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Gulyás G, Kakuk B, Dörmő Á, Járay T, Prazsák I, Csabai Z, Henkrich MM, Boldogkői Z, Tombácz D. Cross-comparison of gut metagenomic profiling strategies. Commun Biol 2024; 7:1445. [PMID: 39505993 DOI: 10.1038/s42003-024-07158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 10/28/2024] [Indexed: 11/08/2024] Open
Abstract
The rapid advancements in sequencing technologies and bioinformatics have enabled metagenomic research of complex microbial systems, but reliable results depend on consistent laboratory and bioinformatics approaches. Current efforts to identify best practices often focus on optimizing specific steps, making it challenging to understand the influence of each stage on microbial population analysis and compare data across studies. This study evaluated DNA extraction, library construction methodologies, sequencing platforms, and computational approaches using a dog stool sample, two synthetic microbial community mixtures, and various sequencing data sources. Our work, the most comprehensive evaluation of metagenomic methods to date. We developed a software tool, termed minitax, which provides consistent results across the range of platforms and methodologies. Our findings showed that the Zymo Research Quick-DNA HMW MagBead Kit, Illumina DNA Prep library preparation method, and the minitax bioinformatics tool were the most effective for high-quality microbial diversity analysis. However, the effectiveness of pipelines or method combinations is sample-specific, making it difficult to identify a universally optimal approach. Therefore, employing multiple approaches is crucial for obtaining reliable outcomes in microbial systems.
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Affiliation(s)
- Gábor Gulyás
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Tamás Járay
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Miksa Máté Henkrich
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary.
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
- MTA-SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary.
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Sauers LA, Bassingthwaite T, Sierra-Rivera B, Hampton KJ, Duffield KR, Gore H, Ramirez JL, Sadd BM. Membership robustness but structural change of the native gut microbiota of bumble bees upon systemic immune induction. Microbiol Spectr 2024; 12:e0086124. [PMID: 39373496 PMCID: PMC11536996 DOI: 10.1128/spectrum.00861-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/26/2024] [Indexed: 10/08/2024] Open
Abstract
Understanding factors influencing the composition and maintenance of beneficial host-associated microbial communities is central to understanding their ecological, evolutionary, and health consequences for hosts. Host immunity is often implicated as a regulator of these microbiota, but immunity may also play a disruptive role, with responses to infection perturbing beneficial communities. Such effects may be more prominent from innate immune responses, with more rapid-acting and often non-specific components, compared to adaptive responses. We investigated how upregulation of antibacterial immunity in the bumble bee Bombus impatiens affects its core gut microbiota, testing the hypothesis that immunity-induced perturbation impacts the microbiota structure. Freshly emerged adult bees were fed a microbiota inoculum before receiving a non-pathogenic immune stimulation injection. We quantified microbial communities using 16S rRNA amplicon sequencing and targeted quantitative PCR. Coarse community membership shows apparent robustness, but we find that immune stimulation alters the abundance of two core community members, Gilliamella and Snodgrassella. Moreover, a positive association in communities between these bacteria is perturbed following a Gram-negative challenge. The observed changes in the gut microbial community are suggestive of immune response-induced dysbiosis, linking ecological interactions across levels between hosts, their pathogens, and their beneficial gut microbiota. The potential for collateral perturbation of the natural gut microbiota following an innate immune response may contribute to immune costs, shaping the evolutionary optimization of immune investment depending on the ecological context. IMPORTANCE Our work demonstrates how innate immunity may influence the host-associated microbiota. While previous work has demonstrated the role of adaptive immunity in regulating the microbiota, we show that stimulation of an innate immune response in bumble bees may disrupt the native gut microbial community by shifting individual abundances of some members and pairwise associations. This work builds upon previous work in bumble bees demonstrating factors determining microbe colonization of hosts and microbiota membership, implicating immune response-induced changes as a factor shaping these important gut communities. While some microbiota members appear unaffected, changes in others and the community overall suggests that collateral perturbation of the native gut microbiota upon an innate immune response may serve as an additional selective pressure that shapes the evolution of host innate immunity.
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Affiliation(s)
- Logan A. Sauers
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Toby Bassingthwaite
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Bryan Sierra-Rivera
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Kylie J. Hampton
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Kristin R. Duffield
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Haley Gore
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - José L. Ramirez
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Ben M. Sadd
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
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3
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Ross FC, Patangia D, Grimaud G, Lavelle A, Dempsey EM, Ross RP, Stanton C. The interplay between diet and the gut microbiome: implications for health and disease. Nat Rev Microbiol 2024; 22:671-686. [PMID: 39009882 DOI: 10.1038/s41579-024-01068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2024] [Indexed: 07/17/2024]
Abstract
Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies.
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Affiliation(s)
- Fiona C Ross
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Dhrati Patangia
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Cork, Ireland
| | - Ghjuvan Grimaud
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Cork, Ireland
| | - Aonghus Lavelle
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eugene M Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- INFANT Centre, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland.
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Ma Y, Chen T, Sun T, Dilimulati D, Xiao Y. The oncomicrobiome: New insights into microorganisms in cancer. Microb Pathog 2024; 197:107091. [PMID: 39481695 DOI: 10.1016/j.micpath.2024.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 10/15/2024] [Accepted: 10/28/2024] [Indexed: 11/02/2024]
Abstract
The discoveries of the oncomicrobiome (intratumoral microbiome) and oncomicrobiota (intratumoral microbiota) represent significant advances in tumor research and have rapidly become of key interest to the field. Within tumors, microorganisms such as bacteria, fungi, viruses, and archaea form the oncomicrobiota and are primarily found within tumor cells, immunocytes, and the intercellular matrix. The oncomicrobiome exhibits marked heterogeneity and is associated with tumor initiation, progression, metastasis, and treatment response. Interactions between the oncomicrobiome and the immune system can modulate host antitumor immunity, influencing the efficacy of immunotherapies. Oncomicrobiome research also faces numerous challenges, including overcoming methodological issues such as low target abundance, susceptibility to contamination, and biases in sample handling and analysis methods across different studies. Furthermore, studies of the oncomicrobiome may be confounded by baseline differences in microbiomes among populations driven by both environmental and genetic factors. Most studies to date have revealed associations between the oncomicrobiome and tumors, but very few have established mechanistic links between the two. This review introduces the relevant concepts, detection methods, sources, and characteristics of the oncomicrobiome. We then describe the composition of the oncomicrobiome in common tumors and its role in shaping the tumor microenvironment. We also discuss the current problems and challenges to be overcome in this rapidly progressing field.
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Affiliation(s)
- Yingying Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingting Sun
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China; Shandong Academy of Medical Sciences, Shandong First Medical University, Jinan, China
| | - Dilinuer Dilimulati
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China; Peking Union Medical College & Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, China.
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5
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Buytaers FE, Berger N, Van der Heyden J, Roosens NHC, De Keersmaecker SCJ. The potential of including the microbiome as biomarker in population-based health studies: methods and benefits. Front Public Health 2024; 12:1467121. [PMID: 39507669 PMCID: PMC11538166 DOI: 10.3389/fpubh.2024.1467121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 10/09/2024] [Indexed: 11/08/2024] Open
Abstract
The key role of our microbiome in influencing our health status, and its relationship with our environment and lifestyle or health behaviors, have been shown in the last decades. Therefore, the human microbiome has the potential to act as a biomarker or indicator of health or exposure to health risks in the general population, if information on the microbiome can be collected in population-based health surveys or cohorts. It could then be associated with epidemiological participant data such as demographic, clinical or exposure profiles. However, to our knowledge, microbiome sampling has not yet been included as biological evidence of health or exposure to health risks in large population-based studies representative of the general population. In this mini-review, we first highlight some practical considerations for microbiome sampling and analysis that need to be considered in the context of a population study. We then present some examples of topics where the microbiome could be included as biological evidence in population-based health studies for the benefit of public health, and how this could be developed in the future. In doing so, we aim to highlight the benefits of having microbiome data available at the level of the general population, combined with epidemiological data from health surveys, and hence how microbiological data could be used in the future to assess human health. We also stress the challenges that remain to be overcome to allow the use of this microbiome data in order to improve proactive public health policies.
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Shaw J, Yu YW. Rapid species-level metagenome profiling and containment estimation with sylph. Nat Biotechnol 2024:10.1038/s41587-024-02412-y. [PMID: 39379646 DOI: 10.1038/s41587-024-02412-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/28/2024] [Indexed: 10/10/2024]
Abstract
Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. On the Critical Assessment of Metagenome Interpretation II (CAMI2) Marine dataset, sylph was the most accurate profiling method of seven tested. For multisample profiling, sylph took >10-fold less central processing unit time compared to Kraken2 and used 30-fold less memory. Sylph's ANI estimates provided an orthogonal signal to abundance, allowing for an ANI-based metagenome-wide association study for Parkinson disease (PD) against 289,232 genomes while confirming known butyrate-PD associations at the strain level. Sylph took <1 min and 16 GB of random-access memory to profile metagenomes against 85,205 prokaryotic and 2,917,516 viral genomes, detecting 30-fold more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.
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Affiliation(s)
- Jim Shaw
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada.
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Yun William Yu
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
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Nagpal S, Srivastava SK. Colon or semicolon: gut sampling microdevices for omics insights. NPJ Biofilms Microbiomes 2024; 10:97. [PMID: 39358351 PMCID: PMC11447266 DOI: 10.1038/s41522-024-00536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/19/2024] [Indexed: 10/04/2024] Open
Abstract
Ingestible microdevices represent a breakthrough in non-invasive sampling of the human gastrointestinal (GI) tract. By capturing the native spatiotemporal microbiome and intricate biochemical gradients, these devices allow a non-invasive multi-omic access to the unperturbed host-microbiota crosstalk, immune/nutritional landscapes and gut-organ connections. We present the current progress of GI sampling microdevices towards personalized metabolism and fostering collaboration among clinicians, engineers, and data scientists.
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Affiliation(s)
- Sunil Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, India
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sarvesh Kumar Srivastava
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India.
- Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, India.
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8
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Puerta-Suárez J, Cardona Maya WD. Are Lactobacillus in the male reproductive tract friends? J Assist Reprod Genet 2024; 41:2849-2850. [PMID: 39136904 PMCID: PMC11535101 DOI: 10.1007/s10815-024-03228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/07/2024] [Indexed: 11/05/2024] Open
Affiliation(s)
- Jenniffer Puerta-Suárez
- Department of Obstetrics and Gynecology, Medical School, University of Antioquia-UdeA, Medellín, Colombia.
| | - Walter D Cardona Maya
- Department of Obstetrics and Gynecology, Medical School, University of Antioquia-UdeA, Medellín, Colombia
- Department of Microbiology and Parasitology, Medical School, University of Antioquia-UdeA, Medellín, Colombia
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9
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Trueba G, Cardenas P, Romo G, Gutierrez B. Reevaluating human-microbiota symbiosis: Strain-level insights and evolutionary perspectives across animal species. Biosystems 2024; 244:105283. [PMID: 39103138 DOI: 10.1016/j.biosystems.2024.105283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
The prevailing consensus in scientific literature underscores the mutualistic bond between the microbiota and the human host, suggesting a finely tuned coevolutionary partnership that enhances the fitness of both parties. This symbiotic relationship has been extensively studied, with certain bacterial attributes being construed as hallmarks of natural selection favoring the benefit of the human host. Some scholars go as far as equating the intricate interplay between humans and their intestinal microbiota to that of endosymbiotic relationships, even conceptualizing microbiota as an integral human organ. However, amidst the prevailing narrative of bacterial species being categorized as beneficial or detrimental to human health, a critical oversight often emerges - the inherent functional diversity within bacterial strains. Such reductionist perspectives risk oversimplifying the complex dynamics at play within the microbiome. Recent genomic analysis at the strain level is highly limited, which is surprising given that strain information provides critical data about selective pressures in the intestine. These pressures appear to focus more on the well-being of bacteria rather than human health. Connected to this is the extent to which animals depend on metabolic activity from intestinal bacteria, which varies widely across species. While omnivores like humans exhibit lower dependency, certain herbivores rely entirely on bacterial activity and have developed specialized compartments to house these bacteria.
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Affiliation(s)
- Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Paul Cardenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - German Romo
- Escuela de Medicina Veterinaria, Universidad San Francisco de Quito, Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador; Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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10
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Lee JY, Bays DJ, Savage HP, Bäumler AJ. The human gut microbiome in health and disease: time for a new chapter? Infect Immun 2024:e0030224. [PMID: 39347570 DOI: 10.1128/iai.00302-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024] Open
Abstract
The gut microbiome, composed of the colonic microbiota and their host environment, is important for many aspects of human health. A gut microbiome imbalance (gut dysbiosis) is associated with major causes of human morbidity and mortality. Despite the central part our gut microbiome plays in health and disease, mechanisms that maintain homeostasis and properties that demarcate dysbiosis remain largely undefined. Here we discuss that sorting taxa into meaningful ecological units reveals that the availability of respiratory electron acceptors, such as oxygen, in the host environment has a dominant influence on gut microbiome health. During homeostasis, host functions that limit the diffusion of oxygen into the colonic lumen shelter a microbial community dominated by primary fermenters from atmospheric oxygen. In turn, primary fermenters break down unabsorbed nutrients into fermentation products that support host nutrition. This symbiotic relationship is disrupted when host functions that limit the luminal availability of host-derived electron acceptors become weakened. The resulting changes in the host environment drive alterations in the microbiota composition, which feature an elevated abundance of facultatively anaerobic microbes. Thus, the part of the gut microbiome that becomes imbalanced during dysbiosis is the host environment, whereas changes in the microbiota composition are secondary to this underlying cause. This shift in our understanding of dysbiosis provides a novel starting point for therapeutic strategies to restore microbiome health. Such strategies can either target the microbes through metabolism-based editing or strengthen the host functions that control their environment.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, USA
| | - Derek J Bays
- Department of Internal Medicine, Division of Infectious Diseases, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Hannah P Savage
- Department of Pathology Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, USA
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Wang Y, Shi YN, Xiang H, Shi YM. Exploring nature's battlefield: organismic interactions in the discovery of bioactive natural products. Nat Prod Rep 2024. [PMID: 39316448 DOI: 10.1039/d4np00018h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Covering: up to March 2024.Microbial natural products have historically been a cornerstone for the discovery of therapeutic agents. Advanced (meta)genome sequencing technologies have revealed that microbes harbor far greater biosynthetic capabilities than previously anticipated. However, despite the application of CRISPR/Cas-based gene editing and high-throughput technologies to activate silent biosynthetic gene clusters, the rapid identification of new natural products has not led to a proportional increase in the discovery rate of lead compounds or drugs. A crucial issue in this gap may be insufficient knowledge about the inherent biological and physiological functions of microbial natural products. Addressing this gap necessitates recognizing that the generation of functional natural products is deeply rooted in the interactions between the producing microbes and other (micro)organisms within their ecological contexts, an understanding that is essential for harnessing their potential therapeutic benefits. In this review, we highlight the discovery of functional microbial natural products from diverse niches, including those associated with humans, nematodes, insects, fungi, protozoa, plants, and marine animals. Many of these findings result from an organismic-interaction-guided strategy using multi-omic approaches. The current importance of this topic lies in its potential to advance drug discovery in an era marked by increasing antimicrobial resistance.
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Affiliation(s)
- Yuyang Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yan-Ni Shi
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Hao Xiang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Ming Shi
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Soldán M, Argalášová Ľ, Hadvinová L, Galileo B, Babjaková J. The Effect of Dietary Types on Gut Microbiota Composition and Development of Non-Communicable Diseases: A Narrative Review. Nutrients 2024; 16:3134. [PMID: 39339734 PMCID: PMC11434870 DOI: 10.3390/nu16183134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 09/14/2024] [Accepted: 09/15/2024] [Indexed: 09/30/2024] Open
Abstract
INTRODUCTION The importance of diet in shaping the gut microbiota is well established and may help improve an individual's overall health. Many other factors, such as genetics, age, exercise, antibiotic therapy, or tobacco use, also play a role in influencing gut microbiota. AIM This narrative review summarizes how three distinct dietary types (plant-based, Mediterranean, and Western) affect the composition of gut microbiota and the development of non-communicable diseases (NCDs). METHODS A comprehensive literature search was conducted using the PubMed, Web of Science, and Scopus databases, focusing on the keywords "dietary pattern", "gut microbiota" and "dysbiosis". RESULTS Both plant-based and Mediterranean diets have been shown to promote the production of beneficial bacterial metabolites, such as short-chain fatty acids (SCFAs), while simultaneously lowering concentrations of trimethylamine-N-oxide (TMAO), a molecule associated with negative health outcomes. Additionally, they have a positive impact on microbial diversity and therefore are generally considered healthy dietary types. On the other hand, the Western diet is a typical example of an unhealthy nutritional approach leading to an overgrowth of pathogenic bacteria, where TMAO levels rise and SCFA production drops due to gut dysbiosis. CONCLUSION The current scientific literature consistently highlights the superiority of plant-based and Mediterranean dietary types over the Western diet in promoting gut health and preventing NCDs. Understanding the influence of diet on gut microbiota modulation may pave the way for novel therapeutic strategies.
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Affiliation(s)
| | - Ľubica Argalášová
- Institute of Hygiene, Faculty of Medicine, Comenius University in Bratislava, Špitálska 24, 813 72 Bratislava, Slovakia; (M.S.); (L.H.); (B.G.); (J.B.)
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13
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Anderson CJ, Boeckaerts L, Chin P, Cardas JB, Xie W, Gonçalves A, Blancke G, Benson S, Rogatti S, Simpson MS, Davey A, Choi SM, Desmet S, Bushman SD, Goeminne G, Vandenabeele P, Desai MS, Vereecke L, Ravichandran KS. Metabolite-based inter-kingdom communication controls intestinal tissue recovery following chemotherapeutic injury. Cell Host Microbe 2024; 32:1469-1487.e9. [PMID: 39197455 DOI: 10.1016/j.chom.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/12/2024] [Accepted: 07/31/2024] [Indexed: 09/01/2024]
Abstract
Cytotoxic chemotherapies have devastating side effects, particularly within the gastrointestinal tract. Gastrointestinal toxicity includes the death and damage of the epithelium and an imbalance in the intestinal microbiota, otherwise known as dysbiosis. Whether dysbiosis is a direct contributor to tissue toxicity is a key area of focus. Here, from both mammalian and bacterial perspectives, we uncover an intestinal epithelial cell death-Enterobacteriaceae signaling axis that fuels dysbiosis. Specifically, our data demonstrate that chemotherapy-induced epithelial cell apoptosis and the purine-containing metabolites released from dying cells drive the inter-kingdom transcriptional re-wiring of the Enterobacteriaceae, including fundamental shifts in bacterial respiration and promotion of purine utilization-dependent expansion, which in turn delays the recovery of the intestinal tract. Inhibition of epithelial cell death or restriction of the Enterobacteriaceae to homeostatic levels reverses dysbiosis and improves intestinal recovery. These findings suggest that supportive therapies that maintain homeostatic levels of Enterobacteriaceae may be useful in resolving intestinal disease.
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Affiliation(s)
- Christopher J Anderson
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Laura Boeckaerts
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Priscilla Chin
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Javier Burgoa Cardas
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wei Xie
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Amanda Gonçalves
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; VIB BioImaging Core, Ghent, Belgium
| | - Gillian Blancke
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sam Benson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Sebastian Rogatti
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Mariska S Simpson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Anna Davey
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Sze Men Choi
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Summer D Bushman
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
| | | | - Peter Vandenabeele
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
| | - Lars Vereecke
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kodi S Ravichandran
- VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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14
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Zhao L, Wu G, Zhao N. Guild-based approach for mitigating information loss and distortion issues in microbiome analysis. J Clin Invest 2024; 134:e185395. [PMID: 39225087 PMCID: PMC11364377 DOI: 10.1172/jci185395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Affiliation(s)
- Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences and Center for Microbiome, Nutrition, and Health, New Jersey Institute for Food, Nutrition, and Health, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Wu
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences and Center for Microbiome, Nutrition, and Health, New Jersey Institute for Food, Nutrition, and Health, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Naisi Zhao
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, Massachusetts, USA
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15
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Sardar P, Almeida A, Pedicord VA. Integrating functional metagenomics to decipher microbiome-immune interactions. Immunol Cell Biol 2024; 102:680-691. [PMID: 38952337 DOI: 10.1111/imcb.12798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.
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Affiliation(s)
- Puspendu Sardar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge School of Biological Sciences, Cambridge, UK
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
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16
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Mermel L. Human Evolution, Microgravity, and Challenges Colonizing Mars. Aerosp Med Hum Perform 2024; 95:720-721. [PMID: 39169488 DOI: 10.3357/amhp.6475.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
INTRODUCTION: Human colonization of Mars has captured the imagination of many. However, the challenges posed are immense. In microgravity, changes in human physiology, immune dysregulation, alterations of our microbiome, and enhanced virulence of various microbes are some of the barriers that stand in the way of a successful endeavor. Countermeasures can be brought to bear, but it remains unclear if success of such a mission in the foreseeable future is realistic or fanciful.Mermel L. Human evolution, microgravity, and challenges colonizing Mars. Aerosp Med Hum Perform. 2024; 95(9):720-721.
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17
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Favaron A, Abdalla Y, McCoubrey LE, Nandiraju LP, Shorthouse D, Gaisford S, Basit AW, Orlu M. Exploring the interactions of JAK inhibitor and S1P receptor modulator drugs with the human gut microbiome: Implications for colonic drug delivery and inflammatory bowel disease. Eur J Pharm Sci 2024; 200:106845. [PMID: 38971433 DOI: 10.1016/j.ejps.2024.106845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/24/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The gut microbiota is a complex ecosystem, home to hundreds of bacterial species and a vast repository of enzymes capable of metabolising a wide range of pharmaceuticals. Several drugs have been shown to affect negatively the composition and function of the gut microbial ecosystem. Janus Kinase (JAK) inhibitors and Sphingosine-1-phosphate (S1P) receptor modulators are drugs recently approved for inflammatory bowel disease through an immediate release formulation and would potentially benefit from colonic targeted delivery to enhance the local drug concentration at the diseased site. However, their impact on the human gut microbiota and susceptibility to bacterial metabolism remain unexplored. With the use of calorimetric, optical density measurements, and metagenomics next-generation sequencing, we show that JAK inhibitors (tofacitinib citrate, baricitinib, filgotinib) have a minor impact on the composition of the human gut microbiota, while ozanimod exerts a significant antimicrobial effect, leading to a prevalence of the Enterococcus genus and a markedly different metabolic landscape when compared to the untreated microbiota. Moreover, ozanimod, unlike the JAK inhibitors, is the only drug subject to enzymatic degradation by the human gut microbiota sourced from six healthy donors. Overall, given the crucial role of the gut microbiome in health, screening assays to investigate the interaction of drugs with the microbiota should be encouraged for the pharmaceutical industry as a standard in the drug discovery and development process.
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Affiliation(s)
- Alessia Favaron
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Youssef Abdalla
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Laura E McCoubrey
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | | | - David Shorthouse
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Simon Gaisford
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Abdul W Basit
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom.
| | - Mine Orlu
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom.
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18
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Verhaert MAM, Aspeslagh S. Immunotherapy efficacy and toxicity: Reviewing the evidence behind patient implementable strategies. Eur J Cancer 2024; 209:114235. [PMID: 39059186 DOI: 10.1016/j.ejca.2024.114235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
The use of immune checkpoint inhibitors (ICI) in cancer treatment is expanding, offering promising outcomes but with an important risk of immune-related adverse events (irAEs). These events, stemming from an overstimulated immune system attacking healthy cells, can necessitate immunosuppressant treatment, disrupt treatment courses, and impact patients' quality of life. The analysis of ICI efficacy data has led to a better understanding of the characteristics of responders. Similarly, we are gaining clearer insights into the characteristics of patients who develop irAEs, prompting an increasing emphasis on modifiable factors associated with irAE risk. These factors include lifestyle choices and the composition of the gut microbiome. Despite comprehensive reviews exploring the microbiome's role in therapy efficacy, understanding its connection with immune-related toxicity remains incomplete. While endeavours to identify predictive biomarkers continue, lifestyle modifications emerge as a promising avenue for enhancing treatment outcomes. This review consolidates the current evidence regarding the impact of the gut microbiome on irAE occurrence. Furthermore, it focuses on actionable strategies for mitigating these adverse events, elucidating the evidence supporting dietary adjustments, supplementation, medication management, and physical activity. With the expanding range of indications for ICI therapy, a significant proportion of oncology patients, including those in early disease stages, are now exposed to these treatments. Acknowledging the importance of averting irAEs in this context, our review offers timely insights crucial for addressing the evolving challenges associated with immunotherapy across diverse oncological settings.
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Affiliation(s)
- Marthe August Marianne Verhaert
- Department of Medical Oncology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium.
| | - Sandrine Aspeslagh
- Department of Medical Oncology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium; Department of Internal Medicine, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
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19
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Kumar T, Maitra S, Rai R, Priyanka, Maitra S, Tirkey NN, Kumari R. The dichotomy between probiotic lactic acid bacteria and Plasmodium: A promising therapeutic avenue. Acta Trop 2024; 257:107284. [PMID: 38857820 DOI: 10.1016/j.actatropica.2024.107284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Our understanding of gut microbial populations and their immense influence on host immunity, health, and diseases has increased deeply in recent years. Numerous reports have identified the role of mosquito and mammalian gut microbiota in the modulation of host susceptibility to Plasmodium infection. Artemisinin resistance in malaria-endemic regions necessitates the development of new, safer, and more affordable treatments to supplement existing therapies. In this review, we compiled a colossal amount of data from numerous studies that have assessed the roles played by gut microbial communities in Plasmodium infection, progression, transmission, and severity. Most interestingly, our study points to the overwhelming evidence from experimental studies in mural malaria to human trials, suggesting that the presence of lactic acid bacteria in the gut microbiota of mammalian hosts provides a great degree of protection against malaria. Therefore, our study provides a compelling narrative for probiotic administration as an adjunct therapy for combatting malaria.
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Affiliation(s)
- Tarkeshwar Kumar
- Department of Zoology, Panch Pargana Kisan College, Ranchi University, Ranchi, Jharkhand, 835204, India.
| | - Satarupa Maitra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Richa Rai
- Department of Zoology, Allahabad University, Prayagraj, Uttar Pradesh, India
| | - Priyanka
- Department of Zoology, Allahabad University, Prayagraj, Uttar Pradesh, India
| | - Satwat Maitra
- Noida International Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India
| | | | - Rajesh Kumari
- Department of Zoology, Allahabad University, Prayagraj, Uttar Pradesh, India
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20
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Zemanick ET, Rosas-Salazar C. The Role of the Microbiome in Pediatric Respiratory Diseases. Clin Chest Med 2024; 45:587-597. [PMID: 39069323 DOI: 10.1016/j.ccm.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Numerous studies have examined the role of the microbiome and microbiome-based therapeutics in many childhood airway and lung diseases. In this narrative review, the authors first give a brief overview of the current methods used in microbiome research. The authors then review the literature linking the microbiome with (1) early-life acute respiratory infections due to respiratory syncytial virus, (2) childhood asthma onset, (3) cystic fibrosis, and (4) bronchopulmonary dysplasia, focusing on recent studies that have used culture-independent methods to characterize the respiratory or gut microbiome in the pediatric population.
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Affiliation(s)
- Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 East 16th Avenue, B-395, Aurora, CO 80045, USA
| | - Christian Rosas-Salazar
- Department of Pediatrics, Vanderbilt University Medical Center and Monroe Carell Jr. Children's Hospital at Vanderbilt, 2200 Children's Way, Doctors' Office Tower, Suite 11215, Nashville, TN 37232, USA.
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21
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Puente-Sánchez F, Pascual-García A, Bastolla U, Pedrós-Alió C, Tamames J. Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity. Commun Biol 2024; 7:1046. [PMID: 39181977 PMCID: PMC11344793 DOI: 10.1038/s42003-024-06616-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
The structure of microbial communities arises from a multitude of factors, including the interactions of microorganisms with each other and with the environment. In this work, we sought to disentangle those drivers by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5000 samples, applying a novel network clustering algorithm aimed to capture conditional taxa co-occurrences. We then examined the phylogenetic and functional composition of the resulting clusters, and searched for global patterns of assembly both at the community level and in the presence/absence of individual metabolic pathways.Our analysis highlighted the prevalence of functional redundancy in microbial communities, particularly between taxa that co-occur in more than one environment, pointing to a relationship between functional redundancy and environmental adaptation. In spite of this, certain pathways were observed in fewer taxa than expected by chance, suggesting the presence of auxotrophy, and presumably cooperation among community members. This hypothetical cooperation may play a role in genome reduction, since we observed a negative relationship between the size of bacterial genomes and the size of the community they belong to.Overall, our results suggest the microbial community assembly is driven by universal principles that operate consistently across different biomes and taxonomic groups.
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Affiliation(s)
- Fernando Puente-Sánchez
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
- Department of Aquatic Sciences and Assessment, Swedish University for Agricultural Sciences (SLU), Lennart Hjelms väg 9, 756 51, Uppsala, Sweden.
| | - Alberto Pascual-García
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Ugo Bastolla
- Computational Biology and Bioinformatics, Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid - CSIC), C/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Carlos Pedrós-Alió
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Javier Tamames
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
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22
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Soliz-Rueda JR, Cuesta-Marti C, O'Mahony SM, Clarke G, Schellekens H, Muguerza B. Gut microbiota and eating behaviour in circadian syndrome. Trends Endocrinol Metab 2024:S1043-2760(24)00189-9. [PMID: 39095231 DOI: 10.1016/j.tem.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/04/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
Eating behaviour and circadian rhythms are closely related. The type, timing, and quantity of food consumed, and host circadian rhythms, directly influence the intestinal microbiota, which in turn impacts host circadian rhythms and regulates food intake beyond homeostatic eating. This Opinion discusses the impact of food intake and circadian disruptions induced by an obesogenic environment on gut-brain axis signalling. We also explore potential mechanisms underlying the effects of altered gut microbiota on food intake behaviour and circadian rhythmicity. Understanding the crosstalk between gut microbiota, circadian rhythms, and unhealthy eating behaviour is crucial to addressing the obesity epidemic, which remains one of the biggest societal challenges of our time.
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Affiliation(s)
- Jorge R Soliz-Rueda
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira I Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Center of Environmental, Food and Toxicological Technology (TecnATox), Tarragona, Spain
| | - Cristina Cuesta-Marti
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - Siobhain M O'Mahony
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Harriët Schellekens
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, Cork, Ireland.
| | - Begoña Muguerza
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira I Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Center of Environmental, Food and Toxicological Technology (TecnATox), Tarragona, Spain
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23
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Meijnikman AS, Nieuwdorp M, Schnabl B. Endogenous ethanol production in health and disease. Nat Rev Gastroenterol Hepatol 2024; 21:556-571. [PMID: 38831008 DOI: 10.1038/s41575-024-00937-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/05/2024]
Abstract
The gut microbiome exerts metabolic actions on distal tissues and organs outside the intestine, partly through microbial metabolites that diffuse into the circulation. The disruption of gut homeostasis results in changes to microbial metabolites, and more than half of the variance in the plasma metabolome can be explained by the gut microbiome. Ethanol is a major microbial metabolite that is produced in the intestine of nearly all individuals; however, elevated ethanol production is associated with pathological conditions such as metabolic dysfunction-associated steatotic liver disease and auto-brewery syndrome, in which the liver's capacity to metabolize ethanol is surpassed. In this Review, we describe the mechanisms underlying excessive ethanol production in the gut and the role of ethanol catabolism in mediating pathogenic effects of ethanol on the liver and host metabolism. We conclude by discussing approaches to target excessive ethanol production by gut bacteria.
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Affiliation(s)
| | - Max Nieuwdorp
- Department of Internal Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, Netherlands
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, Netherlands
- Diabeter Centrum Amsterdam, Amsterdam, Netherlands
| | - 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.
- Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA.
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24
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Itagaki T, Kobayashi H, Sakata KI, Miyamoto I, Hasebe A, Kitagawa Y. Compositional Data and Microbiota Analysis: Imagination and Reality. Microorganisms 2024; 12:1484. [PMID: 39065253 PMCID: PMC11279367 DOI: 10.3390/microorganisms12071484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 06/28/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
The relationships among bacterial flora, diseases, and diet have been described by many authors. An operational taxonomic units (OTUs) are the result of clustering the 16S rRNA gene sequences at a certain cutoff value, and they are considered compositional data. As Pearson's correlation coefficient is difficult to interpret, Aitchison's ratio analysis was used to develop a method to handle compositional data. Multivariate analysis was developed because univariate analysis can be subject to large biases. Simulations regarding absolute abundance based on certain assumptions and some analyses, such as nonparametric multidimensional scaling (NMDS), principal component analysis (PCA), and ratio analysis, were conducted in this study. The same content as a 100% stacked bar graph could be expressed in low dimensions using PCA. However, the relative diversity was not reproducible with NMDS. Various assumptions were made regarding absolute abundance based on the relative abundance. However, which assumptions are true could not be determined. In summary, ratio analysis and PCA are useful for analyzing compositional data and the gut microbiota.
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Affiliation(s)
- Tatsuki Itagaki
- Oral Diagnosis and Medicine, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan; (T.I.); (H.K.); (K.-i.S.); (I.M.); (Y.K.)
- Microbiology, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan
| | - Hirokazu Kobayashi
- Oral Diagnosis and Medicine, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan; (T.I.); (H.K.); (K.-i.S.); (I.M.); (Y.K.)
- Microbiology, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan
| | - Ken-ichiro Sakata
- Oral Diagnosis and Medicine, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan; (T.I.); (H.K.); (K.-i.S.); (I.M.); (Y.K.)
| | - Ikuya Miyamoto
- Oral Diagnosis and Medicine, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan; (T.I.); (H.K.); (K.-i.S.); (I.M.); (Y.K.)
| | - Akira Hasebe
- Microbiology, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan
| | - Yoshimasa Kitagawa
- Oral Diagnosis and Medicine, Faculty of Dental Medicine, Graduate School of Dental Medicine, Hokkaido University, Kita-13 Nishi-7, Kita-ku, Sapporo 060-8586, Japan; (T.I.); (H.K.); (K.-i.S.); (I.M.); (Y.K.)
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25
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Vižlin A, Andersch Björkman Y, Kumar Y, Göthe M, Gillstedt M, Osmančević A. No Evidence of Gut Microbiota Alteration in Psoriasis Patients Switching to Brodalumab after Loss of TNFα Inhibition Effect. Int J Mol Sci 2024; 25:7745. [PMID: 39062988 PMCID: PMC11277239 DOI: 10.3390/ijms25147745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Biological agents used to treat severe psoriasis may alter the gut microbiota, though current knowledge is limited. This study examines whether switching from TNFα inhibitors, from which patients had reduced or lost effect, to brodalumab, an IL-17 inhibitor, affects the gut microbiota in patients with psoriasis and how these changes correlate with the clinical variables of psoriasis severity and depressive symptoms. Fecal samples from patients were collected before the treatment switch and 12 weeks after the switch and were analyzed for the microbiota composition using next-generation sequencing targeting the V3-V5 region of the 16S rRNA gene, followed by bioinformatics analysis. No significant changes in overall gut microbiota composition were observed after the treatment switch, although individual variations in the Firmicutes/Bacteroidetes ratio were noted, and no significant correlations with clinical variables were found. These findings suggest that short-term changes in gut microbiota in patients with psoriasis are limited and that dysbiosis may be influenced by the interplay of various microbial populations rather than specific taxa. This study provides a foundation for further research into the effects of biological treatments on the gut microbiota in patients with psoriasis.
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Affiliation(s)
- Admir Vižlin
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.V.)
| | - Ylva Andersch Björkman
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.V.)
- Department of Dermatology and Venereology, Sahlgrenska University Hospital, Region Västra Götaland, 413 45 Gothenburg, Sweden
| | | | | | - Martin Gillstedt
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.V.)
- Department of Dermatology and Venereology, Sahlgrenska University Hospital, Region Västra Götaland, 413 45 Gothenburg, Sweden
| | - Amra Osmančević
- Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden; (A.V.)
- Department of Dermatology and Venereology, Sahlgrenska University Hospital, Region Västra Götaland, 413 45 Gothenburg, Sweden
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26
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Huang J, Qin TS, Bo Y, Li YJ, Liu RS, Yu Y, Li XD, He JC, Ma AX, Tao DP, Ren WJ, Peng J. The Role of the Intestinal Flora and Its Derivatives in Neurocognitive Disorders: A Narrative Review from Surgical Perspective. Mol Neurobiol 2024:10.1007/s12035-024-04322-1. [PMID: 38985257 DOI: 10.1007/s12035-024-04322-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024]
Abstract
Perioperative neurocognitive dysfunction is a significant concern for population health, impacting postoperative recovery and increasing the financial burden on patients. With an increasing number of surgical procedures being performed, the prevention and management of perioperative neurocognitive dysfunction have garnered significant attention. While factors such as age, lifestyle, genetics, and education are known to influence the development of cognitive dysfunction, recent research has highlighted the role of the gut microbiota in neurological health. An increased abundance of pro-inflammatory gut microbiota can trigger and worsen neuroinflammation, neuronal cell damage, and impaired cellular autophagy. Moreover, the inflammation-promoting gut microbiota can disrupt immune function, impair neuroautophagy, and affect the production and circulation of extracellular vesicles and neurotransmitters. These factors collectively play a role in the onset and advancement of cognitive impairment. This narrative review delves into the molecular mechanisms through which gut microbiota and their derivatives contribute to cognitive impairment, focusing on the impact of anesthesia surgery, changes in gut microbial populations, and perioperative cognitive impairment associations. The study suggests that alterations in the abundance of various bacterial species and their metabolites pre- and post-surgery may be linked to postoperative cognitive impairment. Furthermore, the potential of probiotics or prebiotics in addressing cognitive impairment is discussed, offering a promising avenue for investigating the treatment of perioperative neurocognitive disorders.
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Affiliation(s)
- Jian Huang
- The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, People's Republic of China
| | - Tian-Shou Qin
- The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, People's Republic of China
| | - Yun Bo
- Department of Anesthesiology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
| | - Yu-Jin Li
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
| | - Rong-Sheng Liu
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
| | - Yang Yu
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
| | - Xiao-Dong Li
- The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, People's Republic of China
| | - Jin-Can He
- The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, People's Republic of China
| | - Ai-Xin Ma
- The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, People's Republic of China
| | - Da-Peng Tao
- School of Information Science and Engineering, Yunnan University, Kunming, 650504, China
| | - Wen-Jun Ren
- Department of Cardiovascular Surgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China.
| | - Jun Peng
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
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Qadri H, Shah AH, Almilaibary A, Mir MA. Microbiota, natural products, and human health: exploring interactions for therapeutic insights. Front Cell Infect Microbiol 2024; 14:1371312. [PMID: 39035357 PMCID: PMC11257994 DOI: 10.3389/fcimb.2024.1371312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/03/2024] [Indexed: 07/23/2024] Open
Abstract
The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.
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Affiliation(s)
- Hafsa Qadri
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdul Haseeb Shah
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdullah Almilaibary
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
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28
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Mohr AE, Ortega-Santos CP, Whisner CM, Klein-Seetharaman J, Jasbi P. Navigating Challenges and Opportunities in Multi-Omics Integration for Personalized Healthcare. Biomedicines 2024; 12:1496. [PMID: 39062068 PMCID: PMC11274472 DOI: 10.3390/biomedicines12071496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
The field of multi-omics has witnessed unprecedented growth, converging multiple scientific disciplines and technological advances. This surge is evidenced by a more than doubling in multi-omics scientific publications within just two years (2022-2023) since its first referenced mention in 2002, as indexed by the National Library of Medicine. This emerging field has demonstrated its capability to provide comprehensive insights into complex biological systems, representing a transformative force in health diagnostics and therapeutic strategies. However, several challenges are evident when merging varied omics data sets and methodologies, interpreting vast data dimensions, streamlining longitudinal sampling and analysis, and addressing the ethical implications of managing sensitive health information. This review evaluates these challenges while spotlighting pivotal milestones: the development of targeted sampling methods, the use of artificial intelligence in formulating health indices, the integration of sophisticated n-of-1 statistical models such as digital twins, and the incorporation of blockchain technology for heightened data security. For multi-omics to truly revolutionize healthcare, it demands rigorous validation, tangible real-world applications, and smooth integration into existing healthcare infrastructures. It is imperative to address ethical dilemmas, paving the way for the realization of a future steered by omics-informed personalized medicine.
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Affiliation(s)
- Alex E. Mohr
- Systems Precision Engineering and Advanced Research (SPEAR), Theriome Inc., Phoenix, AZ 85004, USA; (A.E.M.); (C.P.O.-S.); (C.M.W.); (J.K.-S.)
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ 85281, USA
| | - Carmen P. Ortega-Santos
- Systems Precision Engineering and Advanced Research (SPEAR), Theriome Inc., Phoenix, AZ 85004, USA; (A.E.M.); (C.P.O.-S.); (C.M.W.); (J.K.-S.)
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
| | - Corrie M. Whisner
- Systems Precision Engineering and Advanced Research (SPEAR), Theriome Inc., Phoenix, AZ 85004, USA; (A.E.M.); (C.P.O.-S.); (C.M.W.); (J.K.-S.)
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ 85281, USA
| | - Judith Klein-Seetharaman
- Systems Precision Engineering and Advanced Research (SPEAR), Theriome Inc., Phoenix, AZ 85004, USA; (A.E.M.); (C.P.O.-S.); (C.M.W.); (J.K.-S.)
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Paniz Jasbi
- Systems Precision Engineering and Advanced Research (SPEAR), Theriome Inc., Phoenix, AZ 85004, USA; (A.E.M.); (C.P.O.-S.); (C.M.W.); (J.K.-S.)
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29
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Sharon O, Ben Simon E, Shah VD, Desel T, Walker MP. The new science of sleep: From cells to large-scale societies. PLoS Biol 2024; 22:e3002684. [PMID: 38976664 PMCID: PMC11230563 DOI: 10.1371/journal.pbio.3002684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
In the past 20 years, more remarkable revelations about sleep and its varied functions have arguably been made than in the previous 200. Building on this swell of recent findings, this essay provides a broad sampling of selected research highlights across genetic, molecular, cellular, and physiological systems within the body, networks within the brain, and large-scale social dynamics. Based on this raft of exciting new discoveries, we have come to realize that sleep, in this moment of its evolution, is very much polyfunctional (rather than monofunctional), yet polyfunctional for reasons we had never previously considered. Moreover, these new polyfunctional insights powerfully reaffirm sleep as a critical biological, and thus health-sustaining, requisite. Indeed, perhaps the only thing more impressive than the unanticipated nature of these newly emerging sleep functions is their striking divergence, from operations of molecular mechanisms inside cells to entire group societal dynamics.
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Affiliation(s)
- Omer Sharon
- Department of Psychology, University of California, Berkeley, California, United States of America
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - Eti Ben Simon
- Department of Psychology, University of California, Berkeley, California, United States of America
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - Vyoma D. Shah
- Department of Psychology, University of California, Berkeley, California, United States of America
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - Tenzin Desel
- Department of Psychology, University of California, Berkeley, California, United States of America
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - Matthew P. Walker
- Department of Psychology, University of California, Berkeley, California, United States of America
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
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30
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Maiuolo J, Bulotta RM, Ruga S, Nucera S, Macrì R, Scarano F, Oppedisano F, Carresi C, Gliozzi M, Musolino V, Mollace R, Muscoli C, Mollace V. The Postbiotic Properties of Butyrate in the Modulation of the Gut Microbiota: The Potential of Its Combination with Polyphenols and Dietary Fibers. Int J Mol Sci 2024; 25:6971. [PMID: 39000076 PMCID: PMC11240906 DOI: 10.3390/ijms25136971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
The gut microbiota is a diverse bacterial community consisting of approximately 2000 species, predominantly from five phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia. The microbiota's bacterial species create distinct compounds that impact the host's health, including well-known short-chain fatty acids. These are produced through the breakdown of dietary fibers and fermentation of undigested carbohydrates by the intestinal microbiota. The main short-chain fatty acids consist of acetate, propionate, and butyrate. The concentration of butyrate in mammalian intestines varies depending on the diet. Its main functions are use as an energy source, cell differentiation, reduction in the inflammatory process in the intestine, and defense against oxidative stress. It also plays an epigenetic role in histone deacetylases, thus helping to reduce the risk of colon cancer. Finally, butyrate affects the gut-brain axis by crossing the brain-blood barrier, making it crucial to determine the right concentrations for both local and peripheral effects. In recent years, there has been a significant amount of attention given to the role of dietary polyphenols and fibers in promoting human health. Polyphenols and dietary fibers both play crucial roles in protecting human health and can produce butyrate through gut microbiota fermentation. This paper aims to summarize information on the key summits related to the negative correlation between intestinal microbiota diversity and chronic diseases to guide future research on determining the specific activity of butyrate from polyphenols and dietary fibers that can carry out these vital functions.
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Affiliation(s)
- Jessica Maiuolo
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Rosa Maria Bulotta
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Stefano Ruga
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Saverio Nucera
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Roberta Macrì
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Federica Scarano
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Francesca Oppedisano
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Cristina Carresi
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Micaela Gliozzi
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Vincenzo Musolino
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Rocco Mollace
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Roma, Italy;
| | - Carolina Muscoli
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
| | - Vincenzo Mollace
- IRC-FSH Center, Department of Health Sciences, University “Magna Græcia” of Catanzaro, Germaneto, 88100 Catanzaro, Italy; (R.M.B.); (S.R.); (S.N.); (R.M.); (F.S.); (F.O.); (C.C.); (M.G.); (V.M.); (C.M.); (V.M.)
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Roma, Italy;
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31
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Gawey BJ, Mars RA, Kashyap PC. The role of the gut microbiome in disorders of gut-brain interaction. FEBS J 2024. [PMID: 38922780 DOI: 10.1111/febs.17200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/03/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Disorders of Gut-Brain Interaction (DGBI) are widely prevalent and commonly encountered in gastroenterology practice. While several peripheral and central mechanisms have been implicated in the pathogenesis of DGBI, a recent body of work suggests an important role for the gut microbiome. In this review, we highlight how gut microbiota and their metabolites affect physiologic changes underlying symptoms in DGBI, with a particular focus on their mechanistic influence on GI transit, visceral sensitivity, intestinal barrier function and secretion, and CNS processing. This review emphasizes the complexity of local and distant effects of microbial metabolites on physiological function, influenced by factors such as metabolite concentration, duration of metabolite exposure, receptor location, host genetics, and underlying disease state. Large-scale in vitro work has elucidated interactions between host receptors and the microbial metabolome but there is a need for future research to integrate such preclinical findings with clinical studies. The development of novel, targeted therapeutic strategies for DGBI hinges on a deeper understanding of these metabolite-host interactions, offering exciting possibilities for the future of treatment of DGBI.
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Affiliation(s)
- Brent J Gawey
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ruben A Mars
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
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32
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Widder S, Carmody LA, Opron K, Kalikin LM, Caverly LJ, LiPuma JJ. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. Nat Commun 2024; 15:4889. [PMID: 38849369 PMCID: PMC11161516 DOI: 10.1038/s41467-024-49150-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. Understanding PEx ecology is challenged by high inter-patient variability in airway microbial community profiles. We analyze bacterial communities in 880 CF sputum samples collected during an observational prospective cohort study and develop microbiome descriptors to model community reorganization prior to and during 18 PEx. We identify two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx show hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx display stochasticity and increased diversity. A simulation of antimicrobial treatment predicts better efficacy for hierarchically organized communities. This link between PEx, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.
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Affiliation(s)
- Stefanie Widder
- Department of Medicine 1, Research Division Infection Biology, Medical University of Vienna, 1090, Vienna, Austria.
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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33
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Garmendia J, Cebollero‐Rivas P. Environmental exposures, the oral-lung axis and respiratory health: The airway microbiome goes on stage for the personalized management of human lung function. Microb Biotechnol 2024; 17:e14506. [PMID: 38881505 PMCID: PMC11180993 DOI: 10.1111/1751-7915.14506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/19/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
The human respiratory system is constantly exposed to environmental stimuli, sometimes including toxicants, which can trigger dysregulated lung immune responses that lead to respiratory symptoms, impaired lung function and airway diseases. Evidence supports that the microbiome in the lungs has an indispensable role in respiratory health and disease, acting as a local gatekeeper that mediates the interaction between the environmental cues and respiratory health. Moreover, the microbiome in the lungs is intimately intertwined with the oral microbiome through the oral-lung axis. Here, we discuss the intricate three-way relationship between (i) cigarette smoking, which has strong effects on the microbial community structure of the lung; (ii) microbiome dysbiosis and disease in the oral cavity; and (iii) microbiome dysbiosis in the lung and its causal role in patients suffering chronic obstructive pulmonary disease (COPD), a leading cause of morbidity and mortality worldwide. We highlight exciting outcomes arising from recently established interactions in the airway between environmental exposures, microbiome, metabolites-functional attributes and the host, as well as how these associations have the potential to predict the respiratory health status of the host through an airway microbiome health index. For completion, we argue that incorporating (synthetic) microbial community ecology in our contemporary understanding of lung disease presents challenges and also rises novel opportunities to exploit the oral-lung axis and its microbiome towards innovative airway disease diagnostics, prognostics, patient stratification and microbiota-targeted clinical interventions in the context of current therapies.
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Affiliation(s)
- Junkal Garmendia
- Instituto de AgrobiotecnologíaConsejo Superior de Investigaciones Científicas (IdAB‐CSIC)‐Gobierno de NavarraMutilvaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES)MadridSpain
| | - Pilar Cebollero‐Rivas
- Servicio de NeumologíaHospital Universitario de NavarraNavarraSpain
- Universidad Pública de Navarra (UPNa)NavarraSpain
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34
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Scott JS, Li A, Wardill HR. Role of mucositis in predicting gut microbiota composition in people with cancer. Curr Opin Support Palliat Care 2024; 18:73-77. [PMID: 38652454 DOI: 10.1097/spc.0000000000000700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
PURPOSE OF REVIEW Disruption of the precious ecosystem of micro-organisms that reside in the gut - the gut microbiota - is rapidly emerging as a key driver of the adverse side effects/toxicities caused by numerous anti-cancer agents. Although the contribution of the gut microbiota to these toxicities is understood with ever increasing precision, the cause of microbial disruption (dysbiosis) remains poorly understood. Here, we discuss current evidence on the cause(s) of dysbiosis after cancer therapy, positioning breakdown of the intestinal mucosa (mucositis) as a central cause. RECENT FINDINGS Dysbiosis in people with cancer has historically been attributed to extensive antibiotic use. However, evidence now suggests that certain antibiotics have minimal impacts on the microbiota. Indeed, recent evidence shows that the type of cancer therapy predicts microbiota composition independently of antibiotics. Given most anti-cancer drugs have modest effects on microbes directly, this suggests that their impact on the gut microenvironment, in particular the mucosa, which is highly vulnerable to cytotoxicity, is a likely cause of dysbiosis. Here, we outline evidence that support this hypothesis, and discuss the associated clinical implications/opportunities. SUMMARY The concept that mucositis dictates microbiota compositions provides two important implications for clinical practice. Firstly, it reiterates the importance of prioritising the development of novel mucoprotectants that preserve mucosal integrity, and indirectly support microbial stability. Secondly, it provides an opportunity to identify dysbiotic events and associated consequences using readily accessible, minimally invasive biomarkers of mucositis such as plasma citrulline.
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Affiliation(s)
- Jacqui S Scott
- Faculty of Health and Medical Sciences, School of Biomedicine, The University of Adelaide
- Supportive Oncology Research Group, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Anna Li
- Faculty of Health and Medical Sciences, School of Biomedicine, The University of Adelaide
- Supportive Oncology Research Group, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Hannah R Wardill
- Faculty of Health and Medical Sciences, School of Biomedicine, The University of Adelaide
- Supportive Oncology Research Group, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia
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Vandecruys M, De Smet S, De Beir J, Renier M, Leunis S, Van Criekinge H, Glorieux G, Raes J, Vanden Wyngaert K, Nagler E, Calders P, Monbaliu D, Cornelissen V, Evenepoel P, Van Craenenbroeck AH. Revitalizing the Gut Microbiome in Chronic Kidney Disease: A Comprehensive Exploration of the Therapeutic Potential of Physical Activity. Toxins (Basel) 2024; 16:242. [PMID: 38922137 PMCID: PMC11209503 DOI: 10.3390/toxins16060242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Both physical inactivity and disruptions in the gut microbiome appear to be prevalent in patients with chronic kidney disease (CKD). Engaging in physical activity could present a novel nonpharmacological strategy for enhancing the gut microbiome and mitigating the adverse effects associated with microbial dysbiosis in individuals with CKD. This narrative review explores the underlying mechanisms through which physical activity may favorably modulate microbial health, either through direct impact on the gut or through interorgan crosstalk. Also, the development of microbial dysbiosis and its interplay with physical inactivity in patients with CKD are discussed. Mechanisms and interventions through which physical activity may restore gut homeostasis in individuals with CKD are explored.
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Affiliation(s)
- Marieke Vandecruys
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium; (M.V.); or (P.E.)
| | - Stefan De Smet
- Exercise Physiology Research Group, Department of Movement Sciences, KU Leuven, 3000 Leuven, Belgium;
| | - Jasmine De Beir
- Department of Rehabilitation Sciences, Ghent University, 9000 Ghent, Belgium; (J.D.B.); (P.C.)
| | - Marie Renier
- Group Rehabilitation for Internal Disorders, Department of Rehabilitation Sciences, KU Leuven, 3000 Leuven, Belgium; (M.R.); (V.C.)
| | - Sofie Leunis
- Department of Microbiology, Immunology and Transplantation, Abdominal Transplantation, KU Leuven, 3000 Leuven, Belgium; (S.L.); (H.V.C.); (D.M.)
| | - Hanne Van Criekinge
- Department of Microbiology, Immunology and Transplantation, Abdominal Transplantation, KU Leuven, 3000 Leuven, Belgium; (S.L.); (H.V.C.); (D.M.)
| | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (G.G.); (K.V.W.); (E.N.)
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, 3000 Leuven, Belgium;
- VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Karsten Vanden Wyngaert
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (G.G.); (K.V.W.); (E.N.)
| | - Evi Nagler
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (G.G.); (K.V.W.); (E.N.)
| | - Patrick Calders
- Department of Rehabilitation Sciences, Ghent University, 9000 Ghent, Belgium; (J.D.B.); (P.C.)
| | - Diethard Monbaliu
- Department of Microbiology, Immunology and Transplantation, Abdominal Transplantation, KU Leuven, 3000 Leuven, Belgium; (S.L.); (H.V.C.); (D.M.)
- Transplantoux Foundation, 3000 Leuven, Belgium
| | - Véronique Cornelissen
- Group Rehabilitation for Internal Disorders, Department of Rehabilitation Sciences, KU Leuven, 3000 Leuven, Belgium; (M.R.); (V.C.)
| | - Pieter Evenepoel
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium; (M.V.); or (P.E.)
- Department of Nephrology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium; (M.V.); or (P.E.)
- Department of Nephrology, University Hospitals Leuven, 3000 Leuven, Belgium
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Láng L, McArthur S, Lazar AS, Pourtau L, Gaudout D, Pontifex MG, Müller M, Vauzour D. Dietary (Poly)phenols and the Gut-Brain Axis in Ageing. Nutrients 2024; 16:1500. [PMID: 38794738 PMCID: PMC11124177 DOI: 10.3390/nu16101500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
As the population ages, the incidence of age-related neurodegenerative diseases is rapidly increasing, and novel approaches to mitigate this soaring prevalence are sorely needed. Recent studies have highlighted the importance of gut microbial homeostasis and its impact on brain functions, commonly referred to as the gut-brain axis, in maintaining overall health and wellbeing. Nonetheless, the mechanisms by which this system acts remains poorly defined. In this review, we will explore how (poly)phenols, a class of natural compounds found in many plant-based foods and beverages, can modulate the gut-brain axis, and thereby promote neural health. While evidence indicates a beneficial role of (poly)phenol consumption as part of a balanced diet, human studies are scarce and mechanistic insight is still lacking. In this regard, we make the case that dietary (poly)phenols should be further explored to establish their therapeutic efficacy on brain health through modulation of the gut-brain axis, with much greater emphasis on carefully designed human interventions.
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Affiliation(s)
- Léonie Láng
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK; (L.L.); (M.M.)
| | - Simon McArthur
- Faculty of Medicine & Dentistry, Queen Mary, University of London, Blizard Institute, London E1 2AT, UK;
| | - Alpar S. Lazar
- Faculty of Medicine and Health Sciences, The Queen’s Building, University of East Anglia, Norwich NR4 7TJ, UK; (A.S.L.); (M.G.P.)
| | - Line Pourtau
- Activ’Inside, 33750 Beychac et Caillau, France; (L.P.); (D.G.)
| | - David Gaudout
- Activ’Inside, 33750 Beychac et Caillau, France; (L.P.); (D.G.)
| | - Matthew G. Pontifex
- Faculty of Medicine and Health Sciences, The Queen’s Building, University of East Anglia, Norwich NR4 7TJ, UK; (A.S.L.); (M.G.P.)
| | - Michael Müller
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK; (L.L.); (M.M.)
| | - David Vauzour
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK; (L.L.); (M.M.)
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Bethlehem L, Estevinho MM, Grinspan A, Magro F, Faith JJ, Colombel JF. Microbiota therapeutics for inflammatory bowel disease: the way forward. Lancet Gastroenterol Hepatol 2024; 9:476-486. [PMID: 38604201 DOI: 10.1016/s2468-1253(23)00441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 04/13/2024]
Abstract
Microbiota therapeutics that transplant faecal material from healthy donors to people with mild-to-moderate ulcerative colitis have shown the potential to induce remission in about 30% of participants in small, phase 2 clinical trials. Despite this substantial achievement, the field needs to leverage the insights gained from these trials and progress towards phase 3 clinical trials and drug approval, while identifying the distinct clinical niche for this new therapeutic modality within inflammatory bowel disease (IBD) therapeutics. We describe the lessons that can be learned from past studies of microbiota therapeutics, from full spectrum donor stool to defined products manufactured in vitro. We explore the actionable insights these lessons provide on the design of near-term studies and future trajectories for the integration of microbiota therapeutics in the treatment of IBD. If successful, microbiota therapeutics will provide a powerful orthogonal approach (complementing or in combination with existing immunomodulatory drugs) to raise the therapeutic ceiling for the many non-responders and partial responders within the IBD patient population.
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Affiliation(s)
- Lukas Bethlehem
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Manuela Estevinho
- Department of Gastroenterology, Vila Nova de Gaia Espinho Hospital Center, Vila Nova de Gaia, Portugal; Unit of Pharmacology and Therapeutics, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Ari Grinspan
- Dr Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando Magro
- Unit of Pharmacology and Therapeutics, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal; CINTESIS@RISE, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal; Department of Gastroenterology, São João Hospital Center, Porto, Portugal
| | - Jeremiah J Faith
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Dr Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Siegel NA, Jimenez MT, Rocha CS, Rolston M, Dandekar S, Solnick JV, Miller LA. Helicobacter pylori infection in infant rhesus macaque monkeys is associated with an altered lung and oral microbiome. Sci Rep 2024; 14:9998. [PMID: 38693196 PMCID: PMC11063185 DOI: 10.1038/s41598-024-59514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/11/2024] [Indexed: 05/03/2024] Open
Abstract
It is estimated that more than half of the world population has been infected with Helicobacter pylori. Most newly acquired H. pylori infections occur in children before 10 years of age. We hypothesized that early life H. pylori infection could influence the composition of the microbiome at mucosal sites distant to the stomach. To test this hypothesis, we utilized the infant rhesus macaque monkey as an animal model of natural H. pylori colonization to determine the impact of infection on the lung and oral microbiome during a window of postnatal development. From a cohort of 4-7 month-old monkeys, gastric biopsy cultures identified 44% of animals infected by H. pylori. 16S ribosomal RNA gene sequencing of lung washes and buccal swabs from animals showed distinct profiles for the lung and oral microbiome, independent of H. pylori infection. In order of relative abundance, the lung microbiome was dominated by the phyla Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campilobacterota and Actinobacteriota while the oral microbiome was dominated by Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota. In comparison to the oral cavity, the lung was composed of more genera and species that significantly differed by H. pylori status, with a total of 6 genera and species that were increased in H. pylori negative infant monkey lungs. Lung, but not plasma IL-8 concentration was also associated with gastric H. pylori load and lung microbial composition. We found the infant rhesus macaque monkey lung harbors a microbiome signature that is distinct from that of the oral cavity during postnatal development. Gastric H. pylori colonization and IL-8 protein were linked to the composition of microbial communities in the lung and oral cavity. Collectively, these findings provide insight into how H. pylori infection might contribute to the gut-lung axis during early childhood and modulate future respiratory health.
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Affiliation(s)
- Noah A Siegel
- California National Primate Research Center, University of California Davis, Davis, CA, USA
| | - Monica T Jimenez
- California National Primate Research Center, University of California Davis, Davis, CA, USA
| | - Clarissa Santos Rocha
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Matthew Rolston
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Satya Dandekar
- California National Primate Research Center, University of California Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Jay V Solnick
- California National Primate Research Center, University of California Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Lisa A Miller
- California National Primate Research Center, University of California Davis, Davis, CA, USA.
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
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Duan R, Liu Y, Zhang Y, Shi J, Xue R, Liu R, Miao Y, Zhou X, Lv Y, Shen H, Xie X, Ai X. The impact of exercise on the gut microbiota in middle-aged amateur serious runners: a comparative study. Front Physiol 2024; 15:1343219. [PMID: 38737829 PMCID: PMC11082653 DOI: 10.3389/fphys.2024.1343219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Exercise, health, and the gut microbiota (GM) are strongly correlated. Research indicates that professional athletes, especially ultra-marathon runners, have unique GM characteristics. However, more research has focused on elite athletes, with little attention given to amateur sports enthusiasts, especially those in the middle-aged population. Therefore, this study focuses on the impact of long-term running on the composition and potential functions of the GM in middle-aged individuals. Methods We compared the GM of 25 middle-aged serious runnerswith 22 sedentary healthy controls who had minimal exercise habitsusing 16S rRNA gene sequencing. Additionally, we assessed dietary habits using a food frequency questionnaire. Results and Discussion Statistical analysis indicates that there is no significant difference in dietary patterns between the control group and serious runners. Diversity analysis results indicate that there is no significant difference in α diversity between the two groups of GM, but there is a significant difference in β diversity. Analysis of the composition of GM reveals that Ruminococcus and Coprococcus are significantly enriched in serious runners, whereas Bacteroides, Lachnoclostridium, and Lachnospira are enriched in the control group. Differential analysis of functional pathway prediction results reveals significant differences in the functional metabolism levels of GM between serious runners and the control group. Further correlation analysis results indicate that this difference may be closely related to variations in GM. In conclusion, our results suggest that long-term exercise can lead to changes in the composition of the GM. These changes have the potential to impact the overall health of the individual by influencing metabolic regulation.
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Affiliation(s)
- Rui Duan
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Yu Liu
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Yonglian Zhang
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Jinrong Shi
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Rong Xue
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Ruijie Liu
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Yuanxin Miao
- Research Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, Hubei, China
| | - Xianfeng Zhou
- School of Life Sciences and Health Engineering, Hubei University of Technology, Wuhan, China
- Maintainbiotech Ltd., Wuhan, Hubei, China
| | | | - Hexiao Shen
- Maintainbiotech Ltd., Wuhan, Hubei, China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiongwei Xie
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Xu Ai
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
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Elford JD, Becht N, Garssen J, Kraneveld AD, Perez-Pardo P. Buty and the beast: the complex role of butyrate in Parkinson's disease. Front Pharmacol 2024; 15:1388401. [PMID: 38694925 PMCID: PMC11061429 DOI: 10.3389/fphar.2024.1388401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease which is often associated with gastrointestinal (GI) dysfunction. The GI tract is home to a wide range of microorganisms, among which bacteria, that can influence the host through various mechanisms. Products produced by these bacteria can act in the gut but can also exert effects in the brain via what is now well established to be the microbiota-gut-brain axis. In those with PD the gut-bacteria composition is often found to be different to that of non-PD individuals. In addition to compositional changes, the metabolic activity of the gut-microbiota is also changed in PD. Specifically, it is often reported that key producers of short chain fatty acids (SCFAs) as well as the concentration of SCFAs themselves are altered in the stool and blood of those with PD. These SCFAs, among which butyrate, are essential nutrients for the host and are a major energy source for epithelial cells of the GI tract. Additionally, butyrate plays a key role in regulating various host responses particularly in relation to inflammation. Studies have demonstrated that a reduction in butyrate levels can have a critical role in the onset and progression of PD. Furthermore, it has been shown that restoring butyrate levels in those with PD through methods such as probiotics, prebiotics, sodium butyrate supplementation, and fecal transplantation can have a beneficial effect on both motor and non-motor outcomes of the disease. This review presents an overview of evidence for the altered gut-bacteria composition and corresponding metabolite production in those with PD, with a particular focus on the SCFA butyrate. In addition to presenting current studies regarding SCFA in clinical and preclinical reports, evidence for the possibility to target butyrate production using microbiome based approaches in a therapeutic context is discussed.
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Affiliation(s)
- Joshua D. Elford
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nanette Becht
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
- Danone Nutricia Research, Utrecht, Netherlands
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
- Department of Neuroscience, Faculty of Science, Vrije Universiteit, Amsterdam, Netherlands
| | - Paula Perez-Pardo
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
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Ai X, Liu Y, Shi J, Xie X, Li L, Duan R, Lv Y, Xiong K, Miao Y, Zhang Y. Structural characteristics of gut microbiota in longevity from Changshou town, Hubei, China. Appl Microbiol Biotechnol 2024; 108:300. [PMID: 38619710 PMCID: PMC11018559 DOI: 10.1007/s00253-024-13140-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
The gut microbiota (GM) and its potential functions play a crucial role in maintaining host health and longevity. The aim of this study was to investigate the potential relationship between GM and longevity. We collected fecal samples from 92 healthy volunteers (middle-aged and elderly: 43-79 years old; longevity: ≥ 90 years old) from Changshou Town, Zhongxiang City, Hubei, China. In addition, we collected samples from 30 healthy middle-aged and elderly controls (aged 51-70 years) from Wuhan, Hubei. The 16S rDNA V3 + V4 region of the fecal samples was sequenced using high-throughput sequencing technology. Diversity analysis results showed that the elderly group with longevity and the elderly group with low body mass index (BMI) exhibited higher α diversity. However, no significant difference was observed in β diversity. The results of the microbiome composition indicate that Firmicutes, Proteobacteria, and Bacteroidota are the core phyla in all groups. Compared to younger elderly individuals, Akkermansia and Lactobacillus are significantly enriched in the long-lived elderly group, while Megamonas is significantly reduced. In addition, a high abundance of Akkermansia is a significant characteristic of elderly populations with low BMI values. Furthermore, the functional prediction results showed that the elderly longevity group had higher abilities in short-chain fatty acid metabolism, amino acid metabolism, and xenobiotic biodegradation. Taken together, our study provides characteristic information on GM in the long-lived elderly population in Changshou Town. This study can serve as a valuable addition to the current research on age-related GM. KEY POINTS: • The gut microbiota of elderly individuals with longevity and low BMI exhibit higher alpha diversity • Gut microbiota diversity did not differ significantly between genders in the elderly population • Several potentially beneficial bacteria (e.g., Akkermansia and Lactobacillus) are enriched in long-lived individuals.
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Affiliation(s)
- Xu Ai
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China
| | - Yu Liu
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China
| | - Jinrong Shi
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China
| | - Xiongwei Xie
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China
| | - Linzi Li
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China
| | - Rui Duan
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China
| | - Yongling Lv
- Maintainbiotech. Ltd. (Wuhan), Wuhan, 430000, Hubei, China
| | - Kai Xiong
- Maintainbiotech. Ltd. (Wuhan), Wuhan, 430000, Hubei, China
| | - Yuanxin Miao
- Research Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, 448000, Hubei, China.
| | - Yonglian Zhang
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, 448000, Hubei, China.
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Yang S, Wu S, Zhao F, Zhao Z, Shen X, Yu X, Zhang M, Wen F, Sun Z, Menghe B. Diversity Analysis of Intestinal Bifidobacteria in the Hohhot Population. Microorganisms 2024; 12:756. [PMID: 38674700 PMCID: PMC11051944 DOI: 10.3390/microorganisms12040756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
(1) Background: Bifidobacterium plays a pivotal role within the gut microbiota, significantly affecting host health through its abundance and composition in the intestine. Factors such as age, gender, and living environment exert considerable influence on the gut microbiota, yet scant attention has been directed towards understanding the specific effects of these factors on the Bifidobacterium population. Therefore, this study focused on 98 adult fecal samples to conduct absolute and relative quantitative analyses of bifidobacteria. (2) Methods: Using droplet digital PCR and the PacBio Sequel II sequencing platform, this study sought to determine the influence of various factors, including living environment, age, and BMI, on the absolute content and biodiversity of intestinal bifidobacteria. (3) Results: Quantitative results indicated that the bifidobacteria content in the intestinal tract ranged from 106 to 109 CFU/g. Notably, the number of bifidobacteria in the intestinal tract of the school population surpassed that of the off-campus population significantly (p = 0.003). Additionally, the group of young people exhibited a significantly higher count of bifidobacteria than the middle-aged and elderly groups (p = 0.041). The normal-weight group displayed a significantly higher bifidobacteria count than the obese group (p = 0.027). Further analysis of the relative abundance of bifidobacteria under different influencing factors revealed that the living environment emerged as the primary factor affecting the intestinal bifidobacteria structure (p = 0.046, R2 = 2.411). Moreover, the diversity of bifidobacteria in the intestinal tract of college students surpassed that in the out-of-school population (p = 0.034). This was characterized by a notable increase in 11 strains, including B. longum, B. bifidum, and B. pseudolongum, in the intestinal tract of college students, forming a more intricate intestinal bifidobacteria interaction network. (4) Conclusions: In summary, this study elucidated the principal factors affecting intestinal bifidobacteria and delineated their characteristics of intestinal bifidobacteria in diverse populations. By enriching the theory surrounding gut microbiota and health, this study provides essential data support for further investigations into the intricate dynamics of the gut microbiota.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Bilige Menghe
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.Y.); (S.W.); (F.W.)
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Heath H, Mogol AN, Santaliz Casiano A, Zuo Q, Madak-Erdogan Z. Targeting systemic and gut microbial metabolism in ER + breast cancer. Trends Endocrinol Metab 2024; 35:321-330. [PMID: 38220576 DOI: 10.1016/j.tem.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
Estrogen receptor-positive (ER+) breast tumors have a better overall prognosis than ER- tumors; however, there is a sustained risk of recurrence. Mounting evidence indicates that genetic and epigenetic changes associated with resistance impact critical signaling pathways governing cell metabolism. This review delves into recent literature concerning the metabolic pathways regulated in ER+ breast tumors by the availability of nutrients and endocrine therapies and summarizes research on how changes in systemic and gut microbial metabolism can affect ER activity and responsiveness to endocrine therapy. As targeting of metabolic pathways using dietary or pharmacological approaches enters the clinic, we provide an overview of the supporting literature and suggest future directions.
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Affiliation(s)
- Hannah Heath
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ayca Nazli Mogol
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Qianying Zuo
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Zeynep Madak-Erdogan
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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44
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Santos‐Beneit F. What is the role of microbial biotechnology and genetic engineering in medicine? Microbiologyopen 2024; 13:e1406. [PMID: 38556942 PMCID: PMC10982607 DOI: 10.1002/mbo3.1406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Microbial products are essential for developing various therapeutic agents, including antibiotics, anticancer drugs, vaccines, and therapeutic enzymes. Genetic engineering techniques, functional genomics, and synthetic biology unlock previously uncharacterized natural products. This review highlights major advances in microbial biotechnology, focusing on gene-based technologies for medical applications.
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Affiliation(s)
- Fernando Santos‐Beneit
- Institute of Sustainable ProcessesValladolidSpain
- Department of Chemical Engineering and Environmental Technology, School of Industrial EngineeringUniversity of ValladolidValladolidSpain
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Ho PY, Huang KC. Challenges in quantifying functional redundancy and selection in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586891. [PMID: 38586050 PMCID: PMC10996602 DOI: 10.1101/2024.03.26.586891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Microbiomes can exhibit large variations in species abundances but high reproducibility in abundances of functional units, an observation often considered evidence for functional redundancy. Based on such reduction in functional variability, selection is hypothesized to act on functional units in these ecosystems. However, the link between functional redundancy and selection remains unclear. Here, we show that reduction in functional variability does not always imply selection on functional profiles. We propose empirical null models to account for the confounding effects of statistical averaging and bias toward environment-independent beneficial functions. We apply our models to existing data sets, and find that the abundances of metabolic groups within microbial communities from bromeliad foliage do not exhibit any evidence of the previously hypothesized functional selection. By contrast, communities of soil bacteria or human gut commensals grown in vitro are selected for metabolic capabilities. By separating the effects of averaging and functional bias on functional variability, we find that the appearance of functional selection in gut microbiome samples from the Human Microbiome Project is artifactual, and that there is no evidence of selection for any molecular function represented by KEGG orthology. These concepts articulate a basic framework for quantifying functional redundancy and selection, advancing our understanding of the mapping between microbiome taxonomy and function.
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da C. Pinaffi-Langley AC, Melia E, Hays FA. Exploring the Gut-Mitochondrial Axis: p66Shc Adapter Protein and Its Implications for Metabolic Disorders. Int J Mol Sci 2024; 25:3656. [PMID: 38612468 PMCID: PMC11011581 DOI: 10.3390/ijms25073656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
This review investigates the multifaceted role of the p66Shc adaptor protein and the gut microbiota in regulating mitochondrial function and oxidative stress, and their collective impact on the pathogenesis of chronic diseases. The study delves into the molecular mechanisms by which p66Shc influences cellular stress responses through Rac1 activation, Forkhead-type transcription factors inactivation, and mitochondria-mediated apoptosis, alongside modulatory effects of gut microbiota-derived metabolites and endotoxins. Employing an integrative approach, the review synthesizes findings from a broad array of studies, including molecular biology techniques and analyses of microbial metabolites' impacts on host cellular pathways. The results underscore a complex interplay between microbial metabolites, p66Shc activation, and mitochondrial dysfunction, highlighting the significance of the gut microbiome in influencing disease outcomes through oxidative stress pathways. Conclusively, the review posits that targeting the gut microbiota-p66Shc-mitochondrial axis could offer novel therapeutic strategies for mitigating the development and progression of metabolic diseases. This underscores the potential of dietary interventions and microbiota modulation in managing oxidative stress and inflammation, pivotal factors in chronic disease etiology.
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Affiliation(s)
- Ana Clara da C. Pinaffi-Langley
- Department of Nutritional Sciences, College of Allied Health, University of Oklahoma Health Sciences, Oklahoma City, OK 73117, USA; (A.C.d.C.P.-L.); (E.M.)
| | - Elizabeth Melia
- Department of Nutritional Sciences, College of Allied Health, University of Oklahoma Health Sciences, Oklahoma City, OK 73117, USA; (A.C.d.C.P.-L.); (E.M.)
| | - Franklin A. Hays
- Department of Nutritional Sciences, College of Allied Health, University of Oklahoma Health Sciences, Oklahoma City, OK 73117, USA; (A.C.d.C.P.-L.); (E.M.)
- Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK 73117, USA
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Jans M, Vereecke L. A guide to germ-free and gnotobiotic mouse technology to study health and disease. FEBS J 2024. [PMID: 38523409 DOI: 10.1111/febs.17124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/17/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
The intestinal microbiota has major influence on human physiology and modulates health and disease. Complex host-microbe interactions regulate various homeostatic processes, including metabolism and immune function, while disturbances in microbiota composition (dysbiosis) are associated with a plethora of human diseases and are believed to modulate disease initiation, progression and therapy response. The vast complexity of the human microbiota and its metabolic output represents a great challenge in unraveling the molecular basis of host-microbe interactions in specific physiological contexts. To increase our understanding of these interactions, functional microbiota research using animal models in a reductionistic setting are essential. In the dynamic landscape of gut microbiota research, the use of germ-free and gnotobiotic mouse technology, in which causal disease-driving mechanisms can be dissected, represents a pivotal investigative tool for functional microbiota research in health and disease, in which causal disease-driving mechanisms can be dissected. A better understanding of the health-modulating functions of the microbiota opens perspectives for improved therapies in many diseases. In this review, we discuss practical considerations for the design and execution of germ-free and gnotobiotic experiments, including considerations around germ-free rederivation and housing conditions, route and timing of microbial administration, and dosing protocols. This comprehensive overview aims to provide researchers with valuable insights for improved experimental design in the field of functional microbiota research.
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Affiliation(s)
- Maude Jans
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Lars Vereecke
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Belgium
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Widder S, Carmody L, Opron K, Kalikin L, Caverly L, LiPuma J. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. RESEARCH SQUARE 2024:rs.3.rs-4128740. [PMID: 38562856 PMCID: PMC10984025 DOI: 10.21203/rs.3.rs-4128740/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed bacterial communities in 880 CF sputum samples and developed microbiome descriptors to model community reorganization prior to and during 18 PEx. We identified two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx showed hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx displayed stochasticity and increased diversity. A simulation of antimicrobial treatment predicted better efficacy for hierarchically organized communities. This link between PEx type, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.
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García-Gamboa R, Díaz-Torres O, Senés-Guerrero C, Gradilla-Hernández MS, Moya A, Pérez-Brocal V, Garcia-Gonzalez A, González-Avila M. Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight. Sci Rep 2024; 14:5703. [PMID: 38459054 PMCID: PMC10923939 DOI: 10.1038/s41598-024-54782-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
This study examined the interplay between bacterial and fungal communities in the human gut microbiota, impacting on nutritional status and body weight. Cohorts of 10 participants of healthy weight, 10 overweight, and 10 obese individuals, underwent comprehensive analysis, including dietary, anthropometric, and biochemical evaluations. Microbial composition was studied via gene sequencing of 16S and ITS rDNA regions, revealing bacterial (bacteriota) and fungal (mycobiota) profiles. Bacterial diversity exceeded fungal diversity. Statistically significant differences in bacterial communities were found within healthy-weight, overweight, and obese groups. The Bacillota/Bacteroidota ratio (previously known as the Firmicutes/Bacteroidetes ratio) correlated positively with body mass index. The predominant fungal phyla were Ascomycota and Basidiomycota, with the genera Nakaseomyces, Kazachstania, Kluyveromyces, and Hanseniaspora, inversely correlating with weight gain; while Saccharomyces, Debaryomyces, and Pichia correlated positively with body mass index. Overweight and obese individuals who harbored a higher abundance of Akkermansia muciniphila, demonstrated a favorable lipid and glucose profiles in contrast to those with lower abundance. The overweight group had elevated Candida, positively linked to simple carbohydrate consumption. The study underscores the role of microbial taxa in body mass index and metabolic health. An imbalanced gut bacteriota/mycobiota may contribute to obesity/metabolic disorders, highlighting the significance of investigating both communities.
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Affiliation(s)
- Ricardo García-Gamboa
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Av. Normalistas No. 800, col Colinas de la Normal, 44270, Guadalajara, Jalisco, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. General Ramon Corona 2514, Nuevo Mexico, 45138, Zapopan, Jalisco, Mexico
| | - Osiris Díaz-Torres
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, 45138, Zapopan, Jalisco, Mexico
| | - Carolina Senés-Guerrero
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, 45138, Zapopan, Jalisco, Mexico
| | - Misael Sebastián Gradilla-Hernández
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, 45138, Zapopan, Jalisco, Mexico
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Alejandro Garcia-Gonzalez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. General Ramon Corona 2514, Nuevo Mexico, 45138, Zapopan, Jalisco, Mexico
| | - Marisela González-Avila
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Av. Normalistas No. 800, col Colinas de la Normal, 44270, Guadalajara, Jalisco, Mexico.
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Duarte RDC, Iannetta PPM, Gomes AM, Vasconcelos MW. More than a meat- or synthetic nitrogen fertiliser-substitute: a review of legume phytochemicals as drivers of 'One Health' via their influence on the functional diversity of soil- and gut-microbes. FRONTIERS IN PLANT SCIENCE 2024; 15:1337653. [PMID: 38450400 PMCID: PMC10915056 DOI: 10.3389/fpls.2024.1337653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Legumes are essential to healthy agroecosystems, with a rich phytochemical content that impacts overall human and animal well-being and environmental sustainability. While these phytochemicals can have both positive and negative effects, legumes have traditionally been bred to produce genotypes with lower levels of certain plant phytochemicals, specifically those commonly termed as 'antifeedants' including phenolic compounds, saponins, alkaloids, tannins, and raffinose family oligosaccharides (RFOs). However, when incorporated into a balanced diet, such legume phytochemicals can offer health benefits for both humans and animals. They can positively influence the human gut microbiome by promoting the growth of beneficial bacteria, contributing to gut health, and demonstrating anti-inflammatory and antioxidant properties. Beyond their nutritional value, legume phytochemicals also play a vital role in soil health. The phytochemical containing residues from their shoots and roots usually remain in-field to positively affect soil nutrient status and microbiome diversity, so enhancing soil functions and benefiting performance and yield of following crops. This review explores the role of legume phytochemicals from a 'one health' perspective, examining their on soil- and gut-microbial ecology, bridging the gap between human nutrition and agroecological science.
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Affiliation(s)
- Rafael D. C. Duarte
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Pietro P. M. Iannetta
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
- Ecological Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Ana M. Gomes
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Marta W. Vasconcelos
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
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