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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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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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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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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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7
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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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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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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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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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12
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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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13
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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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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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15
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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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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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17
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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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18
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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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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 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] [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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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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21
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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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22
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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 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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23
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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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24
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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 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] [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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25
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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 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] [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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26
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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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27
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Gill SK, Hernaiz-Leonardo JC, Edens TJ, Pascual A, Tang C, Fan J, Thamboo A, Mullings W, Alsaleh S, Alim BM, Javer AR, Manges AR. SinoNasal Microbiota Transfer to treat recalcitrant chronic rhinosinusitis: A case series. Int Forum Allergy Rhinol 2024. [PMID: 38616557 DOI: 10.1002/alr.23352] [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: 11/02/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/16/2024]
Abstract
KEY POINTS SinoNasal Microbiota Transfer (SNMT) was safe with immediate benefit in all recipients, with sustained improvement in two of three recipients for up to 180 days. The addition of antimicrobial photodynamic therapy worsened chronic rhinosinusitis. These promising SNMT results warrant further study of safety and efficacy.
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Affiliation(s)
- Sandeep K Gill
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Juan C Hernaiz-Leonardo
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- St. Paul's Sinus Centre, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thaddeus J Edens
- Devil's Staircase Consulting, West Vancouver, British Columbia, Canada
| | - Athenea Pascual
- St. Paul's Sinus Centre, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chris Tang
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judy Fan
- St. Paul's Sinus Centre, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Thamboo
- St. Paul's Sinus Centre, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Warren Mullings
- Department of Surgery, University Hospital of the West Indies, Mona, Jamaica
| | - Saad Alsaleh
- Department of Otolaryngology-Head and Neck Surgery, King Saud University, Riyadh, Saudi Arabia
| | - Bader M Alim
- St. Paul's Sinus Centre, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Prince Mohammed Bin Abdulaziz Hospital, National Guard Health Affairs, Medina, Saudi Arabia
| | - Amin R Javer
- St. Paul's Sinus Centre, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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28
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Hardison EA, Eliason EJ. Diet effects on ectotherm thermal performance. Biol Rev Camb Philos Soc 2024. [PMID: 38616524 DOI: 10.1111/brv.13081] [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: 08/11/2023] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
The environment is changing rapidly, and considerable research is aimed at understanding the capacity of organisms to respond. Changes in environmental temperature are particularly concerning as most animals are ectothermic, with temperature considered a key factor governing their ecology, biogeography, behaviour and physiology. The ability of ectotherms to persist in an increasingly warm, variable, and unpredictable future will depend on their nutritional status. Nutritional resources (e.g. food availability, quality, options) vary across space and time and in response to environmental change, but animals also have the capacity to alter how much they eat and what they eat, which may help them improve their performance under climate change. In this review, we discuss the state of knowledge in the intersection between animal nutrition and temperature. We take a mechanistic approach to describe nutrients (i.e. broad macronutrients, specific lipids, and micronutrients) that may impact thermal performance and discuss what is currently known about their role in ectotherm thermal plasticity, thermoregulatory behaviour, diet preference, and thermal tolerance. We finish by describing how this topic can inform ectotherm biogeography, behaviour, and aquaculture research.
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Affiliation(s)
- Emily A Hardison
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, 93106, USA
| | - Erika J Eliason
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, 93106, USA
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29
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Pillai P, Gouhier TC. Meta microbiome diversity promotes the evolution of host-microbial mutualisms. J Evol Biol 2024; 37:414-428. [PMID: 38366712 DOI: 10.1093/jeb/voae019] [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: 10/04/2022] [Revised: 12/03/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
Ecological theory suggests that a host organism's internal spatial structure can promote the persistence of mutualistic microbes by allowing for the turnover of tissue occupied by non-beneficial or cheating microbes. This type of regulation, whereby a host preferentially rewards tissue occupied by beneficial members of its microbiome but sanctions tissue occupied by non-beneficial cheaters, is expected to generate a competition-extinction trade-off by allowing beneficial microbes to experience a lower extinction rate than competitively dominant cheaters. Using an adaptive dynamics approach, we demonstrate that although ecologically stable, microbial regulation via sanctioning is not stable in any evolutionary sense, as each individual host will be under pressure to reduce the costs incurred from cheater suppression in order to maximize its own fitness at the expense of the rest of the host population. However, increasing the diversity of non-beneficial cheaters in the host population metamicrobiome can lead to an increase in the relative fitness of hosts that actively sanction non-performing tissue, thus facilitating the evolutionary emergence and persistence of such strategies in host-microbial systems. These counter-intuitive results demonstrate how diversity at multiple levels of biological organization and spatiotemporal scales can interact to facilitate the establishment and maintenance of mutualistic relationships.
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Affiliation(s)
- Pradeep Pillai
- Marine Science Center, Northeastern University, Nahant, MA, United States
| | - Tarik C Gouhier
- Marine Science Center, Northeastern University, Nahant, MA, United States
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30
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Kończak B, Wiesner-Sękala M, Ziembińska-Buczyńska A. THE EUROPEAN TREES PHYLLOSPHERE CHARACTERISTICS AND ITS POTENTIAL IN AIR BIOREMEDIATION. Environ Pollut 2024:123977. [PMID: 38621454 DOI: 10.1016/j.envpol.2024.123977] [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: 01/17/2024] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The air pollution remediation is naturally carried out by plants. Their overground parts called phyllosphere are a type of a natural filter on which pollutants can be adsorb. Moreover, microbial communities living in phyllosphere perform a variety of biochemical processes removing also chemical pollutants. As their pollution is nowadays a burning issue especially for highly developed countries, the development of effective and ecological technologies for air treatment are of the utmost importance. The use of phyllosphere bacteria in the process of air bioremediation is a promising technology. This article reviews the role of phyllospheric bacteria in air bioremediation processes especially linked with the moderate climate plants. Research results published so far indicate that phyllosphere bacteria are able to metabolize the air pollutants but their potential is strictly determined by plant-phyllospheric bacteria interaction. The European tree species most commonly used for this purpose are also presented. The collected information filled the gap in the practical use of tree species in air bioremediation in the moderate climate zone.
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Affiliation(s)
- B Kończak
- Department of Water Protection, Central Mining Institute - National Research Institute , Plac Gwarków 1, 40-166 Katowice, Poland.
| | - M Wiesner-Sękala
- Department of Water Protection, Central Mining Institute - National Research Institute , Plac Gwarków 1, 40-166 Katowice, Poland.
| | - A Ziembińska-Buczyńska
- Department of Environmental Biotechnology, Faculty of Power and Environmental Engineering, Silesian University of Technology, str. Akademicka 2, 44-100 Gliwice, Poland.
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31
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Qu B, Zhang XE, Feng H, Yan B, Bai Y, Liu S, He Y. Microbial perspective on the skin-gut axis and atopic dermatitis. Open Life Sci 2024; 19:20220782. [PMID: 38623584 PMCID: PMC11017189 DOI: 10.1515/biol-2022-0782] [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: 08/23/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 04/17/2024] Open
Abstract
Atopic dermatitis (AD) is a relapsing inflammatory skin condition that has become a global health issue with complex etiology and mounting prevalence. The association of AD with skin and gut microbiota has been revealed by virtue of the continuous development of sequencing technology and genomics analysis. Also, the gut-brain-skin axis and its mutual crosstalk mechanisms have been gradually verified. Accordingly, the microbiota-skin-gut axis also plays an important role in allergic skin inflammation. Herein, we reviewed the relationship between the microbiota-skin-gut axis and AD, explored the underlying signaling molecules and potential pathways, and focused on the potential mechanisms of probiotics, antimicrobial peptides (AMPs), coagulase-negative staphylococci transplantation, fecal microbiota transplantation, AMPs, and addition of essential fatty acids in alleviating AD, with the aim to provide a new perspective for targeting microbiota in the treatment of allergic skin inflammation.
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Affiliation(s)
- Bo Qu
- Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
| | - Xue-er Zhang
- Chengdu University of Traditional Chinese Medicine, No. 37 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
| | - Haoyue Feng
- Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
| | - Bonan Yan
- Chengdu University of Traditional Chinese Medicine, No. 37 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
| | - Yingchun Bai
- Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
| | - Shanlin Liu
- Chengdu University of Traditional Chinese Medicine, No. 37 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
| | - Yuhua He
- Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan Province, P.R. China
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Tolentino B, Nuzhdin S. Eight complete genome sequences of bacteria isolated from laboratory stock of giant kelp gametophytes. Microbiol Resour Announc 2024; 13:e0098423. [PMID: 38488368 PMCID: PMC11008194 DOI: 10.1128/mra.00984-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024] Open
Abstract
We report whole-genome sequences of eight bacteria isolated from laboratory-kept Macrocystis pyrifera gametophytes. The bacterial culture collection is maintained in cryostorage and will be utilized in future applications as inoculants. The genomes were assembled using Oxford Nanopore Technology long-read sequencing.
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Affiliation(s)
| | - Sergey Nuzhdin
- University of Southern California, Los Angeles, California, USA
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33
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Sha H, Lu J, Chen J, Xiong J. Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis. NPJ Biofilms Microbiomes 2024; 10:40. [PMID: 38605016 PMCID: PMC11009345 DOI: 10.1038/s41522-024-00509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 10/03/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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34
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Wang Q, Cole JR. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 2024; 13:e0106323. [PMID: 38436268 PMCID: PMC11008197 DOI: 10.1128/mra.01063-23] [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] [Received: 11/07/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
The RDP Classifier is one of the most popular machine learning approaches for taxonomic classification due to its robustness and relatively high accuracy. Both the RDP taxonomy and RDP Classifier have been updated to incorporate newly described taxa and recent changes to prokaryotic nomenclature.
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Affiliation(s)
- Qiong Wang
- Health & Biosciences, International Flavors & Fragrances, Inc., Wilmington, Delaware, USA
| | - James R. Cole
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
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35
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Kittel E, Crosby T, Kocurek B, Ottesen A, Gieseker C. Microbiota of laboratory channel catfish skin mucosa and aquaria water exposed to chloramine-T trihydrate. Microbiol Resour Announc 2024; 13:e0112523. [PMID: 38509054 PMCID: PMC11008118 DOI: 10.1128/mra.01125-23] [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] [Received: 11/16/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Here, we describe the skin mucosa microbiome of channel catfish (Ictalurus punctatus) before and after exposure to chloramine-T trihydrate. We also describe the aquaria water microbiome after the post-treatment period. These data provide a unique baseline description of skin mucosa and aquaria water microbiome from catfish reared in research aquaria.
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Affiliation(s)
- Elliott Kittel
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, Maryland, USA
| | - Tina Crosby
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, Maryland, USA
| | - Brandon Kocurek
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, Maryland, USA
| | - Andrea Ottesen
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, Maryland, USA
| | - Charles Gieseker
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, Maryland, USA
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36
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Williams A, Sinanaj B, Hoysted GA. Plant-microbe interactions through a lens: tales from the mycorrhizosphere. Ann Bot 2024; 133:399-412. [PMID: 38085925 PMCID: PMC11006548 DOI: 10.1093/aob/mcad191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 04/12/2024]
Abstract
BACKGROUND The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes. SCOPE Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function. CONCLUSIONS Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.
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Affiliation(s)
- Alex Williams
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Grace A Hoysted
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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37
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Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host. Cell Host Microbe 2024; 32:527-542.e9. [PMID: 38513656 DOI: 10.1016/j.chom.2024.03.001] [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: 06/30/2023] [Revised: 12/18/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Inflammatory bowel diseases (IBDs) are chronic conditions characterized by periods of spontaneous intestinal inflammation and are increasing in industrialized populations. Combined with host genetics, diet and gut bacteria are thought to contribute prominently to IBDs, but mechanisms are still emerging. In mice lacking the IBD-associated cytokine, interleukin-10, we show that a fiber-deprived gut microbiota promotes the deterioration of colonic mucus, leading to lethal colitis. Inflammation starts with the expansion of natural killer cells and altered immunoglobulin-A coating of some bacteria. Lethal colitis is then driven by Th1 immune responses to increased activities of mucin-degrading bacteria that cause inflammation first in regions with thinner mucus. A fiber-free exclusive enteral nutrition diet also induces mucus erosion but inhibits inflammation by simultaneously increasing an anti-inflammatory bacterial metabolite, isobutyrate. Our findings underscore the importance of focusing on microbial functions-not taxa-contributing to IBDs and that some diet-mediated functions can oppose those that promote disease.
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Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mengrou Shan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Qinnan Yang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Fuentes
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Grace Y Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Cui C, Li F, Zeng Q, Li C, Shen W, Gao X, Li X, Zhao W, Dong J, Li J, Yang M. Influence of Fertilization Methods and Types on Wheat Rhizosphere Microbiome Community and Functions. J Agric Food Chem 2024; 72:7794-7806. [PMID: 38561246 DOI: 10.1021/acs.jafc.3c09941] [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] [Indexed: 04/04/2024]
Abstract
To investigate the effects of fertilization methods and types on wheat rhizosphere microorganisms, macroelement (N, K) and microelement (Zn) fertilizers were applied on wheat by foliar spraying (FS) and root irrigation (RI) methods in a field experiment. The results indicated that fertilization methods and types can have significant impacts on the diversity and structure of rhizospheric microorganisms in wheat. The application method produced more significant effects than the fertilizer type. RI-N played a more important role in improving the wheat yield and quality and affected the changes in some nitrogen-fixing bacterial communities. Finally, eight strains of bacteria belonging to Pseudomonas azotoformans and P. cedrina showed positive effects on the growth of wheat seedlings. Overall, our study provides a better understanding of the dynamics of wheat rhizosphere microbial communities and their relation to fertilization, yield, and quality, showing that plant growth-promoting rhizobacteria with nitrogen fixing may be a potential approach for more sustainable agriculture production.
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Affiliation(s)
- Chao Cui
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Fang Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Chenyang Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Xiang Gao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Xiaoyan Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Wanchun Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Jian Dong
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Jiangang Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
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Gaifem J, Mendes-Frias A, Wolter M, Steimle A, Garzón MJ, Ubeda C, Nobre C, González A, Pinho SS, Cunha C, Carvalho A, Castro AG, Desai MS, Rodrigues F, Silvestre R. Akkermansia muciniphila and Parabacteroides distasonis synergistically protect from colitis by promoting ILC3 in the gut. mBio 2024; 15:e0007824. [PMID: 38470269 DOI: 10.1128/mbio.00078-24] [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: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the gastrointestinal tract. The etiology of IBD remains elusive, but the disease is suggested to arise from the interaction of environmental and genetic factors that trigger inadequate immune responses and inflammation in the intestine. The gut microbiome majorly contributes to disease as an environmental variable, and although some causative bacteria are identified, little is known about which specific members of the microbiome aid in the intestinal epithelial barrier function to protect from disease. While chemically inducing colitis in mice from two distinct animal facilities, we serendipitously found that mice in one facility showed remarkable resistance to disease development, which was associated with increased markers of epithelial barrier integrity. Importantly, we show that Akkermansia muciniphila and Parabacteroides distasonis were significantly increased in the microbiota of resistant mice. To causally connect these microbes to protection against disease, we colonized susceptible mice with the two bacterial species. Our results demonstrate that A. muciniphila and P. distasonis synergistically drive a protective effect in both acute and chronic models of colitis by boosting the frequency of type 3 innate lymphoid cells in the colon and by improving gut epithelial integrity. Altogether, our work reveals a combined effort of commensal microbes in offering protection against severe intestinal inflammation by shaping gut immunity and by enhancing intestinal epithelial barrier stability. Our study highlights the beneficial role of gut bacteria in dictating intestinal homeostasis, which is an important step toward employing microbiome-driven therapeutic approaches for IBD clinical management. IMPORTANCE The contribution of the gut microbiome to the balance between homeostasis and inflammation is widely known. Nevertheless, the etiology of inflammatory bowel disease, which is known to be influenced by genetics, immune response, and environmental cues, remains unclear. Unlocking novel players involved in the dictation of a protective gut, namely, in the microbiota component, is therefore crucial to develop novel strategies to tackle IBD. Herein, we revealed a synergistic interaction between two commensal bacterial strains, Akkermansia muciniphila and Parabacteroides distasonis, which induce protection against both acute and chronic models of colitis induction, by enhancing epithelial barrier integrity and promoting group 3 innate lymphoid cells in the colonic mucosa. This study provides a novel insight on how commensal bacteria can beneficially act to promote intestinal homeostasis, which may open new avenues toward the use of microbiome-derived strategies to tackle IBD.
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Affiliation(s)
- Joana Gaifem
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Ana Mendes-Frias
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alex Steimle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Maria Jose Garzón
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
- Centers of Biomedical Research Network (CIBER) in Epidemiology and Public Health, Madrid, Spain
| | - Carles Ubeda
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
- Centers of Biomedical Research Network (CIBER) in Epidemiology and Public Health, Madrid, Spain
| | - Clarisse Nobre
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Abigail González
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Salomé S Pinho
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - António Gil Castro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Li SY, Tong MM, Li L, Hui F, Meng FZ, Zhao YL, Guo YM, Guo XY, Shi BL, Yan SM. Rectal microbiomes and serum metabolomics reveal the improved effect of Artemisia ordosica crude polysaccharides on the lactation performance, antioxidant and immune responses of lactating donkeys. J Dairy Sci 2024:S0022-0302(24)00741-0. [PMID: 38608958 DOI: 10.3168/jds.2023-24570] [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: 12/21/2023] [Accepted: 03/02/2024] [Indexed: 04/14/2024]
Abstract
This study is aimed at investigating the effects of dietary supplementation with Artemisia ordosica crude polysaccharides (AOCP) on lactation performance, antioxidant status, and immune status of lactating donkeys and analyzing rectal microbiomes and serum metabolomes. Fourteen lactating Dezhou donkeys with similar age (6.16 ± 0.67 years of BW ± SD), weight (250.06 ± 25.18 kg), days in milk (39.11 ± 7.42 d), and averaged parity of 3 were randomly allocated into 2 treatments: a control group (CON, basal diet) and an AOCP group (AOCP, basal diet with 1.0 g/kg DM AOCP). Ten weeks were allotted for the experiment, 2 weeks for adaptation, and 8 weeks for collecting data and samples. The results showed that supplementation of donkey diets with AOCP increased lactation performance, including dry matter intake, milking yield, estimated milk yield, solids-corrected milk, energy-corrected milk, milk fat yield, milk protein yield, milk lactose yield, milk total solids yield, and milk solid not fat yield. The digestibility of dry matter, crude protein, acid detergent fiber, and neutral detergent fiber was increased in the AOCP group compared with the CON group. The AOCP group increased the concentrations of immunoglobulin A, immunoglobulin G, and immunoglobulin M, the activities of the superoxide dismutase, catalase and total antioxidant capacity in the serum. AOCP decreased the concentrations of tumor necrosis factor-α, nitric oxide, reactive oxygen species, and malondialdehyde in the serum. Compared with the CON group, AOCP increased propionate, butyrate, isovalerate, and total VFA concentrations in rectal feces (P < 0.05). The addition of AOCP to increased diversity (Shannon index) and altered structure of the rectal microflora. As a result of AOCP supplementation, there has been a significant improvement in the colonization of beneficial bacteria, including Lactobacillus, Unclassified_f_Prevotellacea, Ruminococcus, and Fibrobacter genera. In contrast, a decrease in the colonization of the Clostridium_sensu_stricto_1 bacterial genus and other pathogenic bacteria was observed. Meanwhile, metabolomics analysis found that AOCP supplementation upregulated metabolites L-tyrosine content while downregulating 9(S)-HODE, choline, sucrose, LysoPC (18:0), LysoPC (18:1(9Z), and LysoPC (20:2(11Z,14Z)) concentrations. These altered metabolites were involved in the PPAR signaling pathway, prolactin signaling pathway, glycerophospholipid metabolism, carbohydrate digestion and absorption, and tyrosine metabolism pathways, which were mainly related to antioxidant capacity, immune responses, and protein metabolism in the lactating donkeys. As a consequence of feeding AOCP diets, beneficial bacteria were abundant, and antioxidant and protein metabolism-related pathways were enriched, which may enhance lactation performance in donkeys. Therefore, supplementing AOCP diets is a desirable dietary strategy to improve donkey health and lactation performance.
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Affiliation(s)
- S Y Li
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - M M Tong
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - L Li
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - F Hui
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - F Z Meng
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - Y L Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - Y M Guo
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - X Y Guo
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - B L Shi
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - S M Yan
- Contribution number: Basic Research Fund for Universities in Inner Mongolia Autonomous Region (Project No.BR22-13-13).
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41
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Khadka VD, Markey L, Boucher M, Lieberman TD. Commensal skin bacteria exacerbate inflammation and delay skin barrier repair. J Invest Dermatol 2024:S0022-202X(24)00277-X. [PMID: 38604402 DOI: 10.1016/j.jid.2024.03.033] [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: 12/06/2023] [Revised: 03/04/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024]
Abstract
The skin microbiome can both trigger beneficial immune stimulation and pose a potential infection threat. Previous studies have shown that colonization of mouse skin with the model human skin commensal Staphylococcus epidermidis is protective against subsequent excisional wound or pathogen challenge. However, less is known about concurrent skin damage and exposure to commensal microbes, despite growing interest in interventional probiotic therapy. Here, we address this open question by applying commensal skin bacteria at a high dose to abraded skin. While depletion of the skin microbiome via antibiotics delayed repair from damage, probiotic-like application of commensals-- including the mouse commensal Staphylococcus xylosus, three distinct isolates of S. epidermidis, and all other tested human skin commensals-- also significantly delayed barrier repair. Increased inflammation was observed within four hours of S. epidermidis exposure and persisted through day four, at which point the skin displayed a chronic wound-like inflammatory state with increased neutrophil infiltration, increased fibroblast activity, and decreased monocyte differentiation. Transcriptomic analysis suggested that the prolonged upregulation of early canonical proliferative pathways inhibited the progression of barrier repair. These results highlight the nuanced role of members of the skin microbiome in modulating barrier integrity and indicate the need for caution in their development as probiotics.
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Affiliation(s)
- Veda D Khadka
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA, United States; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA, United States
| | - Laura Markey
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA, United States; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA, United States
| | - Magalie Boucher
- Division of Comparative Medicine, Massachusetts Institute of Technology; Cambridge, MA, United States
| | - Tami D Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA, United States; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA, United States; Ragon Institute of Mass General, MIT and Harvard; Cambridge. MA, United States.
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Rueda GH, Causada-Calo N, Borojevic R, Nardelli A, Pinto-Sanchez MI, Constante M, Libertucci J, Mohan V, Langella P, Loonen LMP, Wells JM, Sokol H, Verdu EF, Bercik P. Oral tryptophan activates duodenal aryl hydrocarbon receptor in healthy subjects: a crossover randomized controlled trial. Am J Physiol Gastrointest Liver Physiol 2024. [PMID: 38591144 DOI: 10.1152/ajpgi.00306.2023] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/07/2024] [Indexed: 04/10/2024]
Abstract
Background and Aims: Tryptophan is an essential amino acid transformed by host and gut microbial enzymes into metabolites that regulate mucosal homeostasis through Aryl hydrocarbon receptor (AhR) activation. Alteration of tryptophan metabolism has been associated with chronic inflammation, however whether tryptophan supplementation affects the metabolite repertoire and AhR activation under physiologic conditions in humans, is unknown. Methods: We performed a randomized, double blind, placebo-controlled, crossover study in 20 healthy volunteers. Subjects on a low tryptophan background diet were randomly assigned to a 3-week L-tryptophan supplementation (3 g/day) or placebo, and after a 2-week washout switched to opposite interventions. We assessed gastrointestinal and psychological symptoms by validated questionnaires, AhR activation by cell reporter assay, tryptophan metabolites by liquid chromatography and high-resolution mass spectrometry, cytokine production in isolated monocytes by ELISA and microbiota profile by 16S rRNA Illumina technique. Results: Oral tryptophan supplementation was well tolerated, with no changes in gastrointestinal or psychological scores. Compared with placebo, tryptophan increased AhR activation capacity by duodenal contents, but not by feces. This was paralleled by higher urinary and plasma kynurenine metabolites and indoles. Tryptophan had a modest impact on fecal microbiome profiles, and no significant effect on cytokine production. Conclusions: At the doses used in this study, oral tryptophan supplementation in humans induces microbial indole and host kynurenine metabolic pathways in the small intestine, known to be immunomodulatory. The results should prompt tryptophan intervention strategies in inflammatory conditions of the small intestine where the AhR pathway is impaired.
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Affiliation(s)
- Gaston H Rueda
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Rajka Borojevic
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Andrea Nardelli
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Marco Constante
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Josie Libertucci
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | | | - Linda M P Loonen
- Medicine, Wageningen University & Research, Wageningen, Netherlands
| | - Jerry M Wells
- Wageningen University & Research, Wageningen, Netherlands
| | - Harry Sokol
- Department of Gastroenterology, Hôpital Saint-Antoine, Paris, France
| | - Elena F Verdu
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Premysl Bercik
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
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Mazzella V, Dell'Anno A, Etxebarría N, González-Gaya B, Nuzzo G, Fontana A, Núñez-Pons L. High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits. Commun Biol 2024; 7:422. [PMID: 38589605 PMCID: PMC11001883 DOI: 10.1038/s42003-024-06109-5] [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: 08/04/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.
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Affiliation(s)
- Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, 80077, Ischia, Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | - Antonio Dell'Anno
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Néstor Etxebarría
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia-Bld. 7, 80126, Napoli, Italy
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M, Villaseñor A. Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach. Nat Commun 2024; 15:3004. [PMID: 38589361 PMCID: PMC11001937 DOI: 10.1038/s41467-024-47182-y] [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: 05/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.
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Affiliation(s)
- Tomás Clive Barker-Tejeda
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Elisa Zubeldia-Varela
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Andrea Macías-Camero
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Lola Alonso
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Isabel Adoración Martín-Antoniano
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Instituto de Estudios de las Adicciones IEA-CEU, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - María Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Leticia Mera-Berriatua
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Raphaëlle Bazire
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Paula Cabrera-Freitag
- Pedriatic Allergy Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, and Gregorio Marañón Health Research Institute, Madrid, Spain
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Carles Ubeda
- Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - M Pilar Francino
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO) and Institut de Biologia Integrativa de Sistemes (Universitat de València / Consejo Superior de Investigaciones Científicas), València, Spain
| | - Domingo Barber
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - María Dolores Ibáñez-Sandín
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Marina Pérez-Gordo
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
| | - Alma Villaseñor
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
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Bernard M, Lecoeur A, Coville JL, Bruneau N, Jardet D, Lagarrigue S, Meynadier A, Calenge F, Pascal G, Zerjal T. Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions. Sci Rep 2024; 14:8210. [PMID: 38589474 PMCID: PMC11001975 DOI: 10.1038/s41598-024-58374-3] [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: 06/20/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota of laying hens from feed-efficient and non-efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat-soybean based diet (CTR) or a low-energy, high-fibre corn-sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet-dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short-chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism.
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Affiliation(s)
- Maria Bernard
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
- INRAE, SIGENAE, 78350, Jouy-en-Josas, France.
| | - Alexandre Lecoeur
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Luc Coville
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Bruneau
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Deborah Jardet
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Annabelle Meynadier
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Fanny Calenge
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Tatiana Zerjal
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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Silva FG, Silva SR, Pereira AMF, Cerqueira JL, Conceição C. A Comprehensive Review of Bovine Colostrum Components and Selected Aspects Regarding Their Impact on Neonatal Calf Physiology. Animals (Basel) 2024; 14:1130. [PMID: 38612369 PMCID: PMC11010951 DOI: 10.3390/ani14071130] [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: 03/04/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Colostrum contains macro- and micronutrients necessary to meet the nutritional and energy requirements of the neonatal calf, bioactive components that intervene in several physiological aspects, and cells and microorganisms that modulate the calf's immune system and gut microbiome. Colostrum is sometimes mistaken as transition milk, which, although more nutritive than whole milk, has a distinct biochemical composition. Furthermore, most research about colostrum quality and colostrum management focuses on the transfer of maternal IgG to the newborn calf. The remaining components of colostrum and transition milk have not received the same attention, despite their importance to the newborn animal. In this narrative review, a large body of literature on the components of bovine colostrum was reviewed. The variability of these components was summarized, emphasizing specific components that warrant deeper exploration. In addition, the effects of each component present in colostrum and transition milk on several key physiological aspects of the newborn calf are discussed.
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Affiliation(s)
- Flávio G. Silva
- Veterinary and Animal Research Centre (CECAV), Associate Laboratory of Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal (J.L.C.)
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Department of Zootechnics, School of Science and Technology, University of Évora, Pólo da Mitra Apartado 94, 7006-554 Évora, Portugal; (A.M.F.P.); (C.C.)
- Center for Research and Development in Agrifood Systems and Sustainability, Polytechnic Institute of Viana do Castelo, Agrarian School of Ponte de Lima, Rua D. Mendo Afonso, 147 Refóios do Lima, 4990-706 Ponte de Lima, Portugal
| | - Severiano R. Silva
- Veterinary and Animal Research Centre (CECAV), Associate Laboratory of Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal (J.L.C.)
| | - Alfredo M. F. Pereira
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Department of Zootechnics, School of Science and Technology, University of Évora, Pólo da Mitra Apartado 94, 7006-554 Évora, Portugal; (A.M.F.P.); (C.C.)
| | - Joaquim Lima Cerqueira
- Veterinary and Animal Research Centre (CECAV), Associate Laboratory of Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal (J.L.C.)
- Center for Research and Development in Agrifood Systems and Sustainability, Polytechnic Institute of Viana do Castelo, Agrarian School of Ponte de Lima, Rua D. Mendo Afonso, 147 Refóios do Lima, 4990-706 Ponte de Lima, Portugal
| | - Cristina Conceição
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Department of Zootechnics, School of Science and Technology, University of Évora, Pólo da Mitra Apartado 94, 7006-554 Évora, Portugal; (A.M.F.P.); (C.C.)
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Schoenthaler SJ, Prescott SL, Logan AC. Homicide or Happiness: Did Folate Fortification and Public Health Campaigns Influence Homicide Rates and the Great American Crime Decline? Nutrients 2024; 16:1075. [PMID: 38613108 PMCID: PMC11013728 DOI: 10.3390/nu16071075] [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: 03/07/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
The last several years have witnessed a remarkable growth in research directed at nutrition and behavior, with increased interest in the field of nutritional criminology. It is becoming clear that dietary patterns and specific nutrients play an important role in cognition and behavior, including those related to aggression, violence, and antisocial activity. Included in this expanding knowledge base is the recognition that folate, through multiple pathways, including enzymatic reactions and gut microbiome ecology, plays a critical role in central nervous system functioning. These mechanistic advances allow for a retrospective analysis of a topic that remains unexplained-the sudden and unpredicted drop in homicide and other violent crime rates in the United States and other nations in the 1990s. Here, we revisit this marked reduction in homicide rates through the lens of the coincident public health campaign (and subsequent mandatory fortification) to increase folic acid intake. Based on objectively measured blood folate levels through the National Health and Nutrition Examination Surveys, there is little doubt that tissue folate witnessed a dramatic rise at the national level from 1988 through 2000. Drawing from accumulated and emerging research on the neurobehavioral aspects of folate, it is our contention that this relatively sudden and massive increase in tissue folate levels may have contributed to reductions in violent crime in the United States.
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Affiliation(s)
- Stephen J. Schoenthaler
- Department of Criminal Justice, College of the Arts, Humanities & Social Sciences, California State University, Turlock, CA 95202, USA;
| | - Susan L. Prescott
- Nova Institute for Health, Baltimore, MD 21231, USA
- School of Medicine, University of Western Australia, Perth, WA 6009, Australia
- Department of Family and Community Medicine, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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48
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Abstract
An enzyme that remodels the cell wall of Enterococcus faecium helps these gut bacteria to divide and generate peptide fragments that enhance the immune response against cancer.
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Affiliation(s)
- Rishika Prasad
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Robert R Jenq
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer CenterHoustonUnited States
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49
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Loos D, Filho APDC, Dutilh BE, Barber AE, Panagiotou G. A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists. Cell Rep 2024; 43:114046. [PMID: 38581683 DOI: 10.1016/j.celrep.2024.114046] [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: 07/28/2023] [Revised: 12/22/2023] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.
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Affiliation(s)
- Daniel Loos
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ailton Pereira da Costa Filho
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Bas E Dutilh
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Institute of Biodiversity, Friedrich Schiller University, Jena, Germany; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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50
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Komaki S, Sahoyama Y, Hachiya T, Koseki K, Ogata Y, Hamazato F, Shiozawa M, Nakagawa T, Suda W, Hattori M, Kawakami E. Dimension reduction of microbiome data linked Bifidobacterium and Prevotella to allergic rhinitis. Sci Rep 2024; 14:7983. [PMID: 38575668 PMCID: PMC10995140 DOI: 10.1038/s41598-024-57934-x] [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: 07/21/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis, principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization, to a microbiome dataset from 186 subjects with symptoms of allergic rhinitis (AR) and 106 controls. All the dimension reduction methods supported that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed depending on the distance matrices and the dimension reduction methods. The first composite variables calculated from PCoA and NMDS with the UniFrac distance were strongly associated with AR (FDR adjusted P = 2.4 × 10-4 for PCoA and P = 2.8 × 10-4 for NMDS), and also with the relative abundance of Bifidobacterium and Prevotella. The abundance of Bifidobacterium was also linked to intake of several nutrients, including carbohydrate, saturated fat, and alcohol via composite variables. Notably, the association between the composite variables and AR was much stronger than the association between the relative abundance of individual genera and AR. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.
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Affiliation(s)
| | - Yukari Sahoyama
- Technology Strategy Div., Hitachi High-Tech Corporation, Business Tower, Toranomon Hills, 1-17-1 Minato-ku, Toranomon, Tokyo, 105-6409, Japan.
| | | | - Keita Koseki
- Advanced Data Science Project (ADSP), RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yusuke Ogata
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Fumiaki Hamazato
- Technology Strategy Div., Hitachi High-Tech Corporation, Business Tower, Toranomon Hills, 1-17-1 Minato-ku, Toranomon, Tokyo, 105-6409, Japan
| | - Manabu Shiozawa
- Technology Strategy Div., Hitachi High-Tech Corporation, Business Tower, Toranomon Hills, 1-17-1 Minato-ku, Toranomon, Tokyo, 105-6409, Japan
| | - Tohru Nakagawa
- Hitachi Health Care Center, Hitachi Ltd., Ibaraki, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Eiryo Kawakami
- Advanced Data Science Project (ADSP), RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama City, Kanagawa, 230-0045, Japan
- Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba City, Chiba, 260-8670, Japan
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba City, Chiba, 260-8670, Japan
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