpson), phylogenetic diversity, and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with individual estrogens and metabolic ratios, adjusted for age and BMI. RESULTS In this sample of 164 healthy postmenopausal women, the mean age was 62.9 years (range 47.0-86.0). We found significant inverse associations of observed species with 4-pathway:total estrogens (p = 0.04) and 4-pathway:2-pathway (p = 0.01). Shannon index was positively associated with 2-catechols: methylated 2-catechols (p = 0.04). Chao1 was inversely associated with E1:total estrogens (p = 0.04), and 4-pathway:2-pathway (p = 0.02) and positively associated with 2-pathway:parent estrogens (p = 0.01). Phylogenetic diversity was inversely associated with 4-pathway:total estrogens (p = 0.02), 4-pathway:parent estrogens (p = 0.03), 4-pathway:2-pathway (p = 0.01), and 4-pathway:16-pathway (p = 0.03) and positively associated with 2-pathway:parent estrogens (p = 0.01). F/B ratio was not associated with any of the estrogen measures. CONCLUSION Microbial diversity was associated with several estrogen metabolism ratios implicated in breast cancer risk. Further studies are warranted to confirm these findings in a larger and more representative sample of postmenopausal women, particularly with enrichment of minority participants.
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Affiliation(s)
- Lusine Yaghjyan
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | | | | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Massimiliano S Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | | | - Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
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Mahiddine FY, You I, Park H, Kim MJ. Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation. Vet Res Commun 2023; 47:1629-1640. [PMID: 36977954 DOI: 10.1007/s11259-023-10116-y] [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: 12/16/2022] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.
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Affiliation(s)
- Feriel Yasmine Mahiddine
- Department of Research and Development, Mjbiogen Corp, Seoul, 04788, Republic of Korea
- Department of Theriogenology and Biotechnologies, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Inhwan You
- Department of Research and Development, Mjbiogen Corp, Seoul, 04788, Republic of Korea
- Department of Theriogenology and Biotechnologies, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heekee Park
- Department of Research and Development, Mjbiogen Corp, Seoul, 04788, Republic of Korea
| | - Min Jung Kim
- Department of Research and Development, Mjbiogen Corp, Seoul, 04788, Republic of Korea.
- Department of Theriogenology and Biotechnologies, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
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Garg A, Ellis LB, Love RL, Grewal K, Bowden S, Bennett PR, Kyrgiou M. Vaginal microbiome in obesity and its impact on reproduction. Best Pract Res Clin Obstet Gynaecol 2023; 90:102365. [PMID: 37399714 DOI: 10.1016/j.bpobgyn.2023.102365] [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: 04/01/2023] [Revised: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 07/05/2023]
Abstract
A number of reproductive outcomes have been increasingly found to be affected by the vaginal microbiota. Obesity has become a global epidemic, affecting increasing numbers of reproductive-age women, and has been shown to be a risk factor for a number of adverse female health outcomes. A healthy vaginal microbiome is characterized by Lactobacillus-dominance, in particular Lactobacillus crispatus; obesity has been found to be associated with higher diversity and a lower likelihood of Lactobacillus-dominance. In this review, we summarize the evidence on the vaginal microbiome in obese women and the impact on reproductive outcomes such as conception rates, early pregnancy, and preterm birth. We further explore the mechanisms by which obesity may result in an altered microbial composition and highlight future avenues for therapeutic targeting of the vaginal microbiota.
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Affiliation(s)
- Akanksha Garg
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK; Imperial College Healthcare NHS Trust, London, UK
| | - Laura Burney Ellis
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK; Imperial College Healthcare NHS Trust, London, UK
| | - Ryan Laurence Love
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK; Imperial College Healthcare NHS Trust, London, UK
| | - Karen Grewal
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK; Imperial College Healthcare NHS Trust, London, UK
| | - Sarah Bowden
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK
| | - Phillip R Bennett
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK
| | - Maria Kyrgiou
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK; Imperial College Healthcare NHS Trust, London, UK.
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Gutierrez-Vilchis A, Perfecto-Avalos Y, Garcia-Gonzalez A. Modeling bacteria pairwise interactions in human microbiota by Sparse Identification of Nonlinear Dynamics (SINDy) . ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083503 DOI: 10.1109/embc40787.2023.10341078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The gut microbiota is a community of high complexity; its composition changes due to ecological interactions, these are studied to understand the relationship with the human health. External stimuli like the administration of probiotics, prebiotics, or drugs are known to modify these interactions. The high complexity of microbiota composition can be studied by considering pairwise interactions. Pairwise interactions in bacterial communities consider each species' directionality and impact on one another, e.g., commensalism (unidirectional positive interaction) or competition (bidirectional negative interaction). These interactions can either be interspecies or intraspecies. The Lotka-Volterra (LV) model has been implemented to characterize these bacteria interactions, considering the ecological relationship among the different species presented. One of the main challenges is determining the specific interaction parameters in LV structure from experimental data. This study implemented a novel approach based on the sparse identification of nonlinear dynamic method (SINDy). One of the assumptions in SINDy method implies the knowledge of the data derivative structure. To fulfill this requirement, a differential neural network algorithm was implemented. We assessed the performance of this approach considering both a simulated and experimental interspecies scenario. A two-species bacterial LV model was simulated in the initial validation stage, and the resulting kinetic growth data was recorded. This data was utilized for training a differential neural network algorithm, which was used to derive a time-derivative structure for the dataset. After this step, SINDy method was implemented to calculate the interaction parameters. Three conditions were evaluated in intraspecies competition, obtaining an average identification parametric error of less than 2%. For experimental data, parametric analysis results are sensitive to detect the influence of a drug presence over the intraspecies interaction with a reduction of 50% in its typical values.Clinical Relevance- In this study, we devised a strategy to determine how two species of the human gastrointestinal microbiota interact and the impact of drug administration on these interactions.
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29
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Cho S, Samuel TM, Li T, Howell BR, Baluyot K, Hazlett HC, Elison JT, Zhu H, Hauser J, Sprenger N, Lin W. Interactions between Bifidobacterium and Bacteroides and human milk oligosaccharides and their associations with infant cognition. Front Nutr 2023; 10:1216327. [PMID: 37457984 PMCID: PMC10345227 DOI: 10.3389/fnut.2023.1216327] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
While ample research on independent associations between infant cognition and gut microbiota composition and human milk (HM) oligosaccharides (HMOs) has been reported, studies on how the interactions between gut microbiota and HMOs may yield associations with cognitive development in infancy are lacking. We aimed to determine how HMOs and species of Bacteroides and Bifidobacterium genera interact with each other and their associations with cognitive development in typically developing infants. A total of 105 mother-infant dyads were included in this study. The enrolled infants [2.9-12 months old (8.09 ± 2.48)] were at least predominantly breastfed at 4 months old. A total of 170 HM samples from the mothers and fecal samples of the children were collected longitudinally. Using the Mullen Scales of Early Learning to assess cognition and the scores as the outcomes, linear mixed effects models including both the levels of eight HMOs and relative abundance of Bacteroides and Bifidobacterium species as main associations and their interactions were employed with adjusting covariates; infant sex, delivery mode, maternal education, site, and batch effects of HMOs. Additionally, regression models stratifying infants based on the A-tetrasaccharide (A-tetra) status of the HM they received were also employed to determine if the associations depend on the A-tetra status. With Bacteroides species, we observed significant associations with motor functions, while Bif. catenulatum showed a negative association with visual reception in the detectable A-tetra group both as main effect (value of p = 0.012) and in interaction with LNFP-I (value of p = 0.007). Additionally, 3-FL showed a positive association with gross motor (p = 0.027) and visual reception (p = 0.041). Furthermore, significant associations were observed with the interaction terms mainly in the undetectable A-tetra group. Specifically, we observed negative associations for Bifidobacterium species and LNT [breve (p = 0.011) and longum (p = 0.022)], and positive associations for expressive language with 3'-SL and Bif. bifidum (p = 0.01), 6'-SL and B. fragilis (p = 0.019), and LNFP-I and Bif. kashiwanohense (p = 0.048), respectively. Our findings suggest that gut microbiota and HMOs are both independently and interactively associated with early cognitive development. In particular, the diverse interactions between HMOs and Bacteroides and Bifidobacterium species reveal different candidate pathways through which HMOs, Bifidobacterium and Bacteroides species potentially interact to impact cognitive development in infancy.
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Affiliation(s)
- Seoyoon Cho
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Tinu M. Samuel
- Nestle Product Technology Center-Nutrition, Société des Produits Nestlé S.A., Vevey, Switzerland
| | - Tengfei Li
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Brittany R. Howell
- Fralin Biomedical Research Institute at VTC, Department of Human Development and Family Science, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
| | - Kristine Baluyot
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Heather C. Hazlett
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jed T. Elison
- Institute of Child Development, University of Minnesota, Minneapolis, MN, United States
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonas Hauser
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Norbert Sprenger
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Weili Lin
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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30
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Scott E, Brewer MS, Peralta AL, Issa FA. The Effects of Social Experience on Host Gut Microbiome in Male Zebrafish ( Danio rerio). THE BIOLOGICAL BULLETIN 2023; 244:177-189. [PMID: 38457676 DOI: 10.1086/729377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
AbstractAlthough the gut and the brain vastly differ in physiological function, they have been interlinked in a variety of different neurological and behavioral disorders. The bacteria that comprise the gut microbiome communicate and influence the function of various physiological processes within the body, including nervous system function. However, the effects of social experience in the context of dominance and social stress on gut microbiome remain poorly understood. Here, we examined whether social experience impacts the host zebrafish (Danio rerio) gut microbiome. We studied how social dominance during the first 2 weeks of social interactions changed the composition of zebrafish gut microbiome by comparing gut bacterial composition, diversity, and relative abundance between socially dominant, submissive, social isolates and control group-housed communal fish. Using amplicon sequencing of the 16S rRNA gene, we report that social dominance significantly affects host gut bacterial community composition but not bacterial diversity. At the genus level, Aeromonas and unclassified Enterobacteriaceae relative abundance decreased in dominant individuals while commensal bacteria (e.g., Exiguobacterium and Cetobacterium) increased in relative abundance. Conversely, the relative abundance of Psychrobacter and Acinetobacter was increased in subordinates, isolates, and communal fish compared to dominant fish. The shift in commensal and pathogenic bacteria highlights the impact of social experience and the accompanying stress on gut microbiome, with potentially similar effects in other social organisms.
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31
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Mahboob A, Samuel SM, Mohamed A, Wani MY, Ghorbel S, Miled N, Büsselberg D, Chaari A. Role of flavonoids in controlling obesity: molecular targets and mechanisms. Front Nutr 2023; 10:1177897. [PMID: 37252233 PMCID: PMC10213274 DOI: 10.3389/fnut.2023.1177897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Obesity presents a major health challenge that increases the risk of several non-communicable illnesses, such as but not limited to diabetes, hypertension, cardiovascular diseases, musculoskeletal and neurological disorders, sleep disorders, and cancers. Accounting for nearly 8% of global deaths (4.7 million) in 2017, obesity leads to diminishing quality of life and a higher premature mortality rate among affected individuals. Although essentially dubbed as a modifiable and preventable health concern, prevention, and treatment strategies against obesity, such as calorie intake restriction and increasing calorie burning, have gained little long-term success. In this manuscript, we detail the pathophysiology of obesity as a multifactorial, oxidative stress-dependent inflammatory disease. Current anti-obesity treatment strategies, and the effect of flavonoid-based therapeutic interventions on digestion and absorption, macronutrient metabolism, inflammation and oxidative stress and gut microbiota has been evaluated. The use of several naturally occurring flavonoids to prevent and treat obesity with a long-term efficacy, is also described.
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Affiliation(s)
- Anns Mahboob
- Department of Pre-medical Education, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Samson Mathews Samuel
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Arif Mohamed
- College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | - Sofiane Ghorbel
- Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabil Miled
- College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Ali Chaari
- Department of Pre-medical Education, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
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32
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Burnham CM, McKenney EA, van Heugten KA, Minter LJ, Trivedi S. Effects of age, seasonality, and reproductive status on the gut microbiome of Southern White Rhinoceros (Ceratotherium simum simum) at the North Carolina zoo. Anim Microbiome 2023; 5:27. [PMID: 37147724 PMCID: PMC10163733 DOI: 10.1186/s42523-023-00249-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 04/22/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Managed southern white rhinoceros (Ceratotherium simum simum) serve as assurance populations for wild conspecifics threatened by poaching and other anthropocentric effects, though many managed populations experience subfertility and reproductive failure. Gut microbiome and host health are inextricably linked, and reproductive outcomes in managed southern white rhinoceros may be mediated in part by their diet and gut microbial diversity. Thus, understanding microbial dynamics within managed populations may help improve conservation efforts. We characterized the taxonomic composition of the gut microbiome in the managed population of female southern white rhinoceros (n = 8) at the North Carolina Zoo and investigated the effects of seasonality (summer vs. winter) and age classes (juveniles (n = 2; 0-2 years), subadults (n = 2; 3-7 years), and adults (n = 4; >7 years)) on microbial richness and community structure. Collection of a fecal sample was attempted for each individual once per month from July-September 2020 and January-March 2021 resulting in a total of 41 samples analyzed. Microbial DNA was extracted and sequenced using the V3-V4 region of the 16S rRNA bacterial gene. Total operational taxonomic units (OTUs), alpha diversity (species richness, Shannon diversity), and beta diversity (Bray-Curtis dissimilarity, linear discriminant analysis effect size) indices were examined, and differentially enriched taxa were identified. RESULTS There were differences (p < 0.05) in alpha and beta diversity indices across individuals, age groups, and sampling months. Subadult females had higher levels of Shannon diversity (Wilcoxon, p < 0.05) compared to adult females and harbored a community cluster distinct from both juveniles and adults. Samples collected during winter months (January-March 2021) possessed higher species richness and statistically distinct communities compared to summer months (July-September 2020) (PERMANOVA, p < 0.05). Reproductively active (n = 2) and currently nonreproductive adult females (n = 2) harbored differentially enriched taxa, with the gut microbiome of nonreproductive females significantly enriched (p = 0.001) in unclassified members of Mobiluncus, a genus which possesses species associated with poor reproductive outcomes in other animal species when identified in the cervicovaginal microbiome. CONCLUSION Together, our results increase the understanding of age and season related microbial variation in southern white rhinoceros at the North Carolina Zoo and have identified a potential microbial biomarker for reproductive concern within managed female southern white rhinoceros.
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Affiliation(s)
- Christina M Burnham
- Department of Animal Science, North Carolina State University, 120 W Broughton Dr, Raleigh, NC, 27607, USA
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, 100 Brooks Ave, Raleigh, NC, 27607, USA
| | - Kimberly Ange- van Heugten
- Department of Animal Science, North Carolina State University, 120 W Broughton Dr, Raleigh, NC, 27607, USA
| | - Larry J Minter
- North Carolina Zoo, 4401 Zoo Parkway, Asheboro, NC, 27205, USA
| | - Shweta Trivedi
- Department of Animal Science, North Carolina State University, 120 W Broughton Dr, Raleigh, NC, 27607, USA.
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Comolli J, Walsh DI, Bobrow J, Lennartz CL, Guido NJ, Thorsen T. An in vitro platform for study of the human gut microbiome under an oxygen gradient. Biomed Microdevices 2023; 25:14. [PMID: 37014472 PMCID: PMC10073063 DOI: 10.1007/s10544-023-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2023] [Indexed: 04/05/2023]
Abstract
The complex, dynamic environment of the human lower gastrointestinal tract is colonized by hundreds of bacterial species that impact health and performance. Ex vivo study of the functional interactions between microbial community members in conditions representative of those in the gut is an ongoing challenge. We have developed an in vitro 40-plex platform that provides an oxygen gradient to support simultaneous maintenance of microaerobic and anaerobic microbes from the gut microbiome that can aid in rapid characterization of microbial interactions and direct comparison of individual microbiome samples. In this report, we demonstrate that the platform more closely maintained the microbial diversity and composition of human donor fecal microbiome samples than strict anaerobic conditions. The oxygen gradient established in the platform allowed the stratification and subsequent sampling of diverse microbial subpopulations that colonize microaerobic and anaerobic micro-environments. With the ability to run forty samples in parallel, the platform has the potential to be used as a rapid screening tool to understand how the gut microbiome responds to environmental perturbations such as toxic compound exposure, dietary changes, or pharmaceutical treatments.
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Affiliation(s)
- James Comolli
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - David I Walsh
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Johanna Bobrow
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Chelsea L Lennartz
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Nicholas J Guido
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Todd Thorsen
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA.
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Syama K, Jothi JAA, Khanna N. Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE. BMC Bioinformatics 2023; 24:126. [PMID: 37003965 PMCID: PMC10067187 DOI: 10.1186/s12859-023-05251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND The human microbiome plays a critical role in maintaining human health. Due to the recent advances in high-throughput sequencing technologies, the microbiome profiles present in the human body have become publicly available. Hence, many works have been done to analyze human microbiome profiles. These works have identified that different microbiome profiles are present in healthy and sick individuals for different diseases. Recently, several computational methods have utilized the microbiome profiles to automatically diagnose and classify the host phenotype. RESULTS In this work, a novel deep learning framework based on boosting GraphSAGE is proposed for automatic prediction of diseases from metagenomic data. The proposed framework has two main components, (a). Metagenomic Disease graph (MD-graph) construction module, (b). Disease prediction Network (DP-Net) module. The graph construction module constructs a graph by considering each metagenomic sample as a node in the graph. The graph captures the relationship between the samples using a proximity measure. The DP-Net consists of a boosting GraphSAGE model which predicts the status of a sample as sick or healthy. The effectiveness of the proposed method is verified using real and synthetic datasets corresponding to diseases like inflammatory bowel disease and colorectal cancer. The proposed model achieved a highest AUC of 93%, Accuracy of 95%, F1-score of 95%, AUPRC of 95% for the real inflammatory bowel disease dataset and a best AUC of 90%, Accuracy of 91%, F1-score of 87% and AUPRC of 93% for the real colorectal cancer dataset. CONCLUSION The proposed framework outperforms other machine learning and deep learning models in terms of classification accuracy, AUC, F1-score and AUPRC for both synthetic and real metagenomic data.
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Affiliation(s)
- K Syama
- Department of Computer Science, Birla Institute of Technology and Science Pilani Dubai Campus, Dubai International Academic City , Dubai, UAE
| | - J Angel Arul Jothi
- Department of Computer Science, Birla Institute of Technology and Science Pilani Dubai Campus, Dubai International Academic City , Dubai, UAE.
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Lafuente E, Carles L, Walser J, Giulio M, Wullschleger S, Stamm C, Räsänen K. Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore (
Asellus aquaticus
). Evol Appl 2023; 16:824-848. [PMID: 37124094 PMCID: PMC10130563 DOI: 10.1111/eva.13540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/24/2023] [Accepted: 02/17/2023] [Indexed: 04/03/2023] Open
Abstract
Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.
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Affiliation(s)
- Elvira Lafuente
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | - Louis Carles
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Jean‐Claude Walser
- Department of Environmental Systems Science D‐USYS, Genetic Diversity CentreSwiss Federal Institute of Technology (ETH), ZürichZürichSwitzerland
| | - Marco Giulio
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Simon Wullschleger
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Christian Stamm
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Katja Räsänen
- Eawag: Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Murali A, Giri V, Zickgraf FM, Ternes P, Cameron HJ, Sperber S, Haake V, Driemert P, Kamp H, Funk-Weyer D, Sturla SJ, Rietjens IMCM, van Ravenzwaay B. Connecting Gut Microbial Diversity with Plasma Metabolome and Fecal Bile Acid Changes Induced by the Antibiotics Tobramycin and Colistin Sulfate. Chem Res Toxicol 2023; 36:598-616. [PMID: 36972423 DOI: 10.1021/acs.chemrestox.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The diversity of microbial species in the gut has a strong influence on health and development of the host. Further, there are indications that the variation in expression of gut bacterial metabolic enzymes is less diverse than the taxonomic profile, underlying the importance of microbiome functionality, particularly from a toxicological perspective. To address these relationships, the gut bacterial composition of Wistar rats was altered by a 28 day oral treatment with the antibiotics tobramycin or colistin sulfate. On the basis of 16S marker gene sequencing data, tobramycin was found to cause a strong reduction in the diversity and relative abundance of the microbiome, whereas colistin sulfate had only a marginal impact. Associated plasma and fecal metabolomes were characterized by targeted mass spectrometry-based profiling. The fecal metabolome of tobramycin-treated animals had a high number of significant alterations in metabolite levels compared to controls, particularly in amino acids, lipids, bile acids (BAs), carbohydrates, and energy metabolites. The accumulation of primary BAs and significant reduction of secondary BAs in the feces indicated that the microbial alterations induced by tobramycin inhibit bacterial deconjugation reactions. The plasma metabolome showed less, but still many alterations in the same metabolite groups, including reductions in indole derivatives and hippuric acid, and furthermore, despite marginal effects of colistin sulfate treatment, there were nonetheless systemic alterations also in BAs. Aside from these treatment-based differences, we also uncovered interindividual differences particularly centering on the loss of Verrucomicrobiaceae in the microbiome, but with no apparent associated metabolite alterations. Finally, by comparing the data set from this study with metabolome alterations in the MetaMapTox database, key metabolite alterations were identified as plasma biomarkers indicative of altered gut microbiomes resulting from a wide activity spectrum of antibiotics.
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Affiliation(s)
| | - Varun Giri
- BASF SE, Ludwigshafen am Rhein 67056, Rheinland-Pfalz, Germany
| | | | - Philipp Ternes
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Hunter James Cameron
- BASF Corporation Computational Biology (RTP), Research Triangle Park, 3500 Paramount Parkway, Morrisvile, North Carolina 27560, United States
| | - Saskia Sperber
- BASF SE, Ludwigshafen am Rhein 67056, Rheinland-Pfalz, Germany
| | - Volker Haake
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Peter Driemert
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Hennicke Kamp
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | | | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zurich CH 8092, Switzerland
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Liukkonen M, Hukkanen M, Cossin-Sevrin N, Stier A, Vesterinen E, Grond K, Ruuskanen S. No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings. Anim Microbiome 2023; 5:19. [PMID: 36949549 PMCID: PMC10031902 DOI: 10.1186/s42523-023-00241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. RESULTS Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. CONCLUSIONS We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland.
| | - Mikaela Hukkanen
- Department of Biology, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622, Lyon, France
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Biology, University of Turku, Turku, Finland
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Doulberis M, Papaefthymiou A, Kountouras J. Special Issue “Extragastric Disorders of Helicobacter pylori Infection: From Diagnosis to Treatment”: Editorial. Microorganisms 2023; 11:microorganisms11030677. [PMID: 36985250 PMCID: PMC10059884 DOI: 10.3390/microorganisms11030677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Gut microorganisms represent a very attractive field of contemporary biomedical research since they exhibit complex interactions with their host and shape immunity in health and disease [...]
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Affiliation(s)
- Michael Doulberis
- Gastroklinik, Private Gastroenterological Practice, 8810 Horgen, Switzerland
- Gastroenterology Section, Hirslanden Klinik im Park, 8027 Zurich, Switzerland
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001 Aarau, Switzerland
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
| | - Apostolis Papaefthymiou
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
- First Laboratory of Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Pancreaticobiliary Medicine Unit, University College London Hospitals (UCLH), London W1W 6DN, UK
| | - Jannis Kountouras
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
- Correspondence:
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Cameron SJS, Edwards A, Lambert RJ, Stroud M, Mur LAJ. Participants in the Trans-Antarctic Winter Traverse Expedition Showed Increased Bacterial Load and Diversity in Saliva but Maintained Individual Differences within Stool Microbiota and Across Metabolite Fingerprints. Int J Mol Sci 2023; 24:ijms24054850. [PMID: 36902282 PMCID: PMC10002533 DOI: 10.3390/ijms24054850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Understanding the impact of long-term physiological and environmental stress on the human microbiota and metabolome may be important for the success of space flight. This work is logistically difficult and has a limited number of available participants. Terrestrial analogies present important opportunities to understand changes in the microbiota and metabolome and how this may impact participant health and fitness. Here, we present work from one such analogy: the Transarctic Winter Traverse expedition, which we believe is the first assessment of the microbiota and metabolome from different bodily locations during prolonged environmental and physiological stress. Bacterial load and diversity were significantly higher during the expedition when compared with baseline levels (p < 0.001) in saliva but not stool, and only a single operational taxonomic unit assigned to the Ruminococcaceae family shows significantly altered levels in stool (p < 0.001). Metabolite fingerprints show the maintenance of individual differences across saliva, stool, and plasma samples when analysed using flow infusion electrospray mass spectrometry and Fourier transform infrared spectroscopy. Significant activity-associated changes in terms of both bacterial diversity and load are seen in saliva but not in stool, and participant differences in metabolite fingerprints persist across all three sample types.
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Affiliation(s)
- Simon J. S. Cameron
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Chlorine Gardens, Belfast BT9 5DL, UK
- Correspondence: (S.J.S.C.); (L.A.J.M.)
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK
| | - Robert J. Lambert
- Department of Orthopaedics, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Mike Stroud
- NIHR BRC Nutrition, University of Southampton Medical School, Southampton SO16 6YD, UK
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK
- Correspondence: (S.J.S.C.); (L.A.J.M.)
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Charoenkwan P, Chumnanpuen P, Schaduangrat N, Oh C, Manavalan B, Shoombuatong W. PSRQSP: An effective approach for the interpretable prediction of quorum sensing peptide using propensity score representation learning. Comput Biol Med 2023; 158:106784. [PMID: 36989748 DOI: 10.1016/j.compbiomed.2023.106784] [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: 12/26/2022] [Revised: 02/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023]
Abstract
Quorum sensing peptides (QSPs) are microbial signaling molecules involved in several cellular processes, such as cellular communication, virulence expression, bioluminescence, and swarming, in various bacterial species. Understanding QSPs is essential for identifying novel drug targets for controlling bacterial populations and pathogenicity. In this study, we present a novel computational approach (PSRQSP) for improving the prediction and analysis of QSPs. In PSRQSP, we develop a novel propensity score representation learning (PSR) scheme. Specifically, we utilized the PSR approach to extract and learn a comprehensive set of estimated propensities of 20 amino acids, 400 dipeptides, and 400 g-gap dipeptides from a pool of scoring card method-based models. Finally, to maximize the utility of the propensity scores, we explored a set of optimal propensity scores and combined them to construct a final meta-predictor. Our experimental results showed that combining multiview propensity scores was more beneficial for identifying QSPs than the conventional feature descriptors. Moreover, extensive benchmarking experiments based on the independent test were sufficient to demonstrate the predictive capability and effectiveness of PSRQSP by outperforming the conventional ML-based and existing methods, with an accuracy of 94.44% and AUC of 0.967. PSR-derived propensity scores were employed to determine the crucial physicochemical properties for a better understanding of the functional mechanisms of QSPs. Finally, we constructed an easy-to-use web server for the PSRQSP (http://pmlabstack.pythonanywhere.com/PSRQSP). PSRQSP is anticipated to be an efficient computational tool for accelerating the data-driven discovery of potential QSPs for drug discovery and development.
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Affiliation(s)
- Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Changmin Oh
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, Republic of Korea
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, Republic of Korea.
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
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Hashemi B, Abdollahi M, Abbaspour-Aghdam S, Hazrati A, Malekpour K, Meshgi S, Kafil HS, Ghazi F, Yousefi M, Roshangar L, Ahmadi M. The effect of probiotics on immune responses and their therapeutic application: A new treatment option for multiple sclerosis. Biomed Pharmacother 2023; 159:114195. [PMID: 36630847 DOI: 10.1016/j.biopha.2022.114195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/10/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Multiple sclerosis (MS) is known as a chronic inflammatory disease (CID) that affects the central nervous system and leads to nerve demyelination. However, the exact cause of MS is unknown, but immune system regulation and inhibiting the function of inflammatory pathways may have a beneficial effect on controlling and improving the disease. Studies show that probiotics can alter the gut microbiome, thereby improving and affecting the immune system and inflammatory responses in patients with MS. The results show that probiotics have a good effect on the recovery of patients with MS in humans and animals. The present study investigated the effect of probiotics and possible therapeutic mechanisms of probiotics on immune cells and inflammatory cytokines. This review article showed that probiotics could improve immune cells and inflammatory cytokines in patients with MS and can play an effective role in disease management and control.
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Affiliation(s)
- Behnam Hashemi
- Department of Bacteriology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Maryam Abdollahi
- Department of Bacteriology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Sanaz Abbaspour-Aghdam
- Department of Clinical Biochemistry and Applied Cell Sciences, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ali Hazrati
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kosar Malekpour
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahla Meshgi
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhood Ghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Ahmadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Chu M, Zhang X. Alien species invasion of deep-sea bacteria into mouse gut microbiota. J Adv Res 2023; 45:101-115. [PMID: 35690372 PMCID: PMC10006512 DOI: 10.1016/j.jare.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION Deep sea has numerous bacteria which dominate in the biomass of deep-sea sediments. Some deep-sea bacteria may possess the capacity to destroy mammal health by the alteration of gut microbiota, acting as potential pathogens. OBJECTIVES Pathogenic bacteria are great threats to human health. However, the ultimate origin of pathogenic bacteria has not been intensively explored. In this study, therefore, the influence of deep-sea bacteria on the gut microbiota was evaluated on a global scale. METHODS The bacteria isolated from each of 106 deep-sea sediment samples were transplanted into mice in our study to assess the infectiousness of deep-sea bacteria. RESULTS The results showed that some bacteria from deep sea, an area that has existed since the earth was formed, could proliferate in mouse gut. Based on the infectious evaluation of the bacteria from each of 106 deep-sea sediments, the bacteria isolated from 13 sediments invaded the gut bacterial communities of mice, leading to the significant alteration of mouse gut microbiota. Among the 13 deep-sea sediments, the bacteria isolated from 9 sediments could destroy mouse health by inducing glucose metabolism deterioration, liver damage and inflammatory symptom. As an example, a bacterium was isolated from deep-sea sediment DP040, which was identified to be Bacillus cereus (termed as Bacillus cereus DP040). Bacillus cereus DP040 could invade the gut microbiota of mice to change the gut microbial structure, leading to inflammatory symptom of mice. The deep-sea sediments containing the bacteria destroying the health of mice were distributed in hydrothermal vent, mid-ocean ridge and hadal trench of the Indian Ocean, the Atlantic Ocean and the Pacific Ocean. CONCLUSION Our findings demonstrate that deep sea is an important origin of potential pathogenic bacteria and provide the first biosecurity insight into the alien species invasion of deep-sea bacteria into mammal gut microbiota.
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Affiliation(s)
- Mengqi Chu
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China.
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Hajihosseini M, Amini P, Saidi-Mehrabad A, Dinu I. Infants' gut microbiome data: A Bayesian Marginal Zero-inflated Negative Binomial regression model for multivariate analyses of count data. Comput Struct Biotechnol J 2023; 21:1621-1629. [PMID: 36860341 PMCID: PMC9969297 DOI: 10.1016/j.csbj.2023.02.027] [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: 09/02/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
The infants' gut microbiome is dynamic in nature. Literature has shown high inter-individual variability of gut microbial composition in the early years of infancy compared to adulthood. Although next-generation sequencing technologies are rapidly evolving, several statistical analysis aspects need to be addressed to capture the variability and dynamic nature of the infants' gut microbiome. In this study, we proposed a Bayesian Marginal Zero-inflated Negative Binomial (BAMZINB) model, addressing complexities associated with zero-inflation and multivariate structure of the infants' gut microbiome data. Here, we simulated 32 scenarios to compare the performance of BAMZINB with glmFit and BhGLM as the two other widely similar methods in the literature in handling zero-inflation, over-dispersion, and multivariate structure of the infants' gut microbiome. Then, we showed the performance of the BAMZINB approach on a real dataset using SKOT cohort (I and II) studies. Our simulation results showed that the BAMZINB model performed as well as those two methods in estimating the average abundance difference and had a better fit for almost all scenarios when the signal and sample size were large. Applying BAMZINB on SKOT cohorts showed remarkable changes in the average absolute abundance of specific bacteria from 9 to 18 months for infants of healthy and obese mothers. In conclusion, we recommend using the BAMZINB approach for infants' gut microbiome data taking zero-inflation and over-dispersion properties into account in multivariate analysis when comparing the average abundance difference.
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Affiliation(s)
- Morteza Hajihosseini
- Stanford Department of Urology, Center for Academic Medicine, Palo Alto, CA 94304
| | - Payam Amini
- Department of Biostatistics, School of public Health, IRAN University of Medical Sciences, Tehran, Iran
| | | | - Irina Dinu
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada,Correspondence to: School of Public Health, University of Alberta, 3-278 Edmonton Clinic Health Academy, 11405 - 87 Ave NW, Edmonton, Alberta T6G 1C9, Canada.
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Hou F, Tang J, Liu Y, Tan Y, Wang Y, Zheng L, Liang D, Lin Y, Wang L, Pan Z, Yang R, Bi Y, Zhi F. Safety Evaluation and Probiotic Potency Screening of Akkermansia muciniphila Strains Isolated from Human Feces and Breast Milk. Microbiol Spectr 2023; 11:e0336122. [PMID: 36786638 PMCID: PMC10103750 DOI: 10.1128/spectrum.03361-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Akkermansia muciniphila is considered a next-generation probiotic because of its immense potential to regulate disorders. We isolated 31 strains of A. muciniphila from feces or breast milk of healthy people. After genome sequencing, assembly, and analysis, we selected six strains (AM01 to AM06) for further exploration. We first analyzed their general characteristics, including morphological description, growth characteristics, and physiological and biochemical characteristics, and then confirmed their genetic characteristics, including GC content, putative virulence factors, and antibiotic resistance genes. We next investigated the tolerance of these strains to artificial gastric and intestinal fluids and bile salts to evaluate their survival potential in the digestive tract. Drug sensitivity tests were also conducted based on the analysis of the antibiotic resistance genes of these strains. Furthermore, we examined the genetic stability and acute toxicity of two strains (AM02 and AM06) in mice. Finally, the safety of AM06 was evaluated in normal mice and nude mice. AM06 exhibited adaptability to pH changes. Since AM02 and AM03 showed more resistance to antibiotics than AM01 and AM04 to AM06, their potential clinical application may be limited. Both AM02 and AM06 were genetically and phenotypically stable and safe in normal mice, and AM06 was safe in nude mice. Considering all this together, AM06 is a safe A. muciniphila strain and exhibits a great potential for use as a probiotic strain among the isolated strains. IMPORTANCE In this study, we isolated 30 strains of Akkermansia muciniphila from different samples of human feces, and for the first time we isolated an A. muciniphila strain from human breast milk. This isolation verified the existence of microbes in human breast milk, which suggests that A. muciniphila can be vertically propagated from mother to infant and participates in the formation of the early gut microbiome. We then systematically evaluated the potential for use as a probiotic of this A. muciniphila strains according to the FAO/WHO recommendation. We confirmed that the AM06 strain isolated from breast milk has no virulence factors and is genetically stable and nonpathogenic for both normal mice and nude mice. Moreover, its tolerance to pH changes and bile salts indicates its desirable probiotic properties. Thus, we propose that the AM06 strain of A. muciniphila is safe for use as a probiotic candidate.
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Affiliation(s)
- Fengyi Hou
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyi Tang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yangyang Liu
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ye Wang
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Lijun Zheng
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Debao Liang
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Yuqing Lin
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Likun Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Yu D, Zhou L, Liu X, Xu G. Stable isotope-resolved metabolomics based on mass spectrometry: Methods and their applications. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Jalili M, Nazari M, Magkos F. Fermented Foods in the Management of Obesity: Mechanisms of Action and Future Challenges. Int J Mol Sci 2023; 24:ijms24032665. [PMID: 36768984 PMCID: PMC9916812 DOI: 10.3390/ijms24032665] [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: 12/18/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
Fermented foods are part of the staple diet in many different countries and populations and contain various probiotic microorganisms and non-digestible prebiotics. Fermentation is the process of breaking down sugars by bacteria and yeast species; it not only enhances food preservation but can also increase the number of beneficial gut bacteria. Regular consumption of fermented foods has been associated with a variety of health benefits (although some health risks also exist), including improved digestion, enhanced immunity, and greater weight loss, suggesting that fermented foods have the potential to help in the design of effective nutritional therapeutic approaches for obesity. In this article, we provide a comprehensive overview of the health effects of fermented foods and the corresponding mechanisms of action in obesity and obesity-related metabolic abnormalities.
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Affiliation(s)
- Mahsa Jalili
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Maryam Nazari
- Food Safety Research Center (Salt), Semnan University of Medical Sciences, Semnan JF62+4W5, Iran
| | - Faidon Magkos
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, 1165 Copenhagen, Denmark
- Correspondence:
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Intili G, Paladino L, Rappa F, Alberti G, Plicato A, Calabrò F, Fucarino A, Cappello F, Bucchieri F, Tomasello G, Carini F, Pitruzzella A. From Dysbiosis to Neurodegenerative Diseases through Different Communication Pathways: An Overview. BIOLOGY 2023; 12:biology12020195. [PMID: 36829474 PMCID: PMC9952972 DOI: 10.3390/biology12020195] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
The microbiome research field has rapidly evolved over the last few decades, becoming a major topic of scientific and public interest. The gut microbiota (GM) is the microbial population living in the gut. The GM has many functions, such as maintaining gut homeostasis and host health, providing defense against enteric pathogens, and involvement in immune system development. Several studies have shown that GM is implicated in dysbiosis and is presumed to contribute to neurodegeneration. This review focuses mainly on describing the connection between the intestinal microbiome alterations (dysbiosis) and the onset of neurodegenerative diseases to explore the mechanisms that link the GM to nervous system health, such as the gut-brain axis, as well as the mitochondrial, the adaptive humoral immunity, and the microvesicular pathways. The gut-brain communication depends on a continuous bidirectional flow of molecular signals exchanged through the neural and the systemic circulation. These pathways represent a possible new therapeutic target against neuroinflammation and neurodegeneration. Progress in this context is desperately needed, considering the severity of most neurodegenerative diseases and the current lack of effective treatments.
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Affiliation(s)
- Giorgia Intili
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Letizia Paladino
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90136 Palermo, Italy
| | - Francesca Rappa
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Giusi Alberti
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Alice Plicato
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Federica Calabrò
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Alberto Fucarino
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Francesco Cappello
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90136 Palermo, Italy
| | - Fabio Bucchieri
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Giovanni Tomasello
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Francesco Carini
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Alessandro Pitruzzella
- Biomedicine, Neuroscience, and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90136 Palermo, Italy
- Universitary Consortium of Caltanissetta, University of Palermo, 93100 Caltanissetta, Italy
- Correspondence:
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Huang P, Yi S, Yu L, Tian F, Zhao J, Zhang H, Chen W, Zhai Q. Integrative analysis of the metabolome and transcriptome reveals the influence of Lactobacillus plantarum CCFM8610 on germ-free mice. Food Funct 2023; 14:388-398. [PMID: 36511852 DOI: 10.1039/d2fo03117e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study describes the influence of Lactobacillus plantarum CCFM8610 on the host by employing transcriptome and untargeted metabolomics. According to the enrichment analysis, three pathways, including the complement and coagulation cascade pathway, antigen processing and presentation pathways, and protein processing in the endoplasmic reticulum pathway, were affected by L. plantarum CCFM8610 colonization. According to partial least squares-discriminant analysis, five metabolites, L-methionine, D-tryptophan, indoleacrylic acid, DL-acetylcarnitine, and L-norleucine, were identified as key metabolites in the serum. Furthermore, integrative analysis of the metabolome and transcriptome revealed connections between enriched pathways and differential metabolites, and the regulation strategy of choline by affecting gene expression was proposed. Overall, the effects of L. plantarum CCFM8610 on host health were investigated after excluding the influence of gut microbes, which provides a valuable reference for studying the potential mechanisms of the effect of probiotics on host health.
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Affiliation(s)
- Pan Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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Evaluation of the gut microbiome associated with COVID-19. INFORMATICS IN MEDICINE UNLOCKED 2023; 38:101239. [PMID: 37033411 PMCID: PMC10069162 DOI: 10.1016/j.imu.2023.101239] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/14/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Introduction In 2019, a new virus from the coronavirus family called SARS-CoV-2, infected populations throughout the world. Coronavirus disease 2019 (COVID-19), an illness induced by this virus, attacks vital organs in the body, such as the respiratory system and the gastrointestinal tract. Recent studies have confirmed changes in the gut microbiome caused by the COVID-19 disease. We examined the alteration of the gut microbiome in COVID-19 patients compared to healthy individuals. Materials and methods in this study, the 16s metagenomics dataset, publicly available in the Sequence Read Archive (SRA) database, was used for analysis (accession number PRJNA636824). The analysis processes were performed using the CLC Microbial Genomics Module 20.1.1 (Qiagen). At first, the sequence reads of samples were trimmed and classified into operational taxonomic units (OTUs) with 97% similarity and then assigned to the Greengenes reference database (v138). Differential abundance analysis was used to determine statistically significant differences in OTUs between COVID-19 and healthy groups. Next, biodiversity analyses including the alpha diversity (intragroup diversity) and beta diversity (intergroup diversity) using defined indexes were estimated. Then, the co-occurrence network at the species level was constructed using the Pearson correlation coefficient calculation between pairs of OTUs in R software and visualized using Cytoscape software. Ultimately, the hub OTUs at the species level were identified using the cytoHubba plugin of Cytoscape based on Maximal Clique Centrality (MCC) algorithm. Results The results of the metagenomic analysis revealed that the intestinal microbiome in healthy individuals has a higher biodiversity compared to COVID-19 patients. Indeed, healthy people also have a higher percentage of beneficial bacteria such as bifidobacteria adolescentis compared to COVID-19 patients; in contrast, COVID-19 patients have higher levels of opportunistic and pathogenic bacteria such as Streptococcus anginosus than healthy people. Also, by constructing a co-occurrence network at the species level, Bifidobacterium longum in the healthy group and Veillonella parvulain the COVID-19 group were found as hub species. Conclusion The results of this study shed light on the relationship between the gut microbiome and COVID-19. These results could be helpful for understanding the pathogenesis, clinical features, and treatment of COVID-9.
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Antoine D, Venigalla G, Truitt B, Roy S. Linking the gut microbiome to microglial activation in opioid use disorder. Front Neurosci 2022; 16:1050661. [PMID: 36590299 PMCID: PMC9800800 DOI: 10.3389/fnins.2022.1050661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Substance use disorder (SUD) is a physical and psychological disorder globally prevalent today that has resulted in over 107,000 drug overdose deaths in 2021 in the United States alone. This manuscript reviews the potential relationship between opioid use disorder (OUD), a prevalent subset of SUD, and the microglia, the resident macrophages of the central nervous system (CNS), as they have been found to become significantly more activated during opioid exposure. The inflammatory response mediated by the microglia could contribute to the pathophysiology of SUDs, in particular OUD. Further understanding of the microglia and how they respond to not only signals in the CNS but also signals from other areas of the body, such as the gut microbiome, could explain how the microglia are involved in drug use. Several studies have shown extensive communication between the gut microbiome and the microglia, which may be an important factor in the initiation and development of OUD. Particularly, strategies seeking to manipulate and restore the gut microbiome have been shown to reduce microglial activation and attenuate inflammation. In this review, we discuss the evidence for a link between the microglia and OUD and how the gut microbiome might influence microglial activation to drive the disorder and its associated behaviors. Understanding this connection between microglia and the gut microbiome in the context of drug use may present additional therapeutic targets to treat the different stages of drug use.
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Affiliation(s)
- Danielle Antoine
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States,Department of Neuroscience, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Greeshma Venigalla
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Bridget Truitt
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States,Department of Neuroscience, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Sabita Roy
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States,*Correspondence: Sabita Roy,
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