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Mach N. The forecasting power of the mucin- microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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2
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Li J, Li Y, Zhou L, Li H, Wan T, Tang J, Zhou L, Xie H, Wang L. Microbiome analysis reveals the inducing effect of Pseudomonas on prostatic hyperplasia via activating NF-κB signalling. Virulence 2024; 15:2313410. [PMID: 38378443 PMCID: PMC10880505 DOI: 10.1080/21505594.2024.2313410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Benign prostatic hyperplasia (BPH) is a prevalent disease among middle-aged and elderly males, but its pathogenesis remains unclear. Dysbiosis of the microbiome is increasingly recognized as a significant factor in various human diseases. Prostate tissue also contains a unique microbiome, and its dysbiosis has been proposed to contribute to prostate diseases. Here, we obtained prostate tissues and preoperative catheterized urine from 24 BPH individuals, and 8 normal prostate samples as controls, which followed strict aseptic measures. Using metagenomic next-generation sequencing (mNGS), we found the disparities in the microbiome composition between normal and BPH tissues, with Pseudomonas significantly enriched in BPH tissues, as confirmed by fluorescence in situ hybridization (FISH). Additionally, we showed that the prostate microbiome differed from the urine microbiome. In vitro experiments revealed that lipopolysaccharide (LPS) of Pseudomonas activated NF-κB signalling, leading to inflammation, proliferation, and EMT processes, while inhibiting apoptosis in prostatic cells. Overall, our research determines the presence of microbiome dysbiosis in BPH, and suggests that Pseudomonas, as the dominant microflora, may promote the progression of BPH through LPS activation of NF-κB signalling.
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Affiliation(s)
- Jiaren Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Youyou Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liang Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongming Li
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tengfei Wan
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jin Tang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Xie
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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3
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Li C, Guo X, He Y, Wang J, Hao J, Liu X. Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients. Ann Med 2024; 56:2337712. [PMID: 38614128 PMCID: PMC11017998 DOI: 10.1080/07853890.2024.2337712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/07/2024] [Indexed: 04/15/2024] Open
Abstract
Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.
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Affiliation(s)
- Chen Li
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiaoyan Guo
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yan He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jing Wang
- Department of Clinical laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jianyu Hao
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xinjuan Liu
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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Seo YJ, Lim C, Lim B, Kim JM. Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum. Anim Biotechnol 2024; 35:2331179. [PMID: 38519440 DOI: 10.1080/10495398.2024.2331179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.
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Affiliation(s)
- Young-Jun Seo
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Chiwoong Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
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Liao W, Wei J, Liu C, Luo H, Ruan Y, Mai Y, Yu Q, Cao Z, Xu J, Zheng D, Sheng Z, Zhou X, Liu J. Magnesium-L-threonate treats Alzheimer's disease by modulating the microbiota-gut-brain axis. Neural Regen Res 2024; 19:2281-2289. [PMID: 38488562 PMCID: PMC11034594 DOI: 10.4103/1673-5374.391310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/07/2023] [Accepted: 11/06/2023] [Indexed: 04/24/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202410000-00029/figure1/v/2024-02-06T055622Z/r/image-tiff Disturbances in the microbiota-gut-brain axis may contribute to the development of Alzheimer's disease. Magnesium-L-threonate has recently been found to have protective effects on learning and memory in aged and Alzheimer's disease model mice. However, the effects of magnesium-L-threonate on the gut microbiota in Alzheimer's disease remain unknown. Previously, we reported that magnesium-L-threonate treatment improved cognition and reduced oxidative stress and inflammation in a double-transgenic line of Alzheimer's disease model mice expressing the amyloid-β precursor protein and mutant human presenilin 1 (APP/PS1). Here, we performed 16S rRNA amplicon sequencing and liquid chromatography-mass spectrometry to analyze changes in the microbiome and serum metabolome following magnesium-L-threonate exposure in a similar mouse model. Magnesium-L-threonate modulated the abundance of three genera in the gut microbiota, decreasing Allobaculum and increasing Bifidobacterium and Turicibacter. We also found that differential metabolites in the magnesium-L-threonate-regulated serum were enriched in various pathways associated with neurodegenerative diseases. The western blotting detection on intestinal tight junction proteins (zona occludens 1, occludin, and claudin-5) showed that magnesium-L-threonate repaired the intestinal barrier dysfunction of APP/PS1 mice. These findings suggest that magnesium-L-threonate may reduce the clinical manifestations of Alzheimer's disease through the microbiota-gut-brain axis in model mice, providing an experimental basis for the clinical treatment of Alzheimer's disease.
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Affiliation(s)
- Wang Liao
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Jiana Wei
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
- Special Medical Service Center, Neuroscience Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangdong, Guangdong Province, China
| | - Chongxu Liu
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Haoyu Luo
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yuting Ruan
- Department of Rehabilitation, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yingren Mai
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qun Yu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Zhiyu Cao
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiaxin Xu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Dong Zheng
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zonghai Sheng
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Xianju Zhou
- Special Medical Service Center, Neuroscience Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangdong, Guangdong Province, China
| | - Jun Liu
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
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Neufeld PM, Nettersheim RA, Matschke V, Vorgerd M, Stahlke S, Theiss C. Unraveling the gut-brain axis: the impact of steroid hormones and nutrition on Parkinson's disease. Neural Regen Res 2024; 19:2219-2228. [PMID: 38488556 PMCID: PMC11034592 DOI: 10.4103/1673-5374.391304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/07/2023] [Accepted: 11/24/2023] [Indexed: 04/24/2024] Open
Abstract
This comprehensive review explores the intricate relationship between nutrition, the gut microbiome, steroid hormones, and Parkinson's disease within the context of the gut-brain axis. The gut-brain axis plays a pivotal role in neurodegenerative diseases like Parkinson's disease, encompassing diverse components such as the gut microbiota, immune system, metabolism, and neural pathways. The gut microbiome, profoundly influenced by dietary factors, emerges as a key player. Nutrition during the first 1000 days of life shapes the gut microbiota composition, influencing immune responses and impacting both child development and adult health. High-fat, high-sugar diets can disrupt this delicate balance, contributing to inflammation and immune dysfunction. Exploring nutritional strategies, the Mediterranean diet's anti-inflammatory and antioxidant properties show promise in reducing Parkinson's disease risk. Microbiome-targeted dietary approaches and the ketogenic diet hold the potential in improving brain disorders. Beyond nutrition, emerging research uncovers potential interactions between steroid hormones, nutrition, and Parkinson's disease. Progesterone, with its anti-inflammatory properties and presence in the nervous system, offers a novel option for Parkinson's disease therapy. Its ability to enhance neuroprotection within the enteric nervous system presents exciting prospects. The review addresses the hypothesis that α-synuclein aggregates originate from the gut and may enter the brain via the vagus nerve. Gastrointestinal symptoms preceding motor symptoms support this hypothesis. Dysfunctional gut-brain signaling during gut dysbiosis contributes to inflammation and neurotransmitter imbalances, emphasizing the potential of microbiota-based interventions. In summary, this review uncovers the complex web of interactions between nutrition, the gut microbiome, steroid hormones, and Parkinson's disease within the gut-brain axis framework. Understanding these connections not only offers novel therapeutic insights but also illuminates the origins of neurodegenerative diseases such as Parkinson's disease.
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Affiliation(s)
- Paula Maria Neufeld
- Department of Cytology, Institute of Anatomy, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Ralf A. Nettersheim
- Department of Visceral Surgery, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany
| | - Veronika Matschke
- Department of Cytology, Institute of Anatomy, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany
| | - Sarah Stahlke
- Department of Cytology, Institute of Anatomy, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Carsten Theiss
- Department of Cytology, Institute of Anatomy, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
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Mengis T, Zajac N, Bernhard L, Heggli I, Herger N, Devan J, Marcus R, Brunner F, Laux C, Farshad M, Distler O, Dudli S. Intervertebral disc microbiome in Modic changes: Lack of result replication underscores the need for a consensus in low-biomass microbiome analysis. JOR Spine 2024; 7:e1330. [PMID: 38585427 PMCID: PMC10995447 DOI: 10.1002/jsp2.1330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction The emerging field of the disc microbiome challenges traditional views of disc sterility, which opens new avenues for novel clinical insights. However, the lack of methodological consensus in disc microbiome studies introduces discrepancies. The aims of this study were to (1) compare the disc microbiome of non-Modic (nonMC), Modic type 1 change (MC1), and MC2 discs to findings from prior disc microbiome studies, and (2) investigate if discrepancies to prior studies can be explained with bioinformatic variations. Methods Sequencing of 16S rRNA in 70 discs (24 nonMC, 25 MC1, and 21 MC2) for microbiome profiling. The experimental setup included buffer contamination controls and was performed under aseptic conditions. Methodology and results were contrasted with previous disc microbiome studies. Critical bioinformatic steps that were different in our best-practice approach and previous disc microbiome studies (taxonomic lineage assignment, prevalence cut-off) were varied and their effect on results were compared. Results There was limited overlap of results with a previous study on MC disc microbiome. No bacterial genera were shared using the same bioinformatic parameters. Taxonomic lineage assignment using "amplicon sequencing variants" was more sensitive and detected 48 genera compared to 22 with "operational taxonomic units" (previous study). Increasing filter cut-off from 4% to 50% (previous study) reduced genera from 48 to 4 genera. Despite these differences, both studies observed dysbiosis with an increased abundance of gram-negative bacteria in MC discs as well as a lower beta-diversity. Cutibacterium was persistently detected in all groups independent of the bioinformatic approach, emphasizing its prevalence. Conclusion There is dysbiosis in MC discs. Bioinformatic parameters impact results yet cannot explain the different findings from this and a previous study. Therefore, discrepancies are likely caused by different sample preparations or true biologic differences. Harmonized protocols are required to advance understanding of the disc microbiome and its clinical implications.
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Affiliation(s)
- Tamara Mengis
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Natalia Zajac
- Functional Genomics Center ZurichUniversity and ETH ZurichZurichSwitzerland
| | - Laura Bernhard
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Irina Heggli
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Nick Herger
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Jan Devan
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Roy Marcus
- Department of Radiology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Florian Brunner
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Christoph Laux
- Department of Orthopedics, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Mazda Farshad
- Department of Orthopedics, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Stefan Dudli
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
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Karvanen M, Cars O. The language of antimicrobial and antibiotic resistance is blocking global collective action. Infect Dis (Lond) 2024; 56:487-495. [PMID: 38520678 DOI: 10.1080/23744235.2024.2332455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Sustainable access to effective antibiotics is a foundational need for functioning health care that is increasingly threatened by antibiotic resistance. Although resistance has been known as long as antibiotics have been in clinical use, there are still multiple gaps in the global and local responses. One often cited cause for this complacency is the language that is used to describe the problem and its consequences. In this paper, we survey some examples of the current discussions around antibiotic resistance and seek to offer a path towards unified and understandable messaging that is relevant both to the public and policymakers by using narratives that highlight the individual and societal consequences of antibiotic resistance. Major shortcomings in the current language that hamper both the understanding of antibiotic resistance and needed behaviour change have been identified in scientific papers and special reports. These shortcomings range from terminology that is difficult to understand, through a lack of personal relevance, to a fragmented response in the policy field. We propose that scientists, including behaviour change experts, and other key stakeholders that are engaged in the issue take lead to agreement on the core scientific facts and to formulate a vision that can be a foundation for creation of consistent global narratives. These narratives must in turn be adapted to local contexts. Development of such narratives should be viewed as an essential component in national action plans on AMR to raise awareness, empower citizens and incentivise societal behaviour change, policy development and implementation of governance structures.
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Affiliation(s)
- Matti Karvanen
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Otto Cars
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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9
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Singh A, Luallen RJ. Understanding the factors regulating host- microbiome interactions using Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230059. [PMID: 38497260 PMCID: PMC10945399 DOI: 10.1098/rstb.2023.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/01/2024] [Indexed: 03/19/2024] Open
Abstract
The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host-microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host-microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host-microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Anupama Singh
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Robert J. Luallen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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10
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Ludington WB. The importance of host physical niches for the stability of gut microbiome composition. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230066. [PMID: 38497267 PMCID: PMC10945397 DOI: 10.1098/rstb.2023.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts. Genetics approaches could uncover the mechanisms for recruiting and maintaining the stable and consistent members of the microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- William B. Ludington
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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11
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Hanson MA, Westlake HE, Schrankel CS. Sculpting the microbiome. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230057. [PMID: 38497263 PMCID: PMC10945391 DOI: 10.1098/rstb.2023.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Affiliation(s)
- Mark A. Hanson
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn Cornwall TR10 9FE, UK
| | - Hannah E. Westlake
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn Cornwall TR10 9FE, UK
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12
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Destoumieux-Garzón D, Montagnani C, Dantan L, Nicolas NDS, Travers MA, Duperret L, Charrière GM, Toulza E, Mitta G, Cosseau C, Escoubas JM. Cross-talk and mutual shaping between the immune system and the microbiota during an oyster's life. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230065. [PMID: 38497271 PMCID: PMC10945412 DOI: 10.1098/rstb.2023.0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 03/19/2024] Open
Abstract
The Pacific oyster Crassostrea gigas lives in microbe-rich marine coastal systems subjected to rapid environmental changes. It harbours a diversified and fluctuating microbiota that cohabits with immune cells expressing a diversified immune gene repertoire. In the early stages of oyster development, just after fertilization, the microbiota plays a key role in educating the immune system. Exposure to a rich microbial environment at the larval stage leads to an increase in immune competence throughout the life of the oyster, conferring a better protection against pathogenic infections at later juvenile/adult stages. This beneficial effect, which is intergenerational, is associated with epigenetic remodelling. At juvenile stages, the educated immune system participates in the control of the homeostasis. In particular, the microbiota is fine-tuned by oyster antimicrobial peptides acting through specific and synergistic effects. However, this balance is fragile, as illustrated by the Pacific Oyster Mortality Syndrome, a disease causing mass mortalities in oysters worldwide. In this disease, the weakening of oyster immune defences by OsHV-1 µVar virus induces a dysbiosis leading to fatal sepsis. This review illustrates the continuous interaction between the highly diversified oyster immune system and its dynamic microbiota throughout its life, and the importance of this cross-talk for oyster health. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Delphine Destoumieux-Garzón
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Caroline Montagnani
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Luc Dantan
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Noémie de San Nicolas
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Marie-Agnès Travers
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Léo Duperret
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Guillaume M. Charrière
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Eve Toulza
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Guillaume Mitta
- Ifremer, IRD, ILM, Université de Polynésie Française, UMR EIO, Vairao 98179, French Polynesia
| | - Céline Cosseau
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia,34090 Montpellier, France
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Willmott T, Cottrell EC. RISING STARS: Bumps and bacteria: influence of the maternal microbiota on pregnancy outcomes. J Endocrinol 2024; 261:e230360. [PMID: 38334309 DOI: 10.1530/joe-23-0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
During pregnancy, all major physiological systems undergo remarkable changes, driven largely by alterations in the maternal hormonal milieu. In healthy pregnancies, maternal cardiovascular and metabolic adaptation to pregnancy occurs to support fetal growth and maternal well-being. Impaired maternal adaptation to pregnancy is associated with a range of pregnancy complications, including gestational diabetes and preeclampsia. There is growing recognition of the importance of different maternal microbiota, including in the gut, vagina and oral cavity, in supporting normal maternal adaptations to pregnancy as well as evidence for microbial disturbances associating with pregnancy pathologies. Here, we aim to summarise emerging evidence demonstrating that differences in maternal microbiota associate with pregnancy outcomes and discuss potential therapeutic approaches under development that might restore an 'optimal' microbiome. In particular, we highlight recent work by ourselves and others exploring the role of the oral microbiome in pregnancy, given established links between poor oral health (e.g. periodontitis) and adverse pregnancy outcomes. Our research has focussed on specific nitrate-reducing oral bacteria which play a role in the generation of nitric oxide (NO) and other bioactive nitrogen oxides associated with cardiovascular health and maternal cardiovascular adaption to pregnancy. Ongoing research aims to define whether altered microbial profiles have clinical utility in the prediction of pregnancy pathologies, and whether interventions designed to optimise specific maternal microbiota could help prevent future complications.
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Affiliation(s)
- Thomas Willmott
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Elizabeth C Cottrell
- Maternal and Fetal Health Research Centre, Division of Developmental Biology & Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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14
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Martin FM, Öpik M, Dickie IA. Mycorrhizal research now: from the micro- to the macro-scale. New Phytol 2024; 242:1399-1403. [PMID: 38659112 DOI: 10.1111/nph.19758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, INRAE Grand Est-Nancy, Champenoux, 54280, France
- College of Plant Science and Technology, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 50409, Estonia
| | - Ian A Dickie
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
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15
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Ali MJ. Alterations of Lacrimal Sac Microbiota in Failed Dacryocystorhinostomy: The Lacriome Paper 6. Semin Ophthalmol 2024; 39:324-329. [PMID: 38461372 DOI: 10.1080/08820538.2024.2327481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/02/2024] [Indexed: 03/11/2024]
Abstract
PURPOSE To study the metagenomics of the microbes isolated from the lacrimal sac in patients with failed dacryocystorhinostomy (DCR). METHODS A prospective study was performed on 10 consecutive patients with failed DCR. Lacrimal sac samples were obtained for metagenomic analysis during the revision endoscopic DCR. The samples were collected intraoperatively after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the IlluminaTM platform following DNA extraction and library preparation. The downstream analysis of the samples was performed using various software packaged in the Squeeze Metapipeline v1.3.0 and marker gene-based metagenomic phylogenetic analysis using MetaPhlAn4. RESULTS The five major phyla identified across the samples of failed DCR include Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria (Figure 1). The prevalent species include Stenotrophomonas maltophilia, Pseudomonas juntendi, Streptococcus pneumoniae, Acinetobacter ursingii, Citrobacter koseri, and Cutibacterium acnes (Figure 2). Among the other organisms identified, few were from genera candida and mezorhizobium. Among the viruses, the most abundant was the BeAn 58058 virus. It was interesting to note the occasional presence of plasmodium and toxoplasma species. The functional category distribution of KEGG (Kyoto encyclopedia of genes and genomes) data showed microbial metabolism to be the most involved function, followed by cellular processes. CONCLUSION This is the first whole metagenome sequencing of the lacrimal sac contents from failed DCR patients. The organisms identified varied significantly from those isolated from patients with primary acquired nasolacrimal duct obstruction (PANDO) using similar techniques and reflect altered lacrimal microbiota in surgically unsuccessful DCRs.
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Affiliation(s)
- Mohammad Javed Ali
- Govindram Seksaria Institute of Dacryology, L.V. Prasad Eye Institute, Hyderabad, India
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16
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Sampaio Dotto Fiuza B, Machado de Andrade C, Meirelles PM, Santos da Silva J, de Jesus Silva M, Vila Nova Santana C, Pimentel Pinheiro G, Mpairwe H, Cooper P, Brooks C, Pembrey L, Taylor S, Douwes J, Cruz ÁA, Barreto ML, Pearce N, Figueiredo CA. Gut microbiome signature and nasal lavage inflammatory markers in young people with asthma. J Allergy Clin Immunol Glob 2024; 3:100242. [PMID: 38585449 PMCID: PMC10998106 DOI: 10.1016/j.jacig.2024.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/04/2023] [Accepted: 12/24/2023] [Indexed: 04/09/2024]
Abstract
Background Asthma is a complex disease and a severe global public health problem resulting from interactions between genetic background and environmental exposures. It has been suggested that gut microbiota may be related to asthma development; however, such relationships needs further investigation. Objective This study aimed to characterize the gut microbiota as well as the nasal lavage cytokine profile of asthmatic and nonasthmatic individuals. Methods Stool and nasal lavage samples were collected from 29 children and adolescents with type 2 asthma and 28 children without asthma in Brazil. Amplicon sequencing of the stool bacterial V4 region of the 16S rRNA gene was performed using Illumina MiSeq. Microbiota analysis was performed by QIIME 2 and PICRUSt2. Type 2 asthma phenotype was characterized by high sputum eosinophil counts and positive skin prick tests for house dust mite, cockroach, and/or cat or dog dander. The nasal immune marker profile was assessed using a customized multiplex panel. Results Stool microbiota differed significantly between asthmatic and nonasthmatic participants (P = .001). Bacteroides was more abundant in participants with asthma (P < .05), while Prevotella was more abundant in nonasthmatic individuals (P < .05). In people with asthma, the relative abundance of Bacteroides correlated with IL-4 concentration in nasal lavage samples. Inference of microbiota functional capacity identified differential fatty acid biosynthesis in asthmatic compared to nonasthmatic subjects. Conclusion The stool microbiota differed between asthmatic and nonasthmatic young people in Brazil. Asthma was associated with higher Bacteroides levels, which correlated with nasal IL-4 concentration.
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Affiliation(s)
| | | | - Pedro Milet Meirelles
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução (IN-TREE), Salvador, Brazil
| | | | | | | | | | | | - Philip Cooper
- Fundacion Ecuatoriana Para Investigacion en Salud, Quito, Ecuador
- Universidad Internacional del Ecuador, Quito, Ecuador
- St George’s University of London, London, United Kingdom
| | - Collin Brooks
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Lucy Pembrey
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Steven Taylor
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Jeroen Douwes
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Álvaro A. Cruz
- Fundação ProAR Salvador, Salvador, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Brazil
| | - Mauricio L. Barreto
- Centro de Integração de Dados e Conhecimentos para Saúde, Fiocruz, Salvador, Brazil
| | - Neil Pearce
- Centre for Public Health Research, Massey University, Wellington, New Zealand
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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17
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Lauridsen MM, Grønkjær LL, Khraibut S, Patel N, Deeb JG, Bajaj JS. The Multi-dimensional Challenge of Poor Oral Health in Cirrhosis-Disparities and Solutions. Gastroenterology 2024; 166:717-722. [PMID: 38224859 PMCID: PMC11034712 DOI: 10.1053/j.gastro.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024]
Affiliation(s)
- Mette M Lauridsen
- University Hospital of Southern Denmark, Department for Regional Health Research, Esbjerg, Denmark
- Virginia Commonwealth University, Department of Medicine, Richmond, Virginia, USA
| | - Lea L Grønkjær
- University Hospital of Southern Denmark, Department for Regional Health Research, Esbjerg, Denmark
| | - Sara Khraibut
- Virginia Commonwealth University, Department of Periodontics, School of Dentistry, Richmond, Virginia, USA
| | - Nilang Patel
- Virginia Commonwealth University, Department of Medicine, Richmond, Virginia, USA
| | - Janina Golob Deeb
- Virginia Commonwealth University, Department of Periodontics, School of Dentistry, Richmond, Virginia, USA
| | - Jasmohan S Bajaj
- Virginia Commonwealth University, Department of Medicine, Richmond, Virginia, USA
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18
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Borsinger T, Torchia M, Malskis B, Levy BA, Werth PM, Moschetti WE. Characterizing the Native Microbiome Using Next-Generation Sequencing of Bilateral 'Aseptic' Knees. J Arthroplasty 2024; 39:1317-1322. [PMID: 37952737 DOI: 10.1016/j.arth.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Next generation sequencing (NGS) has proven ability to identify organisms beyond those identified through traditional culture-based techniques in cases of suspected prosthetic joint infection. However, there is concern that some microorganisms identified may represent the natural joint microbiome rather than pathogenic agents. This work sought to evaluate the presence of microorganisms identified with NGS in bilateral native, presumed "aseptic" knees with osteoarthritis. METHODS There were 40 patients undergoing primary unilateral (30) or bilateral (10) total knee arthroplasty enrolled prospectively. During surgery, samples of fluid and tissue were obtained from operative knees, and joint fluid was obtained from nonoperative knees. Samples were sent for NGS analysis and processed according to manufacturer protocols. Patient age, body mass index, comorbidities, prior history of injections, and grade of arthritis were evaluated for association with positive NGS results. RESULTS There were 3 of 80 samples (3.8%) that demonstrated positive NGS. There were two of these that had multiple microorganisms identified (1 knee with 4 microorganisms; 1 knee with 2 microorganisms). An additional 2 samples had positive NGS results below the manufacturer's threshold for reporting. The most common organism identified was Cutibacterium acnes, present in 2 of the 3 positive samples. No patient baseline characteristics were associated with positive NGS results. CONCLUSIONS Some native knee joints with osteoarthritis have positive microorganisms identified with NGS. The presence of microorganisms in the native knee has important implications for better understanding the native joint microbiome as well as utilization of NGS in cases of suspected prosthetic joint infection.
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Affiliation(s)
- Tracy Borsinger
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Michael Torchia
- Department of Orthopaedics, Essentia Health Duluth Clinic, Duluth, Minnesota
| | - Bethany Malskis
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Benjamin A Levy
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Paul M Werth
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Wayne E Moschetti
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
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19
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Trandafir M, Pircalabioru GG, Savu O. Microbiota analysis in individuals with type two diabetes mellitus and end‑stage renal disease: A pilot study. Exp Ther Med 2024; 27:211. [PMID: 38590581 PMCID: PMC11000444 DOI: 10.3892/etm.2024.12500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/30/2024] [Indexed: 04/10/2024] Open
Abstract
Chronic kidney disease (CKD) is a widespread health concern, which affects ~9.1% of the global population and 12-15% of individuals in upper-middle income countries. Notably, ~2% of patients with CKD progress to end-stage renal disease (ESRD), which leads to a substantial decline in the quality of life, an increased risk of mortality and significant financial burden. Patients with ESRD often still suffer from uremia and uremic syndromes, due to the accumulation of toxins between dialysis sessions and the inadequate removal of protein-bound toxins during dialysis. A number of these toxins are produced by the gut microbiota through the fermentation of dietary proteins or cholines. Furthermore, the gut microbial community serves a key role in maintaining metabolic and immune equilibrium in individuals. The present study aimed to investigate the gut microbiota patterns in individuals with type 2 diabetes mellitus (T2DM) and ESRD via quantitative PCR analysis of the 16S and 18S ribosomal RNA of selected members of the gut microbiota. Individuals affected by both T2DM and ESRD displayed distinctive features within their intestinal microbiota. Specifically, there were increased levels of Gammaproteobacteria observed in these patients, and all subjects exhibited a notably increased presence of Enterobacteriaceae compared with healthy individuals. This particular microbial community has established connections with the presence of inflammatory processes in the colon. Moreover, the elevated levels of Enterobacteriaceae may serve as an indicator of an imbalance in the intestinal microbiota, a condition known as dysbiosis. In addition, the Betaproteobacteria phylum was significantly more prevalent in the stool samples of patients with both T2DM and ESRD when compared with the control group. In conclusion, the present pilot study focused on gut microbiome alterations in T2DM and ESRD. Understanding the relationship between dysbiosis and CKD may identify new areas of research and therapeutic interventions aimed at modulating the gut microbiota to improve the health and outcomes of individuals with CKD and ESRD.
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Affiliation(s)
- Maria Trandafir
- Doctoral School, ‘Carol Davila’ University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gratiela Gradisteanu Pircalabioru
- Earth, Environmental and Life Sciences Division, Research Institute of University of Bucharest, 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- eBio-hub Research Center, National University of Science and Technology Politehnica Bucharest, 060811 Bucharest, Romania
| | - Octavian Savu
- Doctoral School, ‘Carol Davila’ University of Medicine and Pharmacy, 050474 Bucharest, Romania
- ‘N.C. Paulescu’ National Institute of Diabetes, Nutrition and Metabolic Diseases, 020042 Bucharest, Romania
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20
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Abstract
PURPOSE OF REVIEW The intestinal microbiome and the gut-liver axis play a major role in health and disease. The human gut harbors trillions of microbes and a disruption of the gut homeostasis can contribute to liver disease. In this review, the progress in the field within the last 3 years is summarized, focusing on metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD), autoimmune liver disease (AILD), and hepatocellular carcinoma (HCC). RECENT FINDINGS Changes in the fecal virome and fungal mycobiome have been described in patients with various liver diseases. Several microbial derived metabolites including endogenous ethanol produced by bacteria, have been mechanistically linked to liver disease such as MASLD. Virulence factors encoded by gut bacteria contribute to ALD, AILD and HCC. Novel therapeutic approaches focused on the microbiome including phages, pre- and postbiotics have been successfully used in preclinical models. Fecal microbiota transplantation has been effective in attenuating liver disease. Probiotics are safe in patients with alcohol-associated hepatitis and improve liver disease and alcohol addiction. SUMMARY The gut-liver axis plays a key role in the pathophysiology of liver diseases. Understanding the microbiota in liver disease can help to develop precise microbiota centered therapies.
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Affiliation(s)
- David Schöler
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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21
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Zhang L, Yuan L, Wen Y, Zhang M, Huang S, Wang S, Zhao Y, Hao X, Li L, Gao Q, Wang Y, Zhang S, Huang S, Liu K, Yu X, Li D, Xu J, Zhao B, Zhang L, Zhang H, Zhou W, Ai C. Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices. New Phytol 2024; 242:1275-1288. [PMID: 38426620 DOI: 10.1111/nph.19653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.
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Affiliation(s)
- Liyu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Liang Yuan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanchen Wen
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Meiling Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shuyu Huang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shiyu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yuanzheng Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Xiangxiang Hao
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Lujun Li
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Qiang Gao
- Jilin Agricultural University, Changchun, 130118, China
| | - Yin Wang
- Jilin Agricultural University, Changchun, 130118, China
| | - Shuiqing Zhang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Shaomin Huang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Kailou Liu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Xichu Yu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Dongchu Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiukai Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Bingqiang Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Lu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huimin Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Chao Ai
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
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22
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Zemke AC, Hilliam Y, Stapleton AL, Kimple AJ, Goralski JL, Shaffer AD, Pilewski JM, Senior BA, Lee SE, Cooper VS. Elexacaftor-tezacaftor-ivacaftor decreases pseudomonas abundance in the sinonasal microbiome in cystic fibrosis. Int Forum Allergy Rhinol 2024; 14:928-938. [PMID: 37837613 DOI: 10.1002/alr.23288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is common in individuals with cystic fibrosis (CF) and is marked by chronic inflammation and episodes of infection that negatively impact quality of life. Several studies have shown that elexacaftor-tezacaftor-ivacaftor (ETI) improves symptoms and examination findings in CF-CRS. The current study determines the effect of ETI on the sinonasal microbiota in CF. METHODS Sinonasal samples were collected under endoscopic visualization before and after starting ETI. Samples were subjected to 16S amplicon sequencing and sequences were processed with the QIIME2 pipeline with subsequent analysis using the vegan R-package. RESULTS Twenty-nine individual baseline samples and 23 sample pairs pre-/post-ETI were available. At baseline, the cohort had samples dominated by Staphylococcus, and alpha diversity was lower than that of a published reference set of individuals without sinonasal disease. Individuals with prior sinus surgery had lower alpha diversity as measured by Shannon Index, Observed Richness, and Faith's phylogenetic diversity Index. Beta diversity differed between individuals with and without allergic rhinitis, with higher Staphylococcus abundance in those with allergic rhinitis. No change in alpha or beta diversity was seen after a median of 9 months on ETI. With ETI, the Pseudomonas genus and the genus containing Burkholderia decreased in samples containing these taxa at baseline. Pseudomonas abundance decreased with treatment as measured by qPCR. Core sinonasal microbiome members Staphylococcus, Corynebacterium, and Streptococcus were unchanged, while Moraxella increased with ETI. CONCLUSIONS Treatment with ETI leads to a reduction in Pseudomonas abundance within the sinonasal microbiome of individuals with Pseudomonas at baseline.
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Affiliation(s)
- Anna C Zemke
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yasmin Hilliam
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Amanda L Stapleton
- Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam J Kimple
- Department of Otolaryngology-Head & Neck Surgery, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jennifer L Goralski
- Division of Pulmonary Diseases & CCM, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amber D Shaffer
- Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph M Pilewski
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brent A Senior
- Department of Otolaryngology-Head & Neck Surgery, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Stella E Lee
- Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Otolaryngology-Head & Neck Surgery, Department of Surgery, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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McAuliffe T, Anderson JC, Larson RJ, Robertson DJ. Systematic scoping review: Use of the faecal immunochemical test residual buffer to enhance colorectal cancer screening. Aliment Pharmacol Ther 2024; 59:1033-1048. [PMID: 38534182 DOI: 10.1111/apt.17947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/07/2023] [Accepted: 03/03/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND The faecal immunochemical test (FIT) is an inexpensive and convenient modality to screen for colorectal cancer. However, its one-time sensitivity for detecting colorectal cancer and cancer precursors is limited. There is growing interest in using the non-haemoglobin contents of FIT residual buffer to enhance colonic neoplasia detection. AIM To establish from the literature a framework to catalogue candidate biomarkers within FIT residual buffer for non-invasive colorectal cancer screening. METHODS The search strategy evaluated PubMed, Scopus, Web of Science, Embase, and Google Scholar for publications through 25 October 2023, with search terms including FIT, buffer, OC-sensor, biomarkers, microbiome, microRNA (miR), colon, rectum, screening, neoplasm, and early detection. Studies employing home-based collection samples using quantitative FIT first processed for haemoglobin were included. One author reviewed all articles; a second author completed a 20% full-text audit to ensure adherence to eligibility criteria. RESULTS A broad search yielded 1669 studies and application of eligibility criteria identified 18 relevant studies. Multiple protein, DNA/RNA, and microbiome biomarkers (notably haptoglobin, miR-16, miR-27a-3p, miR-92a, miR-148a-3p, miR-223, miR-421, let-7b-5p, and Tyzzerella 4) were associated with colorectal neoplasia. Furthermore, studies highlighted the short-term stability of biomarkers for clinical use and long-term stability for research purposes. CONCLUSIONS This scoping review summarises the framework and progress of research on stability of biomarkers in FIT residual buffer and their associations with colorectal neoplasia to guide opportunities for further confirmatory studies to enhance colorectal cancer screening.
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Affiliation(s)
| | - Joseph C Anderson
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Veterans Affairs Medical Center, White River Junction, Vermont, USA
| | - Robin J Larson
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, New Hampshire, USA
| | - Douglas J Robertson
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Veterans Affairs Medical Center, White River Junction, Vermont, USA
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24
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Marques TC, Monteiro HF, Melo DB, Coelho WM, Salman S, Marques LR, Leão KM, Machado VS, Menta P, Dubey D, Sun F, Lima FS. Effect of rumen-protected choline on dairy cow metabolism, immunity, lactation performance, and vaginal discharge microbiome. J Dairy Sci 2024; 107:2864-2882. [PMID: 38101729 DOI: 10.3168/jds.2023-23850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/12/2023] [Indexed: 12/17/2023]
Abstract
Rumen-protected choline (RPC) promotes benefits in milk production, immunity, and health in dairy cows by optimizing lipid metabolism during transition period management and early lactation. However, the RPC success in dairy cows depends on choline bioavailability, which is affected by the type of protection used in rumen-protected choline. Therefore, our objectives were to determine the effects of a novel RPC on dry matter intake (DMI), identify markers of metabolism and immunity, and evaluate lactation performance. Dry Holstein (n = 48) cows at 245 ± 3 d of gestation were blocked by parity and assigned to control or RPC treatment within each block. Cows enrolled in the RPC treatment received 15 g/d of CholiGEM (Kemin Industries, Cavriago RE, Italy) from 21 d prepartum and 30 g/d of CholiGEM from calving to 21 d postpartum. During the transition period, DMI was measured daily, and blood was sampled weekly for energy-related metabolites such as β-hydroxybutyrate (BHB), glucose, and nonesterified fatty acids (NEFA), as well as immune function markers such as haptoglobin (Hp) and lipopolysaccharide-binding protein (LPB). Vaginal discharge samples were collected at the calving and 7 d postpartum and stored in microcentrifuge tubes at -80°C until 16S rRNA sequencing. The main responses of body condition score, body weight, DMI, milk yield, milk components, and immune function markers were analyzed using the GLIMMIX procedure of SAS with the effects of treatment, time, parity, and relevant covariates added to the models. The relative abundance of microbiome α-diversity was evaluated by 3 indexes (Chao1, Shannon, and Simpson) and β-diversity by principal coordinate analysis and permutational multivariate ANOVA. We found no differences in DMI in the pre- and postpartum periods. Cows fed RPC increased the yields of energy- and 3.5% fat-corrected milk and fat yield in primiparous and multiparous cows, with an interaction between treatment and parity for these lactation variables. However, we found no differences in milk protein and lactose up to 150 DIM between treatments. Glucose, NEFA, and BHB had no differences between the treatments. However, RPC decreased BHB numerically (control = 1.07 ± 0.13 vs. RPC = 0.63 ± 0.13) in multiparous on the third week postpartum and tended to reduce the incidence of subclinical ketosis (12.7% vs. 4.2%). No effects for Hp and LPB were found in cows fed RPC. Chao1, Shannon, and Simpson indexes were lower at calving in the RPC treatment than in the Control. However, no differences were found 7 d later for Chao1, Shannon, and Simpson indexes. The vaginal discharge microbiome was altered in cows fed RPC at 7 d postpartum. Fusobacterium, a common pathogen associated with metritis, was reduced in cows fed RPC. Rumen-protected choline enhanced lactation performance and health and altered the vaginal discharge microbiome which is a potential proxy for uterine healthy in dairy cows. The current study's findings corroborate that RPC is a tool to support adaptation to lactation and shed light on opportunities for further research in reproductive health.
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Affiliation(s)
- T C Marques
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616; Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - H F Monteiro
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - D B Melo
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - W M Coelho
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - S Salman
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - L R Marques
- Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - K M Leão
- Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - V S Machado
- Department of Veterinary Sciences, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409
| | - P Menta
- Department of Veterinary Sciences, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409
| | - D Dubey
- Kemin Europa NV, Herentals 2640, Belgium
| | - F Sun
- Kemin Industries Inc., Des Moines, IA 50317
| | - F S Lima
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616.
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25
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Janssens-Böcker C, Wiesweg K, Doberenz C. Native collagen sheet mask improves skin health and appearance: A comprehensive clinical evaluation. J Cosmet Dermatol 2024; 23:1685-1702. [PMID: 38279521 DOI: 10.1111/jocd.16181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/04/2023] [Accepted: 01/03/2024] [Indexed: 01/28/2024]
Abstract
BACKGROUND Collagen, a critical structural protein found abundantly in animal skin and bones, has become increasingly recognized for its potential therapeutic role in skincare. Despite growing interest, the scientific evidence for the efficacy of collagen sheet masks remains limited. The principal objective of our study was to provide insights into the multifaceted role of collagen in skin health, with a specific focus on its application in collagen sheet masks. METHODS The effects of a collagen sheet mask consisting of >92% native bovine collagen were investigated. The soluble protein components of the collagen matrix were analyzed and the influence of soluble collagen components on fibroblast regulation was examined. Scanning Electron Microscope (SEM) analysis was performed for structural analysis and effect on irritated skin. Five different clinical studies were conducted, including a comparison of the diversity of the skin microbiome, the tolerance and local irritating reactions in atopic dermatitis, an evaluation of skin redness after UV radiation, wrinkle reduction, and hydration and skin roughness of the collagen mask in comparison to a pre-soaked cellulose sheet mask. RESULTS The collagen mask contains soluble protein components, including small collagen peptides. The mask showed potential for promoting fibroblast activity. SEM analysis showed a native collagen structure similar to human dermis. The mask maintained the skin microbiome diversity and decreased skin pH levels. It demonstrated good tolerability on both intact and lesional skin and had a significant effect in reducing erythema caused by UV radiation compared to other skincare products. It showed significant improvements in skin hydration and the volume of eye wrinkles and was more effective than pre-soaked cellulose sheet masks. CONCLUSION Collagen sheet masks have the potential to positively impact skin health and appearance by increasing hydration, reducing erythema, minimizing wrinkles, and maintaining a healthy skin microbiome and skin barrier.
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de Deus A, Gonçalves G, da Silva J, de Jesus LC, Azevedo-Santos APS, Dall Agnol H, Pereira SR. Microbiome reveals inflammatory-related bacteria and putative functional pathways involved in human papillomavirus-associated penile squamous cell carcinoma. Andrology 2024; 12:809-820. [PMID: 37840240 DOI: 10.1111/andr.13545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/07/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Penile squamous cell carcinoma (PSCC) is a rare disease that is more prevalent in developing countries, such as Brazil, and is linked to poor genital hygiene, which promotes the proliferation of microorganisms. Dysbiosis has an effect on the local immune response, increases the risk of viral infection, and can generate inflammatory processes. Current knowledge of the microbiota found in penile tissues is limited, and the bacterial diversity of the PSCC remains unknown. In this investigation, the microbiota associated with penile cancer and its potential role in tumor development and progression were identified. METHODS The 16S rRNA gene was analyzed by next-generation sequencing in 19 tumors and their respective non-tumor adjacent tissues to perform taxonomic classification, analysis of core microbiome, abundance, and diversity of amplicon sequence variants (ASVs) (QIIME2 v.2020.2), and in silico functional prediction (PICRUST2, p < 0.05). RESULTS In both tissues, the phyla Proteobacteria and Firmicutes, and genera Alcaligenes and Fusobaterium, were the most prevalent. Tumors presented a greater relative abundance of Fusobacteriota, Campilobacteria, and Fusobacterium (p = 0.04, p = 0.04, and p = 0.039, respectively). In addition, the beta diversity analysis revealed a tendency for the formation of two distinct groups when only advanced tumors (pT2 and pT3) were considered. Further, the functional analysis identified the top 35 pathways, and 79.5% of PSCC samples contained pro-inflammatory microorganisms. CONCLUSION We describe the first microbiome of penile carcinoma, which revealed an abundant and diverse microbiota as well as inflammatory-related taxa (the phyla Proteobacteria and Firmicutes, the genera Fusobacterium and Prevotella, and the species Finegoldia magma and Pseudomonas geniculata) and molecular pathways (chitin derivates degradation, the protocatechuic acid pathway, inositol metabolism, and the sucrose pathway), which have also been linked to inflammation and carcinogenesis. Moreover, we found specific and abundant ASVs in both tumor and non-tumor tissues. Our data encourage further study to better understand the role of these microorganisms in penile carcinogenesis, offering an opportunity for advances in diagnosis, prognosis, and early therapy.
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Affiliation(s)
- Amanda de Deus
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Brazil
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
| | - Gabriele Gonçalves
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
| | - Jenilson da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Brazil
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
| | - Luís Cláudio de Jesus
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Hivana Dall Agnol
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
- Department of Pathology, Federal University of Maranhão, São Luís, Brazil
| | - Silma Regina Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
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27
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Short B, Delaney C, Johnston W, Litherland GJ, Lockhart JC, Williams C, Mackay WG, Ramage G. Informed development of a multi-species biofilm in chronic obstructive pulmonary disease. APMIS 2024; 132:336-347. [PMID: 38379455 DOI: 10.1111/apm.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
Recent evidence indicates that microbial biofilm aggregates inhabit the lungs of COPD patients and actively contribute towards chronic colonization and repeat infections. However, there are no contextually relevant complex biofilm models for COPD research. In this study, a meta-analysis of the lung microbiome in COPD was used to inform development of an optimized biofilm model composed of genera highly associated with COPD. Bioinformatic analysis showed that although diversity matrices of COPD microbiomes were similar to healthy controls, and internal compositions made it possible to accurately differentiate between these cohorts (AUC = 0.939). Genera that best defined these patients included Haemophilus, Moraxella and Streptococcus. Many studies fail to account for fungi; therefore, Candida albicans was included in the creation of an interkingdom biofilm model. These organisms formed a biofilm capable of tolerating high concentrations of antimicrobial therapies with no significant reductions in viability. However, combined therapies of antibiotics and an antifungal resulted in significant reductions in viable cells throughout the biofilm (p < 0.05). This biofilm model is representative of the COPD lung microbiome and results from in vitro antimicrobial challenge experiments indicate that targeting both bacteria and fungi in these interkingdom communities will be required for more positive clinical outcomes.
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Affiliation(s)
- Bryn Short
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - Christopher Delaney
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - William Johnston
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
| | - Gary J Litherland
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - John C Lockhart
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - Craig Williams
- Microbiology Department, Lancaster Royal Infirmary, University of Lancaster, Lancaster, UK
| | - William G Mackay
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
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28
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Bonakdar RA, Sweeney MM, Garvey C, White AA, VanNoord MU. Case Report: Initial Successful Treatment of Migraine and Irritable Bowel Syndrome With a Low-FODMAP Diet. J Am Nutr Assoc 2024; 43:339-344. [PMID: 38108544 DOI: 10.1080/27697061.2023.2288081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVE Migraine and irritable bowel syndrome (IBS) can be difficult-to-treat comorbidities that may be driven by underlying gut-brain axis dysfunction. This report describes utilization of a low-FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet (LFD) in a patient with refractory migraine and co-occurring IBS. METHODS After unremarkable physical and neurological examinations, a 57-year-old woman with IBS and chronic migraine was started on a LFD under the guidance of a registered dietician. Psychometrically validated surveys administered at baseline and initial follow-up assessed patient-reported outcomes related to migraine and IBS symptoms. RESULTS At baseline, the patient reported 80/90 migraine days with average pain of 8/10, a Migraine Disability Assessment (MIDAS) score of 33, and Headache Impact Test-6 (HIT-6) score of 64, the latter 2 scores indicating severe disability. Baseline IBS symptom severity was noted at 9/10. Within 1 week on a LFD, the patient's IBS symptoms and migraines improved in both frequency and intensity of episodes. After 5 weeks on a LFD elimination, the patient's clinical improvement continued and she reported significant reduction in migraines, with average pain of 1/10 and IBS severity of 3/10. The patient also improved from severe to minimal levels of disability on validated measures (MIDAS, HIT-6, and IBS Patient Global Impression of Change). CONCLUSION This is the first case report detailing successful initial treatment of migraine and co-occurring IBS utilizing a dietician-guided LFD. There are a number of important reasons for potential improvement in these gut-brain axis disorders which are reviewed as well as an implication for long-term management and food reintroduction. Larger, randomized trials evaluating a LFD in diverse individuals with migraine and co-occurring IBS are warranted to help confirm these results.
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Affiliation(s)
- Robert A Bonakdar
- Center for Integrative Medicine, Scripps Clinic, La Jolla, California, USA
| | - Megan M Sweeney
- Center for Integrative Medicine, Scripps Clinic, La Jolla, California, USA
| | - Cathy Garvey
- Center for Integrative Medicine, Scripps Clinic, La Jolla, California, USA
| | - Andrew A White
- Department of Allergy, Asthma, and Immunology, Scripps Clinic, San Diego, California, USA
| | - Michelle U VanNoord
- Department of Neurology, Dalessio Headache Center, Scripps Clinic, La Jolla, California, USA
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29
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Baiz MD, Wood AW, Toews DPL. Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone. Proc Biol Sci 2024; 291:20240238. [PMID: 38628125 PMCID: PMC11022011 DOI: 10.1098/rspb.2024.0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection.
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Affiliation(s)
- Marcella D. Baiz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Andrew W. Wood
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
| | - David P. L. Toews
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
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30
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Alexander CC, Gaudier-Diaz MM, Kleinschmit AJ, Dihle PJ, Salger SA, Vega N, Robertson SD. A case study to engage students in the research design and ethics of high-throughput metagenomics. J Microbiol Biol Educ 2024; 25:e0007423. [PMID: 38661414 DOI: 10.1128/jmbe.00074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 04/26/2024]
Abstract
Case studies present students with an opportunity to learn and apply course content through problem solving and critical thinking. Supported by the High-throughput Discovery Science & Inquiry-based Case Studies for Today's Students (HITS) Research Coordination Network, our interdisciplinary team designed, implemented, and assessed two case study modules entitled "You Are What You Eat." Collectively, the case study modules present students with an opportunity to engage in experimental research design and the ethical considerations regarding microbiome research and society. In this manuscript, we provide instructors with tools for adopting or adapting the research design and/or the ethics modules. To date, the case has been implemented using two modalities (remote and in-person) in three courses (Microbiology, Physiology, and Neuroscience), engaging over 200 undergraduate students. Our assessment data demonstrate gains in content knowledge and students' perception of learning following case study implementation. Furthermore, when reflecting on our experiences and student feedback, we identified ways in which the case study could be modified for different settings. In this way, we hope that the "You Are What You Eat" case study modules can be implemented widely by instructors to promote problem solving and critical thinking in the traditional classroom or laboratory setting when discussing next-generation sequencing and/or metagenomics research.
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Affiliation(s)
| | | | | | | | | | - Nic Vega
- Emory University, Atlanta, Georgia, USA
| | - Sabrina D Robertson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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31
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Zhang L, Zhang X, Leach JM, Rahman AF, Yi N. Bayesian compositional models for ordinal response. Stat Methods Med Res 2024:9622802241247730. [PMID: 38654396 DOI: 10.1177/09622802241247730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Ordinal response is commonly found in medicine, biology, and other fields. In many situations, the predictors for this ordinal response are compositional, which means that the sum of predictors for each sample is fixed. Examples of compositional data include the relative abundance of species in microbiome data and the relative frequency of nutrition concentrations. Moreover, the predictors that are strongly correlated tend to have similar influence on the response outcome. Conventional cumulative logistic regression models for ordinal responses ignore the fixed-sum constraint on predictors and their associated interrelationships, and thus are not appropriate for analyzing compositional predictors.To solve this problem, we proposed Bayesian Compositional Models for Ordinal Response to analyze the relationship between compositional data and an ordinal response with a structured regularized horseshoe prior for the compositional coefficients and a soft sum-to-zero restriction on coefficients through the prior distribution. The method was implemented with R package rstan using efficient Hamiltonian Monte Carlo algorithm. We performed simulations to compare the proposed approach and existing methods for ordinal responses. Results revealed that our proposed method outperformed the existing methods in terms of parameter estimation and prediction. We also applied the proposed method to a microbiome study HMP2Data, to find microorganisms linked to ordinal inflammatory bowel disease levels. To make this work reproducible, the code and data used in this paper are available at https://github.com/Li-Zhang28/BCO.
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Affiliation(s)
- Li Zhang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xinyan Zhang
- School of Data Science and Analytics, Kennesaw State University, Kennesaw, GA, USA
| | - Justin M Leach
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Akm F Rahman
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nengjun Yi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024:fiae058. [PMID: 38653719 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼ 240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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33
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Gdanetz K, Dobbins MR, Villani SM, Outwater CA, Slack SM, Nesbitt D, Svircev AM, Lauwers EM, Zeng Q, Cox KD, Sundin GW. Multisite Field Evaluation of Bacteriophages for Fire Blight Management: Incorporation of Ultraviolet Radiation Protectants and Impact on the Apple Flower Microbiome. Phytopathology 2024:PHYTO04230145KC. [PMID: 37581441 DOI: 10.1094/phyto-04-23-0145-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field, as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work, we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected; however, relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage-pathogen dynamics is required to optimize disease control efficacy.
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Affiliation(s)
- Kristi Gdanetz
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Madison R Dobbins
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Sara M Villani
- Department of Entomology and Plant Pathology, Mountain Horticulture and Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, U.S.A
| | - Cory A Outwater
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Suzanne M Slack
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Department of Horticulture, Iowa State University, Ames, IA 50011, U.S.A
| | - Darlene Nesbitt
- London Research and Development Centre, Agriculture and Agri-Food Canada, Vineland Station, ON, Canada L0R 2E0
| | - Antonet M Svircev
- London Research and Development Centre, Agriculture and Agri-Food Canada, Vineland Station, ON, Canada L0R 2E0
| | - Erin M Lauwers
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Northwest Michigan Horticulture Research Center, Michigan State University, Traverse City, MI 49694, U.S.A
| | - Quan Zeng
- Department of Plant Pathology and Ecology, CT Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, U.S.A
| | - Kerik D Cox
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
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34
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Morowitz MJ. From Tofu to T-Bones: How Vegan and Ketogenic Diets Shape Our Immune Defenses. J Leukoc Biol 2024:qiae097. [PMID: 38648518 DOI: 10.1093/jleuko/qiae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Link et al. conducted a controlled study comparing the impacts of ketogenic and vegan diets on energy intake and immune function in humans. Deep -omics analyses revealed distinct effects of each diet on the immune system, including changes in cell populations and blood transcriptomes indicative of diet-induced shifts between adaptive and innate immunity. The study highlights the potentially significant, rapid impact of diet on immune function and health.
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Affiliation(s)
- Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224
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35
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Zhang Z, Zhao H, Chen X, Tian G, Liu G, Cai J, Jia G. Enhancing pig growth and gut health with fermented Jatropha curcas cake: Impacts on microbiota, metabolites, and neurotransmitters. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 38648292 DOI: 10.1111/jpn.13960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/23/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
Given the escalating global crisis in feed protein availability, Jatropha curcas L. cake has attracted significant interest as a viable alternative protein source in animal feed. This experiment was conducted to investigate the effects of fermented Jatropha curcas L. cake (FJCC) as a protein feed in the diet of pigs. A total of 96 growing pigs with an average weight of 27.60 ± 1.59 kg were divided into three dietary groups with varying FJCC inclusion levels (0, 2.5, and 5%) for a 28 d trial. Results showed that the diet with 5% FJCC (FJCC5) demonstrated significant improvements in average daily gain (p = 0.009), feed-to-gain ratio (p = 0.036), nutrient digestibility, and intestinal morphology. Furthermore, the FJCC5 diet resulted in a decrease in pH values in different gut sections (jejunum p = 0.045, cecum p = 0.001, colon p = 0.012), and favorably altered the profile of short-chain fatty acids (SCFAs) with increased butyric acid content (p = 0.005) and total SCFAs (p = 0.019). Additionally, this diet notably decreased IL-6 levels in the jejunum (p = 0.008) and colon (=0.047), significantly reduced IL-1 levels in the hypothalamus (p < 0.001), and lowered IL-1, IL-6, and IL-10 levels in plasma (p < 0.05). Microbiota and metabolite profile analysis revealed an elevated abundance of beneficial microbes (p < 0.05) and key metabolites such as 4-aminobutyric acid (GABA) (p = 0.003) and serotonin (5-HT) (p = 0.022), linked to neuroactive ligand-receptor interaction. Moreover, FJCC5 significantly boosted circulating neurotransmitter levels of 5-HT (p = 0.006) and GABA (p = 0.002) in plasma and hypothalamus, with corresponding increases in precursor amino acids (p < 0.05). These findings suggest that FJCC, particularly at a 5% inclusion rate, can be an effective substitute for traditional protein sources like soybean meal, offering benefits beyond growth enhancement to gut health and potentially impacting the gut-brain axis. This research underscores FJCC's potential as a valuable component in sustainable animal nutrition strategies.
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Affiliation(s)
- Zhenyu Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
- Institute of Animal Husbandry and Veterinary Medicine, Meishan Vocational Technical College, Meishan, China
- Agricultural and Rural Bureau of Dongpo District, Meishan, China
| | - Hua Zhao
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Chen
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangmang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jingyi Cai
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Jia
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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36
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Cerqueira AES, Lima HS, Silva LCF, Veloso TGR, de Paula SO, Santana WC, da Silva CC. Melipona stingless bees and honey microbiota reveal the diversity, composition, and modes of symbionts transmission. FEMS Microbiol Ecol 2024:fiae063. [PMID: 38650068 DOI: 10.1093/femsec/fiae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
The Melipona gut microbes differ from other social bees, with the absence of crucial corbiculate core gut symbionts and the high occurrence of environmental strains. We studied the microbial diversity and composition of three Melipona species and their honey to understand which strains are obtained by horizontal transmission (HT) from the pollination environment; or represent symbionts co-evolved with Melipona by HT from the hive/food stores or vertical transmission (VT) via social interactions. Bees harbored higher microbial alpha diversity and a different and more species-specific bacterial composition than honey. Otherwise, the fungal communities of bee and honey samples are less dissimilar. As expected, the core symbionts Snodgrassella and Gilliamella were absent in bees that had a prevalence of Lactobacillus Firm-5, environmental Lactobacillaceae, Bifidobacteriaceae and Acetobacteraceae. Also, Pectinatus and Floricoccus have habitat preferences for bees, putatively representing novel symbionts from the environment that co-evolved via VT among generations. Fructilactobacillus found in bees possibly had HT to bees from honey stores. Metschnikowia yeasts, consistent in all bees and honey samples, might have HT to bees from food stores. Similarly, Saccharomycetales might have HT from honey or plants/flowers to bees. This work contributes to the understanding of Melipona symbionts and their modes of transmission.
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Affiliation(s)
- Alan Emanuel Silva Cerqueira
- Laboratorio de Microbiologia Ambiental Aplicada, Universidade Federal de Viçosa, Departmento de Microbiologia, Viçosa - Minas Gerais, Brazil
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX
| | - Helena Santiago Lima
- Laboratorio de Microbiologia Ambiental Aplicada, Universidade Federal de Viçosa, Departmento de Microbiologia, Viçosa - Minas Gerais, Brazil
| | - Lívia Carneiro Fidélis Silva
- Laboratorio de Microbiologia Ambiental Aplicada, Universidade Federal de Viçosa, Departmento de Microbiologia, Viçosa - Minas Gerais, Brazil
| | - Tomás Gomes Reis Veloso
- Laboratorio de Associações Micorrízicas, Universidade Federal de Viçosa, Departmento de Microbiologia, Viçosa - Minas Gerais, Brazil
| | - Sérgio Oliveira de Paula
- Laboratorio de Imunovirologia Molecular, Universidade Federal de Viçosa, Departmento de Biologia Geral, Viçosa - Minas Gerais, Brazil
| | - Weyder Cristiano Santana
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Rio Paranaíba - Minas Gerais, Brazil
| | - Cynthia Canêdo da Silva
- Laboratorio de Microbiologia Ambiental Aplicada, Universidade Federal de Viçosa, Departmento de Microbiologia, Viçosa - Minas Gerais, Brazil
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37
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Díez-Sánchez A, Lindholm HT, Vornewald PM, Ostrop J, Yao R, Single AB, Marstad A, Parmar N, Shaw TN, Martín-Alonso M, Oudhoff MJ. LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model. Nat Commun 2024; 15:3412. [PMID: 38649356 PMCID: PMC11035651 DOI: 10.1038/s41467-024-47815-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Postnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, the acquisition of immune tolerance via a balanced immune cell composition, and maturation of the intestinal epithelium. While studies have uncovered an interplay between the first two, less is known about the role of the maturing epithelium. Here we show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium and maintenance of this developed state during adulthood. Using microbiota-depleted mice, we find plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to depend on LSD1-controlled epithelial maturation. We propose that LSD1 controls the expression of epithelial-derived chemokines, such as Cxcl16, and that this is a mode of action for this epithelial-immune cell interplay in local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.
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Affiliation(s)
- Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Håvard T Lindholm
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Pia M Vornewald
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jenny Ostrop
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rouan Yao
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andrew B Single
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Marstad
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tovah N Shaw
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mara Martín-Alonso
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno J Oudhoff
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Health Sciences, Carleton University, Ottawa, Ontario, ON, Canada.
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38
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Jensen O, Trujillo E, Hanson L, Ost KS. Controlling Candida: immune regulation of commensal fungi in the gut. Infect Immun 2024:e0051623. [PMID: 38647290 DOI: 10.1128/iai.00516-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
The intestinal microbiome harbors fungi that pose a significant risk to human health as opportunistic pathogens and drivers of inflammation. Inflammatory and autoimmune diseases are associated with dysbiotic fungal communities and the expansion of potentially pathogenic fungi. The gut is also the main reservoir for disseminated fungal infections. Immune interactions are critical for preventing commensal fungi from becoming pathogenic. Significant strides have been made in defining innate and adaptive immune pathways that regulate intestinal fungi, and these discoveries have coincided with advancements in our understanding of the fungal molecular pathways and effectors involved in both commensal colonization and pathogenesis within the gut. In this review, we will discuss immune interactions important for regulating commensal fungi, with a focus on how specific cell types and effectors interact with fungi to limit their colonization or pathogenic potential. This will include how innate and adaptive immune pathways target fungi and orchestrate antifungal immune responses, in addition to how secreted immune effectors, such as mucus and antimicrobial peptides, regulate fungal colonization and inhibit pathogenic potential. These immune interactions will be framed around our current understanding of the fungal effectors and pathways regulating colonization and pathogenesis within this niche. Finally, we highlight important unexplored mechanisms by which the immune system regulates commensal fungi in the gut.
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Affiliation(s)
- Owen Jensen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Emma Trujillo
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Luke Hanson
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kyla S Ost
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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39
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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 Sci 2024. [PMID: 38643372 DOI: 10.1111/1744-7917.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Hauptfeld E, Pappas N, van Iwaarden S, Snoek BL, Aldas-Vargas A, Dutilh BE, von Meijenfeldt FAB. Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes. Nat Commun 2024; 15:3373. [PMID: 38643272 PMCID: PMC11032395 DOI: 10.1038/s41467-024-47155-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.
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Affiliation(s)
- Ernestina Hauptfeld
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sandra van Iwaarden
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Rosalind Franklin Strasse 1, 07743, Jena, Germany.
| | - F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790AB, Den Burg, The Netherlands.
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41
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Grünwald NJ, Bock CH, Chang JH, De Souza AA, Ponte EMD, du Toit LJ, Dorrance AE, Dung J, Gent D, Goss EM, Lowe-Power TM, Madden LV, Martin FN, McDowell J, Naegele RP, Potnis N, Quesada-Ocampo LM, Sundin GW, Thiessen L, Vinatzer BA, Zeng Q. Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices. Phytopathology 2024:PHYTO12230483IA. [PMID: 38330057 DOI: 10.1094/phyto-12-23-0483-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.
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Affiliation(s)
- Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97331, U.S.A
| | - Clive H Bock
- U.S. Department of Agriculture-Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31008, U.S.A
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lindsey J du Toit
- Department of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A
| | - Anne E Dorrance
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Jeremiah Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741, U.S.A
| | - David Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
| | - Tiffany M Lowe-Power
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
| | - Laurence V Madden
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Frank N Martin
- U.S. Department of Agriculture-Agricultural Research Service, Crop Protection and Improvement Research Center, Salinas, CA 93905, U.S.A
| | - John McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Rachel P Naegele
- U.S. Department of Agriculture-Agricultural Research Service, Sugarbeet and Bean Research Unit, East Lansing, MI 48824, U.S.A
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lindsey Thiessen
- Domestic and Emergency Scientific Support, U.S. Department of Agriculture-Animal & Plant Health Inspection Service-Plant Protection and Quarantine, Raleigh, NC 27606, U.S.A
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A
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42
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Siqueira JF, Silva WO, Romeiro K, Gominho LF, Alves FRF, Rôças IN. Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review. Int Endod J 2024. [PMID: 38634795 DOI: 10.1111/iej.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/21/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis. OBJECTIVES This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis. METHODS The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist. RESULTS From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as-yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 105 to 106 in primary infections and from 103 to 104 in posttreatment infections. DISCUSSION Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta-analysis. CONCLUSIONS There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type. REGISTRATION PROSPERO CRD42021275886.
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Affiliation(s)
- José F Siqueira
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, RJ, Brazil
| | - Warley O Silva
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
| | - Kaline Romeiro
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
| | - Luciana F Gominho
- Department of Restorative Dentistry, Federal University of Paraíba (UFPB), João Pessoa, PB, Brazil
| | - Flávio R F Alves
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, RJ, Brazil
| | - Isabela N Rôças
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, RJ, Brazil
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Zimmermann J, Piecyk A, Sieber M, Petersen C, Johnke J, Moitinho-Silva L, Künzel S, Bluhm L, Traulsen A, Kaleta C, Schulenburg H. Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life. mBio 2024:e0001224. [PMID: 38634692 DOI: 10.1128/mbio.00012-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function. IMPORTANCE The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.
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Affiliation(s)
- Johannes Zimmermann
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Agnes Piecyk
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Michael Sieber
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Julia Johnke
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lucas Moitinho-Silva
- 5Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Lena Bluhm
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Arne Traulsen
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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Zhong KX, Chan AM, Collicutt B, Daspe M, Finke JF, Foss M, Green TJ, Harley CDG, Hesketh AV, Miller KM, Otto SP, Rolheiser K, Saunders R, Sutherland BJG, Suttle CA. The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification. Appl Environ Microbiol 2024; 90:e0005224. [PMID: 38466091 PMCID: PMC11022565 DOI: 10.1128/aem.00052-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/12/2024] Open
Abstract
Pacific oysters (Magallana gigas, a.k.a. Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. To understand these impacts, we exposed early-development Pacific oyster spat to different temperatures (18°C and 24°C) and pCO2 levels (800, 1,600, and 2,800 µatm) in a fully crossed design for 3 weeks. Under all conditions, the microbiome changed over time, with a large decrease in the relative abundance of potentially pathogenic ciliates (Uronema marinum) in all treatments with time. The microbiome composition differed significantly with temperature, but not acidification, indicating that Pacific oyster spat microbiomes can be altered by ocean warming but is resilient to ocean acidification in our experiments. Microbial taxa differed in relative abundance with temperature, implying different adaptive strategies and ecological specializations among microorganisms. Additionally, a small proportion (~0.2% of the total taxa) of the relatively abundant microbial taxa were core constituents (>50% occurrence among samples) across different temperatures, pCO2 levels, or time. Some taxa, including A4b bacteria and members of the family Saprospiraceae in the phyla Chloroflexi (syn. Chloroflexota) and Bacteroidetes (syn. Bacteroidota), respectively, as well as protists in the genera Labyrinthula and Aplanochytrium in the class Labyrinthulomycetes, and Pseudoperkinsus tapetis in the class Ichthyosporea were core constituents across temperatures, pCO2 levels, and time, suggesting that they play an important, albeit unknown, role in maintaining the structural and functional stability of the Pacific oyster spat microbiome in response to ocean warming and acidification. These findings highlight the flexibility of the spat microbiome to environmental changes.IMPORTANCEPacific oysters are the most economically important and widely farmed species of oyster, and their production depends on healthy oyster spat. In turn, spat health and productivity are affected by the associated microbiota; yet, studies have not scrutinized the effects of temperature and pCO2 on the prokaryotic and eukaryotic microbiomes of spat. Here, we show that both the prokaryotic and, for the first time, eukaryotic microbiome of Pacific oyster spat are surprisingly resilient to changes in acidification, but sensitive to ocean warming. The findings have potential implications for oyster survival amid climate change and underscore the need to understand temperature and pCO2 effects on the microbiome and the cascading effects on oyster health and productivity.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy M. Chan
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Maxim Daspe
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan F. Finke
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Megan Foss
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Timothy J. Green
- Centre for Shellfish Research, Vancouver Island University, Nanaimo, British Columbia, Canada
- Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Christopher D. G. Harley
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amelia V. Hesketh
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Sarah P. Otto
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Ben J. G. Sutherland
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada
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Lopez-Lee C, Torres ERS, Carling G, Gan L. Mechanisms of sex differences in Alzheimer's disease. Neuron 2024; 112:1208-1221. [PMID: 38402606 DOI: 10.1016/j.neuron.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/01/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024]
Abstract
Alzheimer's disease (AD) and the mechanisms underlying its etiology and progression are complex and multifactorial. The higher AD risk in women may serve as a clue to better understand these complicated processes. In this review, we examine aspects of AD that demonstrate sex-dependent effects and delve into the potential biological mechanisms responsible, compiling findings from advanced technologies such as single-cell RNA sequencing, metabolomics, and multi-omics analyses. We review evidence that sex hormones and sex chromosomes interact with various disease mechanisms during aging, encompassing inflammation, metabolism, and autophagy, leading to unique characteristics in disease progression between men and women.
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Affiliation(s)
- Chloe Lopez-Lee
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Eileen Ruth S Torres
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Gillian Carling
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA.
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46
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Addison SL, Rúa MA, Smaill SJ, Singh BK, Wakelin SA. Partner or perish: tree microbiomes and climate change. Trends Plant Sci 2024:S1360-1385(24)00064-5. [PMID: 38641475 DOI: 10.1016/j.tplants.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 04/21/2024]
Abstract
Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.
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Affiliation(s)
- S L Addison
- Scion, Rotorua 3010, New Zealand; Western Sydney University, Richmond, New South Wales 2753, Australia.
| | - M A Rúa
- Wright State University, Dayton, OH 45435-0001, USA
| | | | - B K Singh
- Western Sydney University, Richmond, New South Wales 2753, Australia
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47
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Kang X, Lau HCH, Yu J. Modulating gut microbiome in cancer immunotherapy: Harnessing microbes to enhance treatment efficacy. Cell Rep Med 2024; 5:101478. [PMID: 38631285 PMCID: PMC11031381 DOI: 10.1016/j.xcrm.2024.101478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/15/2024] [Accepted: 02/22/2024] [Indexed: 04/19/2024]
Abstract
Immunotherapy has emerged as a robust approach against cancer, yet its efficacy has varied among individuals, accompanied by the occurrence of immune-related adverse events. As a result, the efficacy of immunotherapy is far from satisfactory, and enormous efforts have been invested to develop strategies to improve patient outcomes. The gut microbiome is now well acknowledged for its critical role in immunotherapy, with better understanding on host-microbes interaction in the context of cancer treatment. Also, an increasing number of trials have been conducted to evaluate the potential and feasibility of microbiome-targeting approaches to enhance efficacy of cancer treatment in patients. Here, the role of the gut microbiome and metabolites (e.g., short-chain fatty acids, tryptophan metabolites) in immunotherapy and the underlying mechanisms are explored. The application of microbiome-targeting approaches that aim to improve immunotherapy efficacy (e.g., fecal microbiota transplantation, probiotics, dietary intervention) is also elaborated, with further discussion on current challenges and suggestions for future research.
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Affiliation(s)
- Xing Kang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong.
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48
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Gurung M, Schlegel BT, Rajasundaram D, Fox R, Bode L, Yao T, Lindemann SR, LeRoith T, Read QD, Simecka C, Carroll L, Andres A, Yeruva L. Microbiota from human infants consuming secretors or non-secretors mothers' milk impacts the gut and immune system in mice. mSystems 2024; 9:e0029424. [PMID: 38530054 PMCID: PMC11019842 DOI: 10.1128/msystems.00294-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Maternal secretor status is one of the determinants of human milk oligosaccharides (HMOs) composition, which, in turn, influences the gut microbiota composition of infants. To understand if this change in gut microbiota impacts immune cell composition, intestinal morphology, and gene expression, 21-day-old germ-free C57BL/6 mice were transplanted with fecal microbiota from infants whose mothers were either secretors (SMM) or non-secretors (NSM) or from infants consuming dairy-based formula (MFM). For each group, one set of mice was supplemented with HMOs. HMO supplementation did not significantly impact the microbiota diversity; however, SMM mice had a higher abundance of genus Bacteroides, Bifidobacterium, and Blautia, whereas, in the NSM group, there was a higher abundance of Akkermansia, Enterocloster, and Klebsiella. In MFM, gut microbiota was represented mainly by Parabacteroides, Ruminococcaceae_unclassified, and Clostrodium_sensu_stricto. In mesenteric lymph node, Foxp3+ T cells and innate lymphoid cells type 2 were increased in MFM mice supplemented with HMOs, while in the spleen, they were increased in SMM + HMOs mice. Similarly, serum immunoglobulin A was also elevated in MFM + HMOs group. Distinct global gene expression of the gut was observed in each microbiota group, which was enhanced with HMOs supplementation. Overall, our data show that distinct infant gut microbiota due to maternal secretor status or consumption of dairy-based formula and HMO supplementation impacts immune cell composition, antibody response, and intestinal gene expression in a mouse model. IMPORTANCE Early life factors like neonatal diet modulate gut microbiota, which is important for the optimal gut and immune function. One such factor, human milk oligosaccharides (HMOs), the composition of which is determined by maternal secretor status, has a profound effect on infant gut microbiota. However, how the infant gut microbiota composition determined by maternal secretor status or consumption of infant formula devoid of HMOs impacts infant intestinal ammorphology, gene expression, and immune signature is not well explored. This study provides insights into the differential establishment of infant microbiota derived from infants fed by secretor or non-secretor mothers milk or those consuming infant formula and demonstrates that the secretor status of mothers promotes Bifidobacteria and Bacteroides sps. establishment. This study also shows that supplementation of pooled HMOs in mice changed immune cell composition in the spleen and mesenteric lymph nodes and immunoglobulins in circulation. Hence, this study highlights that maternal secretor status has a role in infant gut microbiota composition, and this, in turn, can impact host gut and immune system.
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Affiliation(s)
- Manoj Gurung
- Microbiome and Metabolism Research Unit (MMRU), USDA-ARS, SEA, Arkansas Children’s Nutrition Center, Little Rock, Arkansas, USA
| | - Brent Thomas Schlegel
- University of Pittsburgh Medical Center (UPMC), Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dhivyaa Rajasundaram
- University of Pittsburgh Medical Center (UPMC), Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Renee Fox
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Lars Bode
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tianming Yao
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana, USA
| | - Stephen R. Lindemann
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana, USA
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Christy Simecka
- Division of Laboratory Animal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laura Carroll
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aline Andres
- Microbiome and Metabolism Research Unit (MMRU), USDA-ARS, SEA, Arkansas Children’s Nutrition Center, Little Rock, Arkansas, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laxmi Yeruva
- Microbiome and Metabolism Research Unit (MMRU), USDA-ARS, SEA, Arkansas Children’s Nutrition Center, Little Rock, Arkansas, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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Ma Y, Chen H, Li H, Zheng M, Zuo X, Wang W, Wang S, Lu Y, Wang J, Li Y, Wang J, Qiu M. Intratumor microbiome-derived butyrate promotes lung cancer metastasis. Cell Rep Med 2024; 5:101488. [PMID: 38565146 PMCID: PMC11031379 DOI: 10.1016/j.xcrm.2024.101488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/01/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Most recurrences of lung cancer (LC) occur within 3 years after surgery, but the underlying mechanism remains unclear. Here, we collect LC tissues with shorter (<3 years, recurrence group) and longer (>3 years, non-recurrence group) recurrence-free survival. By using 16S sequencing, we find that intratumor microbiome diversity is lower in the recurrence group and butyrate-producing bacteria are enriched in the recurrence group. The intratumor microbiome signature and circulating microbiome DNA can accurately predict LC recurrence. We prove that intratumor injection of butyrate-producing bacteria Roseburia can promote subcutaneous tumor growth. Mechanistically, bacteria-derived butyrate promotes LC metastasis by increasing expression of H19 in tumor cells through inhibiting HDAC2 and increasing H3K27 acetylation at the H19 promoter and inducing M2 macrophage polarization. Depletion of macrophages partially abolishes the metastasis-promoting effect of butyrate. Our results provide evidence for the cross-talk between the intratumor microbiome and LC metastasis and suggest the potential prognostic and therapeutic value of the intratumor microbiome.
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Affiliation(s)
- Yi Ma
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Shanghai 200433, China
| | - Haiming Chen
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Haoran Li
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Meiling Zheng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100010, China; Department of Chinese Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Xianglin Zuo
- Department of Science & Technology, Biobank of Jiangsu Cancer Hospital, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Shaodong Wang
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Yiming Lu
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Li
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China.
| | - Jie Wang
- Department of Science & Technology, Biobank of Jiangsu Cancer Hospital, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China.
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50
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Han M, Wang N, Han W, Liu X, Sun T, Xu J. Highly specific vaginal microbiome signature for gynecological cancers. Open Life Sci 2024; 19:20220850. [PMID: 38633411 PMCID: PMC11022122 DOI: 10.1515/biol-2022-0850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/03/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
To investigate the vaginal microbiota signature of patients with gynecologic cancer and evaluate its diagnostic biomarker potential. We incorporated vaginal 16S rRNA-seq data from 529 women and utilized VSEARCH to analyze the raw data. α-Diversity was evaluated utilizing the Chao1, Shannon, and Simpson indices, and β-diversity was evaluated through principal component analysis using Bray-Curtis distances. Linear discriminant analysis effect size (LEfSe) was utilized to determine species differences between groups. A bacterial co-abundance network was constructed utilizing Spearman correlation analysis. A random forest model of gynecologic tumor risk based on genus was constructed and validated to test its diagnostic efficacy. In gynecologic cancer patients, vaginal α-diversity was significantly greater than in controls, and vaginal β-diversity was significantly separated from that of controls; there was no correlation between these characteristics and menopause status among the subject women. Women diagnosed with gynecological cancer exhibited a reduction in the abundance of vaginal Firmicutes and Lactobacillus, while an increase was observed in the proportions of Bacteroidetes, Proteobacteria, Prevotella, Streptococcus, and Anaerococcus. A random forest model constructed based on 56 genus achieved high accuracy (area under the curve = 84.96%) in gynecological cancer risk prediction. Furthermore, there were discrepancies observed in the community complexity of co-abundance networks between gynecologic cancer patients and the control group. Our study provides evidence that women with gynecologic cancer have a unique vaginal flora structure and microorganisms may be involved in the gynecologic carcinogenesis process. A gynecological cancer risk prediction model based on characteristic genera has good diagnostic value.
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Affiliation(s)
- Mengzhen Han
- Department of Breast Medicine 1, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang110000, China
| | - Na Wang
- Department of Breast Medicine 1, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang110000, China
| | - Wenjie Han
- Department of Breast Medicine 1, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang110000, China
| | - Xiaolin Liu
- Liaoning Microhealth Biotechnology Co., Ltd, Shanlin Road, Dadong District, Shenyang110000, China
| | - Tao Sun
- Department of Breast Medicine 1, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital and Institute, No. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning110000, China
| | - Junnan Xu
- Department of Breast Medicine 1, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital and Institute, No. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning110000, China
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