1
|
Lu R, Luo XM. The role of gut microbiota in different murine models of systemic lupus erythematosus. Autoimmunity 2024; 57:2378876. [PMID: 39014962 DOI: 10.1080/08916934.2024.2378876] [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: 04/30/2024] [Accepted: 07/07/2024] [Indexed: 07/18/2024]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by immune system dysfunction that can lead to serious health issues and mortality. Recent investigations highlight the role of gut microbiota alterations in modulating inflammation and disease severity in SLE. This review specifically summaries the variations in gut microbiota composition across various murine models of lupus. By focusing on these differences, we aim to elucidate the intricate relationship between gut microbiota dysbiosis and the development and progression of SLE in preclinical settings.
Collapse
Affiliation(s)
- Ran Lu
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Xin M Luo
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
2
|
Que M, Li S, Xia Q, Li X, Luo X, Zhan G, Luo A. Microbiota-gut-brain axis in perioperative neurocognitive and depressive disorders: Pathogenesis to treatment. Neurobiol Dis 2024; 200:106627. [PMID: 39111702 DOI: 10.1016/j.nbd.2024.106627] [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: 06/04/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
An increasing number of people undergo anesthesia and surgery. Perioperative neurocognitive and depressive disorders are common central nervous system complications with similar pathogeneses. These conditions pose a deleterious threat to human health and a significant societal burden. In recent years, numerous studies have focused on the role of the gut microbiota and its metabolites in the central nervous system via the gut-brain axis. Its involvement in perioperative neurocognitive and depressive disorders has attracted considerable attention. This review aimed to elucidate the role of the gut microbiota and its metabolites in the pathogenesis of perioperative neurocognitive and depressive disorders, as well as the value of targeted interventions and treatments.
Collapse
Affiliation(s)
- Mengxin Que
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiyong Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Xia
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Gaofeng Zhan
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ailin Luo
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
3
|
Boverhoff D, Kool J, Pijnacker R, Ducarmon QR, Zeller G, Shetty S, Sie S, Mulder AC, van der Klis F, Franz E, Mughini-Gras L, van Baarle D, Fuentes S. Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands. Cell Rep 2024; 43:114729. [PMID: 39264809 DOI: 10.1016/j.celrep.2024.114729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/23/2024] [Accepted: 08/22/2024] [Indexed: 09/14/2024] Open
Abstract
Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.
Collapse
Affiliation(s)
- David Boverhoff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Quinten R Ducarmon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sudarshan Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephan Sie
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Annemieke Christine Mulder
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Fiona van der Klis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Debbie van Baarle
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
| |
Collapse
|
4
|
Novielli P, Romano D, Magarelli M, Diacono D, Monaco A, Amoroso N, Vacca M, De Angelis M, Bellotti R, Tangaro S. Personalized identification of autism-related bacteria in the gut microbiome using explainable artificial intelligence. iScience 2024; 27:110709. [PMID: 39286497 PMCID: PMC11402656 DOI: 10.1016/j.isci.2024.110709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/05/2024] [Accepted: 08/07/2024] [Indexed: 09/19/2024] Open
Abstract
Autism spectrum disorder (ASD) affects social interaction and communication. Emerging evidence links ASD to gut microbiome alterations, suggesting that microbial composition may play a role in the disorder. This study employs explainable artificial intelligence (XAI) to examine the contributions of individual microbial species to ASD. By using local explanation embeddings and unsupervised clustering, the research identifies distinct ASD subgroups, underscoring the disorder's heterogeneity. Specific microbial biomarkers associated with ASD are revealed, and the best classifiers achieved an AU-ROC of 0.965 ± 0.005 and an AU-PRC of 0.967 ± 0.008. The findings support the notion that gut microbiome composition varies significantly among individuals with ASD. This work's broader significance lies in its potential to inform personalized interventions, enhancing precision in ASD management and classification. These insights highlight the importance of individualized microbiome profiles for developing tailored therapeutic strategies for ASD.
Collapse
Affiliation(s)
- Pierfrancesco Novielli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Donato Romano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Michele Magarelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - Domenico Diacono
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
- Dipartimento Interateneo di Fisica "M. Merlin", Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Mirco Vacca
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - Maria De Angelis
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
- Dipartimento Interateneo di Fisica "M. Merlin", Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Sabina Tangaro
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| |
Collapse
|
5
|
da Silva VG, Smith NW, Mullaney JA, Wall C, Roy NC, McNabb WC. Food-breastmilk combinations alter the colonic microbiome of weaning infants: an in silico study. mSystems 2024; 9:e0057724. [PMID: 39191378 PMCID: PMC11406890 DOI: 10.1128/msystems.00577-24] [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: 04/22/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
The introduction of solid foods to infants, also known as weaning, is a critical point for the development of the complex microbial community inhabiting the human colon, impacting host physiology in infancy and later in life. This research investigated in silico the impact of food-breastmilk combinations on growth and metabolite production by colonic microbes of New Zealand weaning infants using the metagenome-scale metabolic model named Microbial Community. Eighty-nine foods were individually combined with breastmilk, and the 12 combinations with the strongest influence on the microbial production of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were identified. Fiber-rich and polyphenol-rich foods, like pumpkin and blackcurrant, resulted in the greatest increase in predicted fluxes of total SCFAs and individual fluxes of propionate and acetate when combined, respectively, with breastmilk. Identified foods were further combined with other foods and breastmilk, resulting in 66 multiple food-breastmilk combinations. These combinations altered in silico the impact of individual foods on the microbial production of SCFAs and BCFAs, suggesting that the interaction between the dietary compounds composing a meal is the key factor influencing colonic microbes. Blackcurrant combined with other foods and breastmilk promoted the greatest increase in the production of acetate and total SCFAs, while pork combined with other foods and breastmilk decreased the production of total BCFAs.IMPORTANCELittle is known about the influence of complementary foods on the colonic microbiome of weaning infants. Traditional in vitro and in vivo microbiome methods are limited by their resource-consuming concerns. Modeling approaches represent a promising complementary tool to provide insights into the behavior of microbial communities. This study evaluated how foods combined with other foods and human milk affect the production of short-chain fatty acids and branched-chain fatty acids by colonic microbes of weaning infants using a rapid and inexpensive in silico approach. Foods and food combinations identified here are candidates for future experimental investigations, helping to fill a crucial knowledge gap in infant nutrition.
Collapse
Affiliation(s)
- Vitor G da Silva
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nick W Smith
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jane A Mullaney
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- AgResearch, Palmerston North, New Zealand
| | - Clare Wall
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Nutrition and Dietetics, The University of Auckland, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| |
Collapse
|
6
|
Dommann J, Kerbl-Knapp J, Albertos Torres D, Egli A, Keiser J, Schneeberger PHH. A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities. mSystems 2024:e0085924. [PMID: 39254034 DOI: 10.1128/msystems.00859-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 08/19/2024] [Indexed: 09/11/2024] Open
Abstract
Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cramér's V = 0.857, and Theil's U = 0.316). For species-level community profiling, we found strong correlations (rs > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average rs = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.
Collapse
Affiliation(s)
- Julian Dommann
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Jakob Kerbl-Knapp
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Diana Albertos Torres
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Pierre H H Schneeberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| |
Collapse
|
7
|
Dora D, Szőcs E, Soós Á, Halasy V, Somodi C, Mihucz A, Rostás M, Mógor F, Lohinai Z, Nagy N. From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy. Front Immunol 2024; 15:1434804. [PMID: 39301033 PMCID: PMC11410641 DOI: 10.3389/fimmu.2024.1434804] [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: 05/18/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024] Open
Abstract
This comprehensive review undertakes a multidisciplinary exploration of the gut-lung axis, from the foundational aspects of anatomy, embryology, and histology, through the functional dynamics of pathophysiology, to implications for clinical science. The gut-lung axis, a bidirectional communication pathway, is central to understanding the interconnectedness of the gastrointestinal- and respiratory systems, both of which share embryological origins and engage in a continuous immunological crosstalk to maintain homeostasis and defend against external noxa. An essential component of this axis is the mucosa-associated lymphoid tissue system (MALT), which orchestrates immune responses across these distant sites. The review delves into the role of the gut microbiome in modulating these interactions, highlighting how microbial dysbiosis and increased gut permeability ("leaky gut") can precipitate systemic inflammation and exacerbate respiratory conditions. Moreover, we thoroughly present the implication of the axis in oncological practice, particularly in lung cancer development and response to cancer immunotherapies. Our work seeks not only to synthesize current knowledge across the spectrum of science related to the gut-lung axis but also to inspire future interdisciplinary research that bridges gaps between basic science and clinical application. Our ultimate goal was to underscore the importance of a holistic understanding of the gut-lung axis, advocating for an integrated approach to unravel its complexities in human health and disease.
Collapse
Affiliation(s)
- David Dora
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Emőke Szőcs
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Ádám Soós
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Viktória Halasy
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Csenge Somodi
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Anna Mihucz
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Melinda Rostás
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Fruzsina Mógor
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Zoltan Lohinai
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Nándor Nagy
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| |
Collapse
|
8
|
Bibi S, Kerbiriou C, Uzma, Mckirdy S, Kostrytsia A, Rasheed H, Eqani SAMAS, Gerasimidis K, Nurulain SM, Ijaz UZ. Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116959. [PMID: 39232295 DOI: 10.1016/j.ecoenv.2024.116959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 08/16/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Endemic fluorosis refers to the condition when individuals are exposed to excessive amounts of fluoride ion due to living in a region characterized by elevated levels of fluorine in the drinking water, food, and/or air. In Pakistan, a substantial proportion of the population is thereby affected, posing a public health concern. OBJECTIVES Assessing how the gut microbiota and its metabolic profiles are impacted by chronic exposure to fluoride in drinking water (that caused Dental Fluorosis) as well as to perceive how this microbiota is connected to adverse health outcomes prevailing with fluoride exposure. METHODS Drinking water (n=27) and biological samples (n=100) of blood, urine and feces were collected from 70 high fluoride exposed (with Dental Fluorosis) and 30 healthy control (without Dental Fluorosis) subjects. Water and urinary fluoride concentrations were determined. Serum/plasma biochemical testing was performed. Fecal DNA extraction, 16S rRNA analysis of microbial taxa, their predicted metabolic function and fecal short chain fatty acids (SCFAs) quantification were carried out. RESULTS The study revealed that microbiota taxonomic shifts and their metabolic characterization had been linked to certain host clinical parameters under the chronic fluoride exposure. Some sets of genera showed strong specificity to water and urine fluoride concentrations, Relative Fat Mass index and SCFAs. The SCFAs response in fluoride-exposed samples was observed to be correlated with bacterial taxa that could contribute to adverse health effects. CONCLUSIONS Microbial dysbiosis as a result of endemic fluorosis exhibits a structure that is associated with risk of metabolic deregulation and is implicated in various diseases. Our results may form the development of novel interventions and may have utility in diagnosis and monitoring.
Collapse
Affiliation(s)
- Sara Bibi
- Department of Biosciences, COMSATS University Islamabad, 45550, Pakistan; Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow G11 6EW, UK
| | - Caroline Kerbiriou
- School of Medicine, Dentistry & Nursing, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Uzma
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow G11 6EW, UK
| | - Shona Mckirdy
- School of Medicine, Dentistry & Nursing, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Anastasiia Kostrytsia
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow G11 6EW, UK
| | - Hifza Rasheed
- National Water Quality Laboratory, Pakistan Council of Research in Water Resources (PCRWR), Islamabad, Pakistan
| | | | | | | | - Umer Zeeshan Ijaz
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow G11 6EW, UK; Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L69 7BE, UK; National University of Ireland, University Road, Galway H91 TK33, Ireland.
| |
Collapse
|
9
|
Cheng T, Wen P, Yu R, Zhang F, Li H, Xu X, Zhao D, Liu F, Su W, Zheng Z, Yang H, Yao J, Jin L. Integrative microbiome and metabolome profiles reveal the impacts of periodontitis via oral-gut axis in first-trimester pregnant women. J Transl Med 2024; 22:819. [PMID: 39227984 PMCID: PMC11370083 DOI: 10.1186/s12967-024-05579-9] [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: 05/24/2024] [Accepted: 08/04/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Periodontitis results from host-microbe dysbiosis and the resultant dysregulated immunoinflammatory response. Importantly, it closely links to numerous systemic comorbidities, and perplexingly contributes to adverse pregnancy outcomes (APOs). Currently, there are limited studies on the distal consequences of periodontitis via oral-gut axis in pregnant women. This study investigated the integrative microbiome-metabolome profiles through multi-omics approaches in first-trimester pregnant women and explored the translational potentials. METHODS We collected samples of subgingival plaques, saliva, sera and stool from 54 Chinese pregnant women at the first trimester, including 31 maternal periodontitis (Perio) subjects and 23 Non-Perio controls. By integrating 16S rRNA sequencing, untargeted metabolomics and clinical traits, we explored the oral-gut microbial and metabolic connection resulting from periodontitis among early pregnant women. RESULTS We demonstrated a novel bacterial distinguisher Coprococcus from feces of periodontitis subjects in association with subgingival periodontopathogens, being different from other fecal genera in Lachnospiraceae family. The ratio of fecal Coprococcus to Lachnoclostridium could discriminate between Perio and Non-Perio groups as the ratio of subgingival Porphyromonas to Rothia did. Furthermore, there were differentially abundant fecal metabolic features pivotally enriched in periodontitis subjects like L-urobilin and kynurenic acid. We revealed a periodontitis-oriented integrative network cluster, which was centered with fecal Coprococcus and L-urobilin as well as serum triglyceride. CONCLUSIONS The current findings about the notable influence of periodontitis on fecal microbiota and metabolites in first-trimester pregnant women via oral-gut axis signify the importance and translational implications of preconceptional oral/periodontal healthcare for enhancing maternal wellbeing.
Collapse
Affiliation(s)
- Tianfan Cheng
- Division of Periodontology & Implant Dentistry, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China.
| | - Ping Wen
- Institute of Maternal and Child Medicine & Shenzhen Key Laboratory of Maternal and Child Health and Diseases, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Rong Yu
- Institute of Maternal and Child Medicine & Shenzhen Key Laboratory of Maternal and Child Health and Diseases, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Feng Zhang
- Division of Stomatology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Huijun Li
- Division of Stomatology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Xiaoyi Xu
- Institute of Maternal and Child Medicine & Shenzhen Key Laboratory of Maternal and Child Health and Diseases, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
- Center for Disease Control and Prevention, Shenzhen, China
| | - Dan Zhao
- Division of Periodontology & Implant Dentistry, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
- Department of Implant Dentistry, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Fang Liu
- Division of Obstetrics & Gynecology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Weilan Su
- Division of Obstetrics & Gynecology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Zheng Zheng
- Division of Obstetrics & Gynecology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Hong Yang
- Division of Obstetrics & Gynecology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Jilong Yao
- Division of Obstetrics & Gynecology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Lijian Jin
- Division of Periodontology & Implant Dentistry, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
10
|
Liwinski T, Auer MK, Schröder J, Pieknik I, Casar C, Schwinge D, Henze L, Stalla GK, Lang UE, von Klitzing A, Briken P, Hildebrandt T, Desbuleux JC, Biedermann SV, Holterhus PM, Bang C, Schramm C, Fuss J. Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals. BMC Med 2024; 22:346. [PMID: 39218875 PMCID: PMC11367877 DOI: 10.1186/s12916-024-03548-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts. METHODS Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT. RESULTS While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R2 = 4.1%, P = 0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism. CONCLUSIONS This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes. TRIAL REGISTRATION Clinicaltrials.gov NCT02185274.
Collapse
Affiliation(s)
- Timur Liwinski
- Clinic for Adult Psychiatry, University Psychiatric Clinics, University of Basel, Wilhelm Klein-Strasse 27, Basel, CH-4002, Switzerland
| | - Matthias K Auer
- Medizinische Klinik and Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| | - Johanna Schröder
- Department of Psychology, Institute for Clinical Psychology and Psychotherapy, Medical School Hamburg, Hamburg, Germany
| | - Ina Pieknik
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| | - Christian Casar
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Dorothee Schwinge
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Lara Henze
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Günter K Stalla
- Medizinische Klinik and Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
- Medicover Neuroendocrinology, Munich, Germany
| | - Undine E Lang
- Clinic for Adult Psychiatry, University Psychiatric Clinics, University of Basel, Wilhelm Klein-Strasse 27, Basel, CH-4002, Switzerland
| | - Alina von Klitzing
- Institute for Sex Research, Sexual Medicine and Forensic Psychiatry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peer Briken
- Institute for Sex Research, Sexual Medicine and Forensic Psychiatry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Hildebrandt
- Department of Gynecology and Obstetrics, CCC Erlangen EMN, Friedrich Alexander University, Erlangen, Germany
| | - Jeanne C Desbuleux
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| | - Sarah V Biedermann
- Department of Psychiatry and Psychotherapy, Social and Emotional Neuroscience Group, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul-Martin Holterhus
- Division of Pediatric Endocrinology and Diabetes, Department of Children and Adolescent Medicine I, University Hospital of Schleswig-Holstein, Campus Kiel/Christian-Albrechts University of Kiel, Kiel, D-24105, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, Kiel, 24105, Germany
| | - Christoph Schramm
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Centre for Translational Immunology (HCTI), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Fuss
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| |
Collapse
|
11
|
Guo Y, Wang S, Wu X, Zhao R, Chang S, Ma C, Song S, Zeng S. Multi-Omics Reveals the Role of Arachidonic Acid Metabolism in the Gut-Follicle Axis for the Antral Follicular Development of Holstein Cows. Int J Mol Sci 2024; 25:9521. [PMID: 39273467 PMCID: PMC11395146 DOI: 10.3390/ijms25179521] [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: 07/06/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
In vitro embryonic technology is crucial for improving farm animal reproduction but is hampered by the poor quality of oocytes and insufficient development potential. This study investigated the relationships among changes in the gut microbiota and metabolism, serum features, and the follicular fluid metabolome atlas. Correlation network maps were constructed to reveal how the metabolites affect follicular development by regulating gene expression in granulosa cells. The superovulation synchronization results showed that the number of follicle diameters from 4 to 8 mm, qualified oocyte number, cleavage, and blastocyst rates were improved in the dairy heifers (DH) compared with the non-lactating multiparous dairy cows (NDC) groups. The gut microbiota was decreased in Rikenellaceae_RC9_gut_group, Alistipes, and Bifidobacterium, but increased in Firmicutes, Cyanobacteria, Fibrobacterota, Desulfobacterota, and Verrucomicrobiota in the NDC group, which was highly associated with phospholipid-related metabolites of gut microbiota and serum. Metabolomic profiling of the gut microbiota, serum, and follicular fluid further demonstrated that the co-metabolites were phosphocholine and linoleic acid. Moreover, the expression of genes related to arachidonic acid metabolism in granulosa cells was significantly correlated with phosphocholine and linoleic acid. The results in granulosa cells showed that the levels of PLCB1 and COX2, participating in arachidonic acid metabolism, were increased in the DH group, which improved the concentrations of PGD2 and PGF2α in the follicular fluid. Finally, the expression levels of apoptosis-related proteins, cytokines, and steroidogenesis-related genes in granulosa cells and the concentrations of steroid hormones in follicular fluid were determinants of follicular development. According to our results, gut microbiota-related phosphocholine and linoleic acid participate in arachidonic acid metabolism in granulosa cells through the gut-follicle axis, which regulates follicular development. These findings hold promise for enhancing follicular development and optimizing oocyte quality in subfertile dairy cows.
Collapse
Affiliation(s)
- Yajun Guo
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shiwei Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xuan Wu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Rong Zhao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Siyu Chang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chen Ma
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuang Song
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shenming Zeng
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
12
|
Crawford J, Liu S, Tao R, Kramer P, Bender S, Tao F. The ketogenic diet mitigates opioid-induced hyperalgesia by restoring short-chain fatty acids-producing bacteria in the gut. Pain 2024; 165:e106-e114. [PMID: 38452211 PMCID: PMC11333194 DOI: 10.1097/j.pain.0000000000003212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
ABSTRACT Opioids are commonly prescribed to patients with chronic pain. Chronic opioid usage comes with a slew of serious side effects, including opioid-induced hyperalgesia (OIH). The patients with long-term opioid treatment experience paradoxical increases in nociceptive hypersensitivity, namely, OIH. Currently, treatment options for OIH are extremely lacking. In this study, we show that the ketogenic diet recovers the abnormal pain behavior caused by chronic morphine treatment in male mice, and we further show that the therapeutic effect of the ketogenic diet is mediated through gut microbiome. Our 16S rRNA sequencing demonstrates that chronic morphine treatment causes changes in mouse gut microbiota, specifically a decrease in short-chain fatty acids-producing bacteria, and the sequencing data also show that the ketogenic diet rescues those bacteria in the mouse gut. More importantly, we show that supplementation with short-chain fatty acids (butyrate, propionate, and acetate) can delay the onset of OIH, indicating that short-chain fatty acids play a direct role in the development of OIH. Our findings suggest that gut microbiome could be targeted to treat OIH, and the ketogenic diet can be used as a complementary approach for pain relief in patients with chronic opioid treatment. We only used male mice in this study, and thus, our findings cannot be generalized to both sexes.
Collapse
Affiliation(s)
- Joshua Crawford
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, Dallas, Texas, USA
| | - Sufang Liu
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, Dallas, Texas, USA
| | - Ran Tao
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, Dallas, Texas, USA
| | - Phillip Kramer
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, Dallas, Texas, USA
| | - Steven Bender
- Department of Oral and Maxillofacial Surgery, Texas A&M University School of Dentistry, Dallas, Texas, USA
| | - Feng Tao
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, Dallas, Texas, USA
| |
Collapse
|
13
|
Liang Y, Khanthaphixay B, Reynolds J, Leigh PJ, Lim ML, Yoon JY. A smartphone-based approach for comprehensive soil microbiome profiling. APPLIED PHYSICS REVIEWS 2024; 11:031412. [PMID: 39221035 PMCID: PMC11307194 DOI: 10.1063/5.0174176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/09/2024] [Indexed: 09/04/2024]
Abstract
The soil microbiome is crucial for nutrient cycling, health, and plant growth. This study presents a smartphone-based approach as a low-cost and portable alternative to traditional methods for classifying bacterial species and characterizing microbial communities in soil samples. By harnessing bacterial autofluorescence detection and machine learning algorithms, the platform achieved an average accuracy of 88% in distinguishing common soil-related bacterial species despite the lack of biomarkers, nucleic acid amplification, or gene sequencing. Furthermore, it successfully identified dominant species within various bacterial mixtures with an accuracy of 76% and three-level soil health identification at an accuracy of 80%-82%, providing insights into microbial community dynamics. The influence of other soil conditions (pH and moisture) was relatively minor, showcasing the platform's robustness. Various field soil samples were also tested with this platform at 80% accuracy compared with the laboratory analyses, demonstrating the practicality and usability of this approach for on-site soil analysis. This study highlights the potential of the smartphone-based system as a valuable tool for soil assessment, microbial monitoring, and environmental management.
Collapse
Affiliation(s)
- Yan Liang
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
| | - Bradley Khanthaphixay
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Jocelyn Reynolds
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Preston J. Leigh
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Melissa L. Lim
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
| | | |
Collapse
|
14
|
Jan T, Negi R, Sharma B, Kumar S, Singh S, Rai AK, Shreaz S, Rustagi S, Chaudhary N, Kaur T, Kour D, Sheikh MA, Kumar K, Yadav AN, Ahmed N. Next generation probiotics for human health: An emerging perspective. Heliyon 2024; 10:e35980. [PMID: 39229543 PMCID: PMC11369468 DOI: 10.1016/j.heliyon.2024.e35980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/05/2024] Open
Abstract
Over recent years, the scientific community has acknowledged the crucial role of certain microbial strains inhabiting the intestinal ecosystem in promoting human health, and participating in various beneficial functions for the host. These microorganisms are now referred to as next-generation probiotics and are currently considered as biotherapeutic products and food or nutraceutical supplements. However, the majority of next-generation probiotic candidates pose nutritional demands and exhibit high sensitivity towards aerobic conditions, leading to numerous technological hurdles in large-scale production. This underscores the need for the development of suitable delivery systems capable of enhancing the viability and functionality of these probiotic strains. Currently, potential candidates for next generation probiotics (NGP) are being sought among gut bacteria linked to health, which include strains from the genera Bacteroids, Faecalibacterium, Akkermansia and Clostridium. In contrast to Lactobacillus spp. and Bifidobacterium spp., NGP, particularly Bacteroids spp. and Clostridium spp., appear to exhibit greater ambiguity regarding their potential to induce infectious diseases. The present review provides a comprehensive overview of NGPs in terms of their health beneficial effects, regulation framework and risk assessment targeting relevant criteria for commercialization in food and pharmaceutical markets.
Collapse
Affiliation(s)
- Tawseefa Jan
- Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Rajeshwari Negi
- Department of Genetics, Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Babita Sharma
- Department of Microbiology, Akal College of Basic Science, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Sanjeev Kumar
- Faculty of Agricultural Sciences, GLA University, Mathura, Uttar Pradesh, India
| | - Sangram Singh
- Department of Biochemistry, Dr. Ram Manohar Lohia Avadh University, Ayodhya, Uttar Pradesh, India
| | - Ashutosh Kumar Rai
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Sheikh Shreaz
- Desert Agriculture and Ecosystem Department, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Sarvesh Rustagi
- Depratment of Food Technology, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Nisha Chaudhary
- Depratment of Food Science and Technology, Agriculture University, Jodhpur, Rajasthan, India
| | - Tanvir Kaur
- Department of Genetics, Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Divjot Kour
- Department of Microbiology, Akal College of Basic Science, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Mohd Aaqib Sheikh
- Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Krishan Kumar
- Department of Food Technology, Rajiv Gandhi University, Doimukh, Arunachal Pradesh, India
| | - Ajar Nath Yadav
- Department of Genetics, Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
- Centre of Research Impact and Outcome, Chitkara University, Rajpura, Punjab, India
- Chitkara Center for Research and Development, Chitkara University, Himachal Pradesh, India
| | - Naseer Ahmed
- Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| |
Collapse
|
15
|
Zass L, Mwapagha LM, Louis-Jacques AF, Allali I, Mulindwa J, Kiran A, Hanachi M, Souiai O, Mulder N, Oduaran OH. Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit. Database (Oxford) 2024; 2024:baae062. [PMID: 39167718 PMCID: PMC11338178 DOI: 10.1093/database/baae062] [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: 04/10/2024] [Revised: 06/28/2024] [Accepted: 08/15/2024] [Indexed: 08/23/2024]
Abstract
Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.
Collapse
Affiliation(s)
- Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Lamech M Mwapagha
- Department of Biology, Chemistry and Physics, Faculty of Health, Natural Resources and Applied Sciences, Namibia University of Science and Technology, Private Bag 13388, 13 Jackson Kaujeua Street, Windhoek, Namibia
| | - Adetola F Louis-Jacques
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Florida, 1600 SW Archer Road, Gainesville, FL 32610, USA
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Julius Mulindwa
- Department of Biochemistry and Sports Sciences, College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Anmol Kiran
- Malawi-Liverpool-Wellcome Trust, P.O. Box 30096, Blantyre 3, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, 13, Place Pasteur, B.P. 74, Tunis 1002, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, 13, Place Pasteur, B.P. 74, Tunis 1002, Tunisia
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 9 Jubilee Road, Parktown 2193, Johannesburg, Johannesburg, South Africa
| |
Collapse
|
16
|
Mohr AE, Jasbi P, van Woerden I, Chi J, Gu H, Bruening M, Whisner CM. Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort. GUT MICROBES REPORTS 2024; 1:1-23. [PMID: 39221110 PMCID: PMC11361303 DOI: 10.1080/29933935.2024.2387936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.
Collapse
Affiliation(s)
- Alex E. Mohr
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Personalized Diagnostics, School of Molecular Sciences, Arizona State University, Tempe, AZ USA
| | - Irene van Woerden
- Community and Public Health, Idaho State University, Pocatello, ID, USA
| | - Jinhua Chi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Meg Bruening
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Nutritional Sciences, College of Health and Human Development, Pennsylvania State University, University Park, PA, USA
| | - Corrie M. Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
17
|
Barbero-Herranz R, Garriga-García M, Moreno-Blanco A, Palacios E, Ruiz-Sala P, Vicente-Santamaría S, Stanescu S, Belanger-Quintana A, Pintos-Morell G, Arconada B, del Campo R, Avendaño-Ortiz J. The Role of the Gut Microbiota in Sanfilippo Syndrome's Physiopathology: An Approach in Two Affected Siblings. Int J Mol Sci 2024; 25:8856. [PMID: 39201540 PMCID: PMC11354487 DOI: 10.3390/ijms25168856] [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: 06/22/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Sanfilippo syndrome, or mucopolysaccharidosis type III (MPS III), is a rare lysosomal disease caused by congenital enzymatic deficiencies in heparan sulfate (HS) degradation, leading to organ dysfunction. The most severe hallmark of MPS III comprises neurological alterations, although gastrointestinal symptoms (GISs) have also been shown to be relevant in many patients. Here, we explored the contribution of the gut microbiota to MPS III GISs. We analyzed the composition and functionality of the gut microbiota in two MPS III siblings with the same mutation (c.544C > T, c.1080delC, in the SGSH gene) and the same diet, but with differences in their GISs, including recurrent diarrhea in one of them. Using 16S sequencing, we observed that the MPS III patients exhibited decreased alpha diversity and a lower abundance of Lachnospiraceae and Bifidobacteriaceae accompanied by a higher abundance of the Ruminococcaceae and Rikenellaceae families than the healthy control subjects. Comparing siblings, we found an increased abundance of Bacteroidaceae and a lower abundance of Ruminococcaceae and Akkermansiaceae in the GIS-free patient. This patient also had a higher relative abundance of Sus genes (SusA, SusB, SusE, and SusG) involved in glycosaminoglycan metabolism. We found higher HS levels in the stool of the two MPS III patients than in healthy volunteers, particularly in the patient with GISs. Functionally, whole fecal metabolites from the patient with GISs induced oxidative stress in vitro in healthy monocytes. Finally, the Bacteroides thetaiotaomicron strain isolated from MPS III stool samples exhibited HS degradation ability. Overall, our results reveal different microbiota compositions and functionalities in MPS III siblings, who exhibited differential gastrointestinal symptomatology. Our study may serve as a gateway to explore the impact of the gut microbiota and its potential to enhance the quality of life in Sanfilippo syndrome patients.
Collapse
Affiliation(s)
- Raquel Barbero-Herranz
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (R.B.-H.); (A.M.-B.); (E.P.)
| | - María Garriga-García
- Endocrinology and Nutrition Service, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.G.-G.); (S.V.-S.)
| | - Ana Moreno-Blanco
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (R.B.-H.); (A.M.-B.); (E.P.)
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Esther Palacios
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (R.B.-H.); (A.M.-B.); (E.P.)
| | - Pedro Ruiz-Sala
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Autonomous University of Madrid (UAM), IdiPaz, 28049 Madrid, Spain;
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28049 Madrid, Spain
| | - Saioa Vicente-Santamaría
- Endocrinology and Nutrition Service, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.G.-G.); (S.V.-S.)
| | - Sinziana Stanescu
- Unidad de Enfermedades Metabólicas Hospital, CSUR, MetabERN, Pediatric Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (S.S.); (A.B.-Q.)
| | - Amaya Belanger-Quintana
- Unidad de Enfermedades Metabólicas Hospital, CSUR, MetabERN, Pediatric Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (S.S.); (A.B.-Q.)
| | - Guillem Pintos-Morell
- Vall d’Hebron Institut de Recerca (VHIR), Unidad de Enfermedades Raras, Hospital Vall d’Hebron Barcelona Hospital Campus, Comité Médico Consultivo MPS-Lisosomales, 08035 Barcelona, Spain;
| | - Beatriz Arconada
- Federación Española de Enfermedades Raras (FEDER), 28009 Madrid, Spain;
| | - Rosa del Campo
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (R.B.-H.); (A.M.-B.); (E.P.)
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Faculty of Health Sciences, Alfonso X El Sabio University, Villanueva de la Cañada, 28691 Madrid, Spain
| | - José Avendaño-Ortiz
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (R.B.-H.); (A.M.-B.); (E.P.)
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| |
Collapse
|
18
|
Yin XF, Ye T, Chen HL, Liu J, Mu XF, Li H, Wang J, Hu YJ, Cao H, Kang WQ. The microbiome compositional and functional differences between rectal mucosa and feces. Microbiol Spectr 2024; 12:e0354923. [PMID: 38916335 PMCID: PMC11302734 DOI: 10.1128/spectrum.03549-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population. IMPORTANCE This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.
Collapse
Affiliation(s)
- Xiao-Fei Yin
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Taoyu Ye
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Han-Lin Chen
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Junyan Liu
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Xue-Feng Mu
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hao Li
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Jun Wang
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
- Shenzhen Digital Life Institute, Shenzhen, China
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Yuan-Jia Hu
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hongzhi Cao
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
- Shenzhen Digital Life Institute, Shenzhen, China
- Department of Digital Health, South China Hospital of Shenzhen University, Shenzhen, China
| | - Wen-Quan Kang
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| |
Collapse
|
19
|
Schweitzer M, Wlasak M, Wassermann B, Marcher F, Poglitsch C, Pirker J, Berg G. 'Tiny Biome Tales': A gamified review about the influence of lifestyle choices on the human microbiome. Microb Biotechnol 2024; 17:e14544. [PMID: 39119866 PMCID: PMC11310763 DOI: 10.1111/1751-7915.14544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
In the last two decades, new discoveries from microbiome research have changed our understanding of human health. It became evident that daily habits and lifestyle choices shape the human microbiome and ultimately determine health or disease. Therefore, we developed 'Tiny Biome Tales' (https://microbiome.gamelabgraz.at/), a science pedagogy video game designed like a scientific review based exclusively on peer-reviewed articles, to teach about the influence of lifestyle choices on the human microbiome during pregnancy, early and adult life, and related health consequences. Despite the scientific character, it can be played by a broad audience. Here, we also present a scientific assessment and showed that playing the game significantly contributed to knowledge gain. The innovative style of the 'gamified review' represents an ideal platform to disseminate future findings from microbiome research by updating existing and adding new scenes to the game.
Collapse
Affiliation(s)
- Matthias Schweitzer
- Institute of Environmental BiotechnologyGraz University of TechnologyGrazAustria
| | - Maximilian Wlasak
- Institute of Interactive Systems and Data ScienceGraz University of TechnologyGrazAustria
| | - Birgit Wassermann
- Institute of Environmental BiotechnologyGraz University of TechnologyGrazAustria
| | - Florian Marcher
- Institute of Interactive Systems and Data ScienceGraz University of TechnologyGrazAustria
| | - Christian Poglitsch
- Institute of Interactive Systems and Data ScienceGraz University of TechnologyGrazAustria
| | - Johanna Pirker
- Institute of Interactive Systems and Data ScienceGraz University of TechnologyGrazAustria
- Institut für InformatikLudwig‐Maximilians‐UniversitätMunichGermany
| | - Gabriele Berg
- Institute of Environmental BiotechnologyGraz University of TechnologyGrazAustria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)PotsdamGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| |
Collapse
|
20
|
Hoisington AJ, Choy K, Khair S, Dyamenahalli KU, Najarro KM, Wiktor AJ, Frank DN, Burnham EL, McMahan RH, Kovacs EJ. Recent alcohol intake impacts microbiota in adult burn patients. Alcohol 2024; 118:25-35. [PMID: 38604285 PMCID: PMC11179986 DOI: 10.1016/j.alcohol.2024.04.003] [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: 10/12/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Alcohol use is associated with an increased incidence of negative health outcomes in burn patients due to biological mechanisms that include a dysregulated inflammatory response and increased intestinal permeability. This study used phosphatidylethanol (PEth) in blood, a direct biomarker of recent alcohol use, to investigate associations between a recent history of alcohol use and the fecal microbiota, short chain fatty acids, and inflammatory markers in the first week after a burn injury for nineteen participants. Burn patients were grouped according to PEth levels of low or high and differences in the overall fecal microbial community were observed between these cohorts. Two genera that contributed to the differences and had higher relative abundance in the low PEth burn patient group were Akkermansia, a mucin degrading bacteria that improves intestinal barrier function, and Bacteroides, a potentially anti-inflammatory bacteria. There was no statistically significant difference between levels of short chain fatty acids or intestinal permeability across the two groups. To our knowledge, this study represents the first report to evaluate the effects of burn injury and recent alcohol use on early post burn microbiota dysbiosis, inflammatory response, and levels of short chain fatty acids. Future studies in this field are warranted to better understand the factors associated with negative health outcomes and develop interventional trials.
Collapse
Affiliation(s)
- Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA; Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA; Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson Air Force Base, OH, USA
| | - Kevin Choy
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shanawaj Khair
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kiran U Dyamenahalli
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kevin M Najarro
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Veterans Health Administration, Eastern Colorado Health Care System, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
| | - Arek J Wiktor
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Daniel N Frank
- GI and Liver Innate Immune Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; Department of Medicine, Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ellen L Burnham
- Department of Medicine, Division of Infectious Diseases, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; Alcohol Research Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rachel H McMahan
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Veterans Health Administration, Eastern Colorado Health Care System, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
| | - Elizabeth J Kovacs
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA; Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Veterans Health Administration, Eastern Colorado Health Care System, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA; Alcohol Research Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
21
|
Kattel A, Aro V, Lahtvee P, Kazantseva J, Jõers A, Nahku R, Belouah I. Exploring the resilience and stability of a defined human gut microbiota consortium: An isothermal microcalorimetric study. Microbiologyopen 2024; 13:e1430. [PMID: 39115291 PMCID: PMC11307317 DOI: 10.1002/mbo3.1430] [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: 04/12/2024] [Revised: 07/08/2024] [Accepted: 07/20/2024] [Indexed: 08/11/2024] Open
Abstract
The gut microbiota significantly contributes to human health and well-being. The aim of this study was to evaluate the stability and resilience of a consortium composed of three next-generation probiotics (NGPs) candidates originally found in the human gut. The growth patterns of Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Faecalibacterium prausnitzii were studied both individually and consortium. The growth kinetics of Akkermansia muciniphila (A. muciniphila), Bacteroides thetaiotaomicron (B. thetaiotaomicron), and Faecalibacterium prausnitzii (F. prausnitzii) were characterized both individually and in consortium using isothermal microcalorimetry and 16S ribosomal RNA next-generation sequencing. The consortium reached stability after three passages and demonstrated resilience to changes in its initial composition. The concentration of butyrate produced was nearly twice as high in the consortium compared to the monoculture of F. prausnitzii. The experimental conditions and methodologies used in this article are a solid foundation for developing further complex consortia.
Collapse
Affiliation(s)
- Anna Kattel
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
| | - Valter Aro
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| | | | | | - Arvi Jõers
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| | - Ranno Nahku
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
| | - Isma Belouah
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| |
Collapse
|
22
|
Pieczyńska-Zając JM, Malinowska AM, Pruszyńska-Oszmałek E, Kołodziejski PA, Drzymała-Czyż S, Bajerska J. Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome. Nutrition 2024; 124:112450. [PMID: 38669829 DOI: 10.1016/j.nut.2024.112450] [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: 01/09/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVE It has been suggested that dysbiosis of the gut microbiota is associated with the pathogenesis of Polycystic Ovary Syndrome (PCOS), and that improper diet can aggravate these changes. This study thus aimed to investigate the effects of a high-fat/high-fructose (HF/HFr) diet on the gut microbial community and their metabolites in prepubertal female mice with letrozole (LET)-induced PCOS. We also tested the correlations between the relative abundance of microbial taxa and selected PCOS parameters. RESEARCH METHODS & PROCEDURES Thirty-two C57BL/6 mice were randomly divided into four groups (n = 8) and implanted with LET or a placebo, with simultaneous administration of a HF/HFr diet or standard diet (StD) for 5 wk. The blood and intestinal contents were collected after the sacrifice. RESULTS Placebo + HF/HFr and LET + HF/HFr had significantly higher microbial alpha diversity than either group fed StD. The LET-implanted mice fed StD had a significantly higher abundance of Prevotellaceae_UCG-001 than the placebo mice fed StD. Both groups fed the HF/HFr diet had significantly lower fecal levels of short-chain fatty acids than the placebo mice fed StD, while the LET + HF/HFr animals had significantly higher concentrations of lipopolysaccharides in blood serum than either the placebo or LET mice fed StD. Opposite correlations were observed between Turicibacter and Lactobacillus and the lipid profile, CONCLUSION: HF/HFr diet had a much stronger effect on the composition of the intestinal microbiota of prepubertal mice than LET itself.
Collapse
Affiliation(s)
| | - Anna Maria Malinowska
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ewa Pruszyńska-Oszmałek
- Department of Animal Physiology, Biochemistry and Biostructure, Poznań University of Life Sciences, Poznań, Poland
| | - Paweł Antoni Kołodziejski
- Department of Animal Physiology, Biochemistry and Biostructure, Poznań University of Life Sciences, Poznań, Poland
| | | | - Joanna Bajerska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, Poland.
| |
Collapse
|
23
|
Garcia-Villatoro EL, Ufondu A, Callaway ES, Allred KF, Safe SH, Chapkin RS, Jayaraman A, Allred CD. Aryl hydrocarbon receptor activity in intestinal epithelial cells in the formation of colonic tertiary lymphoid tissues. Am J Physiol Gastrointest Liver Physiol 2024; 327:G154-G174. [PMID: 38563893 DOI: 10.1152/ajpgi.00274.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
After birth, the development of secondary lymphoid tissues (SLTs) in the colon is dependent on the expression of the aryl hydrocarbon receptor (AhR) in immune cells as a response to the availability of AhR ligands. However, little is known about how AhR activity from intestinal epithelial cells (IECs) may influence the development of tertiary lymphoid tissues (TLTs). As organized structures that develop at sites of inflammation or infection during adulthood, TLTs serve as localized centers of adaptive immune responses, and their presence has been associated with the resolution of inflammation and tumorigenesis in the colon. Here, we investigated the effect of the conditional loss of AhR activity in IECs in the formation and immune cell composition of TLTs in a model of acute inflammation. In females, loss of AhR activity in IECs reduced the formation of TLTs without significantly changing disease outcomes or immune cell composition within TLTs. In males lacking AhR expression in IECs, increased disease activity index, lower expression of functional-IEC genes, increased number of TLTs, increased T-cell density, and lower B- to T-cell ratio were observed. These findings may represent an unfavorable prognosis when exposed to dextran sodium sulfate (DSS)-induced epithelial damage compared with females. Sex and loss of IEC AhR also resulted in changes in microbial populations in the gut. Collectively, these data suggest that the formation of TLTs in the colon is influenced by sex and AhR expression in IECs.NEW & NOTEWORTHY This is the first research of its kind to demonstrate a clear connection between biological sex and the development of tertiary lymphoid tissues (TLT) in the colon. In addition, the research finds that in a preclinical model of inflammatory bowel disease, the expression of the aryl hydrocarbon receptor (AhR) influences the development of these structures in a sex-specific manner.
Collapse
Affiliation(s)
- E L Garcia-Villatoro
- Department of Nutrition, Texas A&M University, College Station, Texas, United States
| | - A Ufondu
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States
| | - E S Callaway
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States
| | - K F Allred
- Department of Nutrition, Texas A&M University, College Station, Texas, United States
- Department of Nutrition, University of North Carolina Greensboro, Greensboro, North Carolina, United States
| | - S H Safe
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, United States
| | - R S Chapkin
- Department of Nutrition, Texas A&M University, College Station, Texas, United States
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas, United States
| | - A Jayaraman
- Department of Nutrition, Texas A&M University, College Station, Texas, United States
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States
| | - C D Allred
- Department of Nutrition, Texas A&M University, College Station, Texas, United States
- Department of Nutrition, University of North Carolina Greensboro, Greensboro, North Carolina, United States
| |
Collapse
|
24
|
Lin Q, Dorsett Y, Mirza A, Tremlett H, Piccio L, Longbrake EE, Choileain SN, Hafler DA, Cox LM, Weiner HL, Yamamura T, Chen K, Wu Y, Zhou Y. Meta-analysis identifies common gut microbiota associated with multiple sclerosis. Genome Med 2024; 16:94. [PMID: 39085949 PMCID: PMC11293023 DOI: 10.1186/s13073-024-01364-x] [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: 06/16/2023] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Previous studies have identified a diverse group of microbial taxa that differ between patients with multiple sclerosis (MS) and the healthy population. However, interpreting findings on MS-associated microbiota is challenging, as there is no true consensus. It is unclear whether there is gut microbiota commonly altered in MS across studies. METHODS To answer this, we performed a meta-analysis based on the 16S rRNA gene sequencing data from seven geographically and technically diverse studies comprising a total of 524 adult subjects (257 MS and 267 healthy controls). Analysis was conducted for each individual study after reprocessing the data and also by combining all data together. The blocked Wilcoxon rank-sum test and linear mixed-effects regression were used to identify differences in microbial composition and diversity between MS and healthy controls. Network analysis was conducted to identify bacterial correlations. A leave-one-out sensitivity analysis was performed to ensure the robustness of the findings. RESULTS The microbiome community structure was significantly different between studies. Re-analysis of data from individual studies revealed a lower relative abundance of Prevotella in MS across studies, compared to controls. Meta-analysis found that although alpha and beta diversity did not differ between MS and controls, a higher abundance of Actinomyces and a lower abundance of Faecalibacterium were reproducibly associated with MS. Additionally, network analysis revealed that the recognized negative Bacteroides-Prevotella correlation in controls was disrupted in patients with MS. CONCLUSIONS Our meta-analysis identified common gut microbiota associated with MS across geographically and technically diverse studies.
Collapse
Affiliation(s)
- Qingqi Lin
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Yair Dorsett
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Ali Mirza
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Helen Tremlett
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Brain and Mind Centre, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Erin E Longbrake
- Departments of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Siobhan Ni Choileain
- Departments of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Laura M Cox
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, 02115, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, 02115, USA
| | - Takashi Yamamura
- Department of Immunology, National Institute of Neuroscience, Tokyo, Japan
| | - Kun Chen
- Department of Statistics, University of Connecticut, Storrs, CT, USA
| | - Yufeng Wu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| |
Collapse
|
25
|
Zhou L, Yan Z, Yang S, Lu G, Nie Y, Ren Y, Xue Y, Shi JS, Xu ZH, Geng Y. High methionine intake alters gut microbiota and lipid profile and leads to liver steatosis in mice. Food Funct 2024; 15:8053-8069. [PMID: 38989659 DOI: 10.1039/d4fo01613k] [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: 07/12/2024]
Abstract
Methionine is an important sulfur-containing amino acid. Health effects of both methionine restriction (MR) and methionine supplementation (MS) have been studied. This study aimed to investigate the impact of a high-methionine diet (HMD) (1.64% methionine) on both the gut and liver functions in mice through multi-omic analyses. Hepatic steatosis and compromised gut barrier function were observed in mice fed the HMD. RNA-sequencing (RNA-seq) analysis of liver gene expression patterns revealed the upregulation of lipid synthesis and degradation pathways, cholesterol metabolism and inflammation-related nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Metagenomic sequencing of cecal content demonstrated a shift in gut microbial composition with an increased abundance of opportunistic pathogens and gut microbial functions with up-regulated lipopolysaccharide (LPS) biosynthesis in mice fed HMD. Metabolomic study of cecal content showed an altered gut lipid profile and the level of bioactive lipids, including docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), palmitoylethanolamide (PEA), linoleoyl ethanolamide (LEA) and arachidonoyl ethanolamide (AEA), that carry anti-inflammatory effects significantly reduced in the gut of mice fed the HMD. Correlation analysis demonstrated that gut microbiota was highly associated with liver and gut functions and gut bioactive lipid content. In conclusion, this study suggested that the HMD exerted negative impacts on both the gut and liver, and an adequate amount of methionine intake should be carefully determined to ensure normal physiological function without causing adverse effects.
Collapse
Affiliation(s)
- Lingxi Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhen Yan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
| | - Songfan Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
| | - Gexue Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
| | - Yawen Nie
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
| | - Yilin Ren
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yuzheng Xue
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
| | - Zheng-Hong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Innovation Center for Advanced Brewing Science and Technology, Sichuan University, Chengdu, China.
| | - Yan Geng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China.
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, China
| |
Collapse
|
26
|
Nicze M, Dec A, Borówka M, Krzyżak D, Bołdys A, Bułdak Ł, Okopień B. Molecular Mechanisms behind Obesity and Their Potential Exploitation in Current and Future Therapy. Int J Mol Sci 2024; 25:8202. [PMID: 39125772 PMCID: PMC11311839 DOI: 10.3390/ijms25158202] [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: 06/28/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Obesity is a chronic disease caused primarily by the imbalance between the amount of calories supplied to the body and energy expenditure. Not only does it deteriorate the quality of life, but most importantly it increases the risk of cardiovascular diseases and the development of type 2 diabetes mellitus, leading to reduced life expectancy. In this review, we would like to present the molecular pathomechanisms underlying obesity, which constitute the target points for the action of anti-obesity medications. These include the central nervous system, brain-gut-microbiome axis, gastrointestinal motility, and energy expenditure. A significant part of this article is dedicated to incretin-based drugs such as GLP-1 receptor agonists (e.g., liraglutide and semaglutide), as well as the brand new dual GLP-1 and GIP receptor agonist tirzepatide, all of which have become "block-buster" drugs due to their effectiveness in reducing body weight and beneficial effects on the patient's metabolic profile. Finally, this review article highlights newly designed molecules with the potential for future obesity management that are the subject of ongoing clinical trials.
Collapse
Affiliation(s)
- Michał Nicze
- Department of Internal Medicine and Clinical Pharmacology, Faculty of Medical Sciences, Medical University of Silesia in Katowice, Medyków 18, 40-752 Katowice, Poland (A.B.); (B.O.)
| | | | | | | | | | - Łukasz Bułdak
- Department of Internal Medicine and Clinical Pharmacology, Faculty of Medical Sciences, Medical University of Silesia in Katowice, Medyków 18, 40-752 Katowice, Poland (A.B.); (B.O.)
| | | |
Collapse
|
27
|
Aldisi D, Sabico S, Almiman A, Al-Farraj A, Basaeed TA, Wani K, Hussain SD, Ansari MGA, McTernan PG, Al-Daghri NM. Is freeze-dried superfood kale supplementation healthier than common green peas? Outcomes of a cross-over trial. Front Nutr 2024; 11:1370677. [PMID: 39114118 PMCID: PMC11303336 DOI: 10.3389/fnut.2024.1370677] [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: 01/15/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024] Open
Abstract
Kale (Brassica oleracea species) is considered a functional food whose macronutrient and phytochemical contents are considered beneficial and widely considered as a superfood. In the present 6-week cross-over trial with a 2-week washout period, we compared the beneficial effects of freeze-dried kale over peas among Arab women with obesity. A total of 124 Saudi women with obesity were allocated to receive either freeze-dried kale (n = 62) or freeze-dried peas (n = 62) given in the form of 3-gram sachets thrice daily for 2 weeks, followed by a 2-week washout period and a cross-over of 4 weeks. Anthropometric measurements, glucose, lipids and markers of gut barrier function were assessed at baseline and post-intervention. Participants who took kale supplementation first resulted in significant weight reduction (p = 0.02) which was not observed among those who took peas first. Participants receiving pea supplementation first experienced a significant decline in Hba1c (p = 0.005) and CD14 (p = 0.03), but C-peptide increased (p = 0.05). Crossover analysis revealed significant carryover effects in most variables with non-significant combined treatment effects. Among the variables with no carryover effect with significant combined treatment effect include HbA1c which was in favor of the pea group (p = 0.005) and C-peptide which was modestly in favor of the kale group (p = 0.05). While both freeze dried kale and pea supplementation appear beneficial, supplementation of freeze-dried pea appears to be more effective in terms of acute glycemic control than kale. The study suggests that common but less-hyped vegetables such as pea maybe equally, if not more beneficial than the more expensive promoted superfoods such as kale. Longer clinical trials using a parallel design instead of cross-over are recommended to strengthen present findings.
Collapse
Affiliation(s)
- Dara Aldisi
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaun Sabico
- Chair for Biomarkers of Chronic Diseases, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abeer Almiman
- Chair for Biomarkers of Chronic Diseases, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Amani Al-Farraj
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Taghreed A. Basaeed
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Kaiser Wani
- Chair for Biomarkers of Chronic Diseases, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Syed D. Hussain
- Chair for Biomarkers of Chronic Diseases, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed G. A. Ansari
- Chair for Biomarkers of Chronic Diseases, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Philip G. McTernan
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Nasser M. Al-Daghri
- Chair for Biomarkers of Chronic Diseases, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
28
|
Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL, Christakis NA. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. Cell Rep 2024; 43:114442. [PMID: 38968070 PMCID: PMC11290354 DOI: 10.1016/j.celrep.2024.114442] [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: 01/09/2024] [Revised: 04/27/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic data from a community-based cohort of 1,871 people from 19 isolated villages in the Mesoamerican highlands of western Honduras, we report associations between bacterial species and human phenotypes and factors. Among them, socioeconomic factors account for 51.44% of the total associations. Meta-analysis of species-level profiles across several datasets identified several species associated with body mass index, consistent with previous findings. Furthermore, the inclusion of strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially for some factors like household wealth (e.g., wealthier individuals harbor different strains of Eubacterium rectale). Our analysis suggests a role that gut microbiome surveillance can play in understanding broad features of individual and public health.
Collapse
Affiliation(s)
- Shivkumar Vishnempet Shridhar
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Francesco Beghini
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Marcus Alexander
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Adarsh Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| | - Nicholas A Christakis
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Medicine, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
29
|
Mombeek LMM, Boesmans W, Wilson DM. Genomic stress in diseases stemming from defects in the second brain. Neurogastroenterol Motil 2024:e14860. [PMID: 39004995 DOI: 10.1111/nmo.14860] [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: 02/15/2024] [Revised: 06/04/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024]
Abstract
This review discusses the less-explored realm of DNA damage and repair within the enteric nervous system (ENS), often referred to as the "second brain." While the central nervous system has been extensively studied for its DNA repair mechanisms and associated neuropathologies, the ENS, which can autonomously coordinate gastrointestinal function, experiences unique challenges and vulnerabilities related to its genome integrity. The susceptibility of the ENS to DNA damage is exacerbated by its limited protective barriers, resulting in not only endogenous genotoxic exposures, such as oxidative stress, but also exogenous threats, such as ingested environmental contaminants, local inflammatory responses, and gut dysbiosis. Here, we discuss the evidence for DNA repair defects in enteric neuropathies, most notably, the reported relationship between inherited mutations in RAD21 and LIG3 with chronic intestinal pseudo-obstruction and mitochondrial gastrointestinal encephalomyopathy disorders, respectively. We also introduce the lesser-recognized gastrointestinal complications in DNA repair syndromes, including conditions like Cockayne syndrome. The review concludes by pointing out the potential role of DNA repair defects in not only congenital disorders but also aging-related gut dysfunction, as well as the crucial need for further research to establish direct causal links between DNA damage accumulation and ENS-specific pathologic phenotypes.
Collapse
Affiliation(s)
- Lobke Marie M Mombeek
- Faculty of Medicine and Life Sciences, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Werend Boesmans
- Faculty of Medicine and Life Sciences, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- Department of Pathology, GROW Research Institute for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - David M Wilson
- Faculty of Medicine and Life Sciences, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Yu J, Chen X, Yang X, Zhang B. Understanding gut dysbiosis for hepatocellular carcinoma diagnosis and treatment. Trends Endocrinol Metab 2024:S1043-2760(24)00163-2. [PMID: 38969601 DOI: 10.1016/j.tem.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 07/07/2024]
Abstract
The gut microbiome can play a crucial role in hepatocellular carcinoma (HCC) progression through the enterohepatic circulation, primarily acting via metabolic reprogramming and alterations in the hepatic immune microenvironment triggered by microbe-associated molecular patterns (MAMPs), metabolites, and fungi. In addition, the gut microbiome shows potential as a biomarker for early HCC diagnosis and for assessing the efficacy of immunotherapy in unresectable HCC. This review examines how gut microbiota dysbiosis, with varied functional profiles, contributes to HCCs of different etiologies. We discuss therapeutic strategies to modulate the gut microbiome including diets, antibiotics, probiotics, fecal microbiota transplantation, and nano-delivery systems, and underscore their potential as an adjunctive treatment modality for HCC.
Collapse
Affiliation(s)
- Jingjing Yu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
32
|
Meyer C, Brockmueller A, Ruiz de Porras V, Shakibaei M. Microbiota and Resveratrol: How Are They Linked to Osteoporosis? Cells 2024; 13:1145. [PMID: 38994996 PMCID: PMC11240679 DOI: 10.3390/cells13131145] [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: 05/28/2024] [Revised: 06/18/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024] Open
Abstract
Osteoporosis (OP), which is characterized by a decrease in bone density and increased susceptibility to fractures, is closely linked to the gut microbiota (GM). It is increasingly realized that the GM plays a key role in the maintenance of the functioning of multiple organs, including bone, by producing bioactive metabolites such as short-chain fatty acids (SCFA). Consequently, imbalances in the GM, referred to as dysbiosis, have been identified with a significant reduction in beneficial metabolites, such as decreased SCFA associated with increased chronic inflammatory processes, including the activation of NF-κB at the epigenetic level, which is recognized as the main cause of many chronic diseases, including OP. Furthermore, regular or long-term medications such as antibiotics and many non-antibiotics such as proton pump inhibitors, chemotherapy, and NSAIDs, have been found to contribute to the development of dysbiosis, highlighting an urgent need for new treatment approaches. A promising preventive and adjuvant approach is to combat dysbiosis with natural polyphenols such as resveratrol, which have prebiotic functions and ensure an optimal microenvironment for beneficial GM. Resveratrol offers a range of benefits, including anti-inflammatory, anti-oxidant, analgesic, and prebiotic effects. In particular, the GM has been shown to convert resveratrol, into highly metabolically active molecules with even more potent beneficial properties, supporting a synergistic polyphenol-GM axis. This review addresses the question of how the GM can enhance the effects of resveratrol and how resveratrol, as an epigenetic modulator, can promote the growth and diversity of beneficial GM, thus providing important insights for the prevention and co-treatment of OP.
Collapse
Affiliation(s)
- Christine Meyer
- Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-University Munich, Pettenkoferstr. 11, D-80336 Munich, Germany
| | - Aranka Brockmueller
- Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-University Munich, Pettenkoferstr. 11, D-80336 Munich, Germany
| | - Vicenç Ruiz de Porras
- CARE Program, Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Badalona, 08916 Barcelona, Spain
- Badalona Applied Research Group in Oncology (B⋅ARGO), Catalan Institute of Oncology, Camí de les Escoles, s/n, Badalona, 08916 Barcelona, Spain
- GRET and Toxicology Unit, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Mehdi Shakibaei
- Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-University Munich, Pettenkoferstr. 11, D-80336 Munich, Germany
| |
Collapse
|
33
|
Popov IV, Koopmans B, Venema K. Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2). J Appl Microbiol 2024; 135:lxae170. [PMID: 38986506 DOI: 10.1093/jambio/lxae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/16/2024] [Accepted: 07/08/2024] [Indexed: 07/12/2024]
Abstract
AIMS This study aimed to compare the effects of linear and branched fructooligosaccharides (FOS) extracted from chicory and grass (Lolium perenne), respectively on human microbiota composition, diversity, and metabolism. METHODS AND RESULTS To test the effects of linear and branched FOS on human microbiota we used the artificial in vitro human colon model (TIM-2). Microbiota composition and diversity were assessed by V3-V4 16S rRNA metagenomic sequencing, followed by differential taxa abundance and alpha/beta diversity analyses. SCFA/BCFA production was evaluated by gas chromatography-mass spectrometry. As a result, branched FOS had the most beneficial effects on microbial diversity and metabolite production. Also, branched FOS significantly increased the abundance of commensal bacteria associated with maintaining healthy gut functions and controlling inflammation, such as Butyricicoccus, Erysipelotrichaceae, Phascolarctobacterium, and Sutterella. Linear FOS also significantly increased the abundance of some other commensal gut bacteria (Anaerobutyricum, Lachnospiraceae, Faecalibacterium), but there were no differences in diversity metrics compared to the control. CONCLUSIONS The study revealed that branched FOS had the most beneficial effects compared to the linear FOS in vitro, concerning microbiota modulation, and metabolite production, making this a good candidate for further studies in food biotechnology.
Collapse
Affiliation(s)
- Igor V Popov
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University-Campus Venlo, 5928 SZ Venlo, The Netherlands
- Faculty of Bioengineering and Veterinary Medicine, Don State Technical University, 344000 Rostov-on-Don, Russia
| | | | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University-Campus Venlo, 5928 SZ Venlo, The Netherlands
| |
Collapse
|
34
|
Sanford PA, Blaby I, Yoshikuni Y, Woolston BM. An efficient cre-based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum. Biotechnol Bioeng 2024. [PMID: 38956879 DOI: 10.1002/bit.28796] [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: 03/30/2024] [Revised: 05/20/2024] [Accepted: 06/16/2024] [Indexed: 07/04/2024]
Abstract
Acetogenic Clostridia are obligate anaerobes that have emerged as promising microbes for the renewable production of biochemicals owing to their ability to efficiently metabolize sustainable single-carbon feedstocks. Additionally, Clostridia are increasingly recognized for their biosynthetic potential, with recent discoveries of diverse secondary metabolites ranging from antibiotics to pigments to modulators of the human gut microbiota. Lack of efficient methods for genomic integration and expression of large heterologous DNA constructs remains a major challenge in studying biosynthesis in Clostridia and using them for metabolic engineering applications. To overcome this problem, we harnessed chassis-independent recombinase-assisted genome engineering (CRAGE) to develop a workflow for facile integration of large gene clusters (>10 kb) into the human gut acetogen Eubacterium limosum. We then integrated a non-ribosomal peptide synthetase gene cluster from the gut anaerobe Clostridium leptum, which previously produced no detectable product in traditional heterologous hosts. Chromosomal expression in E. limosum without further optimization led to production of phevalin at 2.4 mg/L. These results further expand the molecular toolkit for a highly tractable member of the Clostridia, paving the way for sophisticated pathway engineering efforts, and highlighting the potential of E. limosum as a Clostridial chassis for exploration of anaerobic natural product biosynthesis.
Collapse
Affiliation(s)
- Patrick A Sanford
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Ian Blaby
- Joint Genome Institute, Lawrence Berkeley National Laboratory, The US Department of Energy, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Lawrence Berkeley National Laboratory, The US Department of Energy, Berkeley, California, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
| |
Collapse
|
35
|
Liu Y, Fachrul M, Inouye M, Méric G. Harnessing human microbiomes for disease prediction. Trends Microbiol 2024; 32:707-719. [PMID: 38246848 DOI: 10.1016/j.tim.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.
Collapse
Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Human Genomics and Evolution Unit, St Vincent's Institute of Medical Research, Victoria, Australia; Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia; Central Clinical School, Monash University, Melbourne, Victoria, Australia; Department of Medical Science, Molecular Epidemiology, Uppsala University, Uppsala, Sweden; Department of Cardiovascular Research, Translation, and Implementation, La Trobe University, Melbourne, Victoria, Australia.
| |
Collapse
|
36
|
Quinn-Bohmann N, Wilmanski T, Sarmiento KR, Levy L, Lampe JW, Gurry T, Rappaport N, Ostrem EM, Venturelli OS, Diener C, Gibbons SM. Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nat Microbiol 2024; 9:1700-1712. [PMID: 38914826 DOI: 10.1038/s41564-024-01728-4] [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: 03/09/2023] [Accepted: 05/09/2024] [Indexed: 06/26/2024]
Abstract
Microbially derived short-chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated with disease. A systems-scale mechanistic understanding of this heterogeneity is lacking. Here we use a microbial community-scale metabolic modelling (MCMM) approach to predict individual-specific SCFA production profiles to assess the impact of different dietary, prebiotic and probiotic inputs. We evaluate the quantitative accuracy of our MCMMs using in vitro and ex vivo data, plus published human cohort data. We find that MCMM SCFA predictions are significantly associated with blood-derived clinical chemistries, including cardiometabolic and immunological health markers, across a large human cohort. Finally, we demonstrate how MCMMs can be leveraged to design personalized dietary, prebiotic and probiotic interventions aimed at optimizing SCFA production in the gut. Our model represents an approach to direct gut microbiome engineering for precision health and nutrition.
Collapse
Affiliation(s)
- Nick Quinn-Bohmann
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | | | | | - Lisa Levy
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Thomas Gurry
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Myota GmbH, Berlin, Germany
| | - Noa Rappaport
- Center for Phenomic Health, Buck Institute for Research on Aging, Novato, CA, USA
| | - Erin M Ostrem
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christian Diener
- Institute for Systems Biology, Seattle, WA, USA.
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, USA.
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- eScience Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
37
|
Celano G, Calabrese FM, Riezzo G, D’Attoma B, Ignazzi A, Di Chito M, Sila A, De Nucci S, Rinaldi R, Linsalata M, Apa CA, Mancini L, De Angelis M, Giannelli G, De Pergola G, Russo F. A Multi-Omics Approach to Disclose Metabolic Pathways Impacting Intestinal Permeability in Obese Patients Undergoing Very Low Calorie Ketogenic Diet. Nutrients 2024; 16:2079. [PMID: 38999827 PMCID: PMC11243313 DOI: 10.3390/nu16132079] [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: 05/07/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024] Open
Abstract
A very low calorie ketogenic diet (VLCKD) impacts host metabolism in people marked by an excess of visceral adiposity, and it affects the microbiota composition in terms of taxa presence and relative abundances. As a matter of fact, there is little available literature dealing with microbiota differences in obese patients marked by altered intestinal permeability. With the aim of inspecting consortium members and their related metabolic pathways, we inspected the microbial community profile, together with the set of volatile organic compounds (VOCs) from untargeted fecal and urine metabolomics, in a cohort made of obese patients, stratified based on both normal and altered intestinal permeability, before and after VLCKD administration. Based on the taxa relative abundances, we predicted microbiota-derived metabolic pathways whose variations were explained in light of our cohort symptom picture. A totally different number of statistically significant pathways marked samples with altered permeability, reflecting an important shift in microbiota taxa. A combined analysis of taxa, metabolic pathways, and metabolomic compounds delineates a set of markers that is useful in describing obesity dysfunctions and comorbidities.
Collapse
Affiliation(s)
- Giuseppe Celano
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (G.C.); (C.A.A.); (L.M.); (M.D.A.)
| | - Francesco Maria Calabrese
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (G.C.); (C.A.A.); (L.M.); (M.D.A.)
| | - Giuseppe Riezzo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (G.R.); (B.D.); (A.I.); (M.L.)
| | - Benedetta D’Attoma
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (G.R.); (B.D.); (A.I.); (M.L.)
| | - Antonia Ignazzi
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (G.R.); (B.D.); (A.I.); (M.L.)
| | - Martina Di Chito
- Center of Nutrition for the Research and the Care of Obesity and Metabolic Diseases, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (M.D.C.); (A.S.); (S.D.N.); (R.R.); (G.D.P.)
| | - Annamaria Sila
- Center of Nutrition for the Research and the Care of Obesity and Metabolic Diseases, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (M.D.C.); (A.S.); (S.D.N.); (R.R.); (G.D.P.)
| | - Sara De Nucci
- Center of Nutrition for the Research and the Care of Obesity and Metabolic Diseases, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (M.D.C.); (A.S.); (S.D.N.); (R.R.); (G.D.P.)
| | - Roberta Rinaldi
- Center of Nutrition for the Research and the Care of Obesity and Metabolic Diseases, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (M.D.C.); (A.S.); (S.D.N.); (R.R.); (G.D.P.)
| | - Michele Linsalata
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (G.R.); (B.D.); (A.I.); (M.L.)
| | - Carmen Aurora Apa
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (G.C.); (C.A.A.); (L.M.); (M.D.A.)
| | - Leonardo Mancini
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (G.C.); (C.A.A.); (L.M.); (M.D.A.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy; (G.C.); (C.A.A.); (L.M.); (M.D.A.)
| | - Gianluigi Giannelli
- Scientific Direction, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy;
| | - Giovanni De Pergola
- Center of Nutrition for the Research and the Care of Obesity and Metabolic Diseases, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (M.D.C.); (A.S.); (S.D.N.); (R.R.); (G.D.P.)
| | - Francesco Russo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (G.R.); (B.D.); (A.I.); (M.L.)
| |
Collapse
|
38
|
Naghipour S, Cox AJ, Fisher JJ, Plan M, Stark T, West N, Peart JN, Headrick JP, Du Toit EF. Circulating TMAO, the gut microbiome and cardiometabolic disease risk: an exploration in key precursor disorders. Diabetol Metab Syndr 2024; 16:133. [PMID: 38886825 PMCID: PMC11181661 DOI: 10.1186/s13098-024-01368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Elevations in the gut metabolite trimethylamine-N-oxide (TMAO) have been linked to cardiovascular and metabolic diseases. Whether elevated TMAO levels reflect early mechanistic involvement or a sequela of evolving disease awaits elucidation. The purpose of this study was to further explore these potential associations. METHODS We investigated relationships between circulating levels of TMAO and its pre-cursor substrates, dietary factors, gut microbiome profiles and disease risk in individuals with a Healthy BMI (18.5 < BMI < 25, n = 41) or key precursor states for cardiometabolic disease: Overweight (25 < BMI < 30 kg/m2, n = 33), Obese (BMI > 30, n = 27) and Metabolic Syndrome (MetS; ≥ 3 ATPIII report criteria, n = 39). RESULTS Unexpectedly, plasma [TMAO] did not vary substantially between groups (means of 3-4 µM; p > 0.05), although carnitine was elevated in participants with MetS. Gut microbial diversity and Firmicutes were also significantly reduced in the MetS group (p < 0.05). Exploratory analysis across diverse parameters reveals significant correlations between circulating [TMAO] and seafood intake (p = 0.007), gut microbial diversity (p = 0.017-0.048), and plasma [trimethylamine] (TMA; p = 0.001). No associations were evident with anthropometric parameters or cardiometabolic disease risk. Most variance in [TMAO] within and between groups remained unexplained. CONCLUSIONS Data indicate that circulating [TMAO] may be significantly linked to seafood intake, levels of TMA substrate and gut microbial diversity across healthy and early disease phenotypes. However, mean concentrations remain < 5 µM, with little evidence of links between TMAO and cardiometabolic disease risk. These observations suggest circulating TMAO may not participate mechanistically in cardiometabolic disease development, with later elevations likely a detrimental sequela of extant disease.
Collapse
Affiliation(s)
- Saba Naghipour
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, 4215, Australia
| | - Amanda J Cox
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, 4215, Australia
- Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia
| | - Joshua J Fisher
- School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Manuel Plan
- Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD, 4072, Australia
- Metabolomics Facility, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD, 4006, Australia
| | - Terra Stark
- Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Nic West
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, 4215, Australia
- Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia
| | - Jason N Peart
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, 4215, Australia
| | - John P Headrick
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, 4215, Australia
| | - Eugene F Du Toit
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, 4215, Australia.
| |
Collapse
|
39
|
Primorac D, Ciechanover A. Personalized medicine: the future is here. Croat Med J 2024; 65:169-173. [PMID: 38868962 PMCID: PMC11157250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
|
40
|
Álvarez-Herms J. Summatory Effects of Anaerobic Exercise and a 'Westernized Athletic Diet' on Gut Dysbiosis and Chronic Low-Grade Metabolic Acidosis. Microorganisms 2024; 12:1138. [PMID: 38930520 PMCID: PMC11205432 DOI: 10.3390/microorganisms12061138] [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: 04/14/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Anaerobic exercise decreases systemic pH and increases metabolic acidosis in athletes, altering the acid-base homeostasis. In addition, nutritional recommendations advising athletes to intake higher amounts of proteins and simple carbohydrates (including from sport functional supplements) could be detrimental to restoring acid-base balance. Here, this specific nutrition could be classified as an acidic diet and defined as 'Westernized athletic nutrition'. The maintenance of a chronic physiological state of low-grade metabolic acidosis produces detrimental effects on systemic health, physical performance, and inflammation. Therefore, nutrition must be capable of compensating for systemic acidosis from anaerobic exercise. The healthy gut microbiota can contribute to improving health and physical performance in athletes and, specifically, decrease the systemic acidic load through the conversion of lactate from systemic circulation to short-chain fatty acids in the proximal colon. On the contrary, microbial dysbiosis results in negative consequences for host health and physical performance because it results in a greater accumulation of systemic lactate, hydrogen ions, carbon dioxide, bacterial endotoxins, bioamines, and immunogenic compounds that are transported through the epithelia into the blood circulation. In conclusion, the systemic metabolic acidosis resulting from anaerobic exercise can be aggravated through an acidic diet, promoting chronic, low-grade metabolic acidosis in athletes. The individuality of athletic training and nutrition must take into consideration the acid-base homeostasis to modulate microbiota and adaptive physiological responses.
Collapse
Affiliation(s)
- Jesús Álvarez-Herms
- Phymolab, Physiology and Molecular Laboratory, 40170 Collado Hermoso, Segovia, Spain
| |
Collapse
|
41
|
Pujolassos M, Susín A, Calle M. Microbiome compositional data analysis for survival studies. NAR Genom Bioinform 2024; 6:lqae038. [PMID: 38666212 PMCID: PMC11044448 DOI: 10.1093/nargab/lqae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/23/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The growing interest in studying the relationship between the human microbiome and our health has also extended to time-to-event studies where researchers explore the connection between the microbiome and the occurrence of a specific event of interest. The analysis of microbiome obtained through high throughput sequencing techniques requires the use of specialized Compositional Data Analysis (CoDA) methods designed to accommodate its compositional nature. There is a limited availability of statistical tools for microbiome analysis that incorporate CoDA, and this is even more pronounced in the context of survival analysis. To fill this methodological gap, we present coda4microbiome for survival studies, a new methodology for the identification of microbial signatures in time-to-event studies. The algorithm implements an elastic-net penalized Cox regression model adapted to compositional covariates. We illustrate coda4microbiome algorithm for survival studies with a case study about the time to develop type 1 diabetes for non-obese diabetic mice. Our algorithm identified a bacterial signature composed of 21 genera associated with diabetes development. coda4microbiome for survival studies is integrated in the R package coda4microbiome as an extension of the existing functions for cross-sectional and longitudinal studies.
Collapse
Affiliation(s)
- Meritxell Pujolassos
- Bioscience Department, Faculty of Sciences, Technology and Engineering, University of Vic – Central University of Catalunya, Vic 08500, Spain
| | - Antoni Susín
- Mathematical Department, UPC-Barcelona Tech, Barcelona 08034, Spain
| | - M.Luz Calle
- Bioscience Department, Faculty of Sciences, Technology and Engineering, University of Vic – Central University of Catalunya, Vic 08500, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic 08500, Spain
| |
Collapse
|
42
|
Pimenta AI, Bernardino RM, Pereira IAC. Role of sulfidogenic members of the gut microbiota in human disease. Adv Microb Physiol 2024; 85:145-200. [PMID: 39059820 DOI: 10.1016/bs.ampbs.2024.04.003] [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: 07/28/2024]
Abstract
The human gut flora comprises a dynamic network of bacterial species that coexist in a finely tuned equilibrium. The interaction with intestinal bacteria profoundly influences the host's development, metabolism, immunity, and overall health. Furthermore, dysbiosis, a disruption of the gut microbiota, can induce a variety of diseases, not exclusively associated with the intestinal tract. The increased consumption of animal protein, high-fat and high-sugar diets in Western countries has been implicated in the rise of chronic and inflammatory illnesses associated with dysbiosis. In particular, this diet leads to the overgrowth of sulfide-producing bacteria, known as sulfidogenic bacteria, which has been linked to inflammatory bowel diseases and colorectal cancer, among other disorders. Sulfidogenic bacteria include sulfate-reducing bacteria (Desulfovibrio spp.) and Bilophila wadsworthia among others, which convert organic and inorganic sulfur compounds to sulfide through the dissimilatory sulfite reduction pathway. At high concentrations, sulfide is cytotoxic and disrupts the integrity of the intestinal epithelium and mucus barrier, triggering inflammation. Besides producing sulfide, B. wadsworthia has revealed significant pathogenic potential, demonstrated in the ability to cause infection, adhere to intestinal cells, promote inflammation, and compromise the integrity of the colonic mucus layer. This review delves into the mechanisms by which taurine and sulfide-driven gut dysbiosis contribute to the pathogenesis of sulfidogenic bacteria, and discusses the role of these gut microbes, particularly B. wadsworthia, in human diseases.
Collapse
Affiliation(s)
- Andreia I Pimenta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel M Bernardino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Shi J, Zhou W, Chen G, Yi W, Sun Y, Zeng X. The Utilization by Bacteroides spp. of a Purified Polysaccharide from Fuzhuan Brick Tea. Foods 2024; 13:1666. [PMID: 38890895 PMCID: PMC11172108 DOI: 10.3390/foods13111666] [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: 03/28/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
In the present study, four Bacteroides species that could degrade Fuzhuan brick tea polysaccharide-3 (FBTPS-3) were isolated from human feces and identified to be Bacteroides ovatus, B. uniformis, B. fragilis and B. thetaiotaomicron. The four Bacteroides species showed growth on FBTPS-3 as the carbon source, and B. ovatus showed the best capability for utilizing FBTPS-3 among the four species since B. ovatus could utilize more FBTPS-3 during 24 h fermentation. Moreover, the four Bacteroides species could metabolize FBTPS-3 and promote the production of acetic, propionic and isovaleric acids. Transcriptome analysis of B. ovatus revealed that 602 genes were up-regulated by FBTPS-3, including two carbohydrate-active enzyme clusters and four polysaccharide utilization loci (PULs). The PUL 1 contained GH28 family that could hydrolyze rhamnogalacturonan and other pectic substrates, which was in line with our previous work that rhamnose and galacturonic acid were the main component monosaccharides of FBTPS-3. Collectively, the results suggested that FBTPS-3 could be utilized by Bacteroides spp., and it might be developed as a promising prebiotic targeting Bacteroidetes in intestinal environment.
Collapse
Affiliation(s)
| | | | | | | | | | - Xiaoxiong Zeng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (J.S.); (W.Z.); (G.C.); (W.Y.); (Y.S.)
| |
Collapse
|
45
|
Jones R, Robinson AT, Beach LB, Lindsey ML, Kirabo A, Hinton A, Erlandson KM, Jenkins ND. Exercise to Prevent Accelerated Vascular Aging in People Living With HIV. Circ Res 2024; 134:1607-1635. [PMID: 38781293 PMCID: PMC11126195 DOI: 10.1161/circresaha.124.323975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Given advances in antiretroviral therapy, the mortality rate for HIV infection has dropped considerably over recent decades. However, people living with HIV (PLWH) experience longer life spans coupled with persistent immune activation despite viral suppression and potential toxicity from long-term antiretroviral therapy use. Consequently, PLWH face a cardiovascular disease (CVD) risk more than twice that of the general population, making it the leading cause of death among this group. Here, we briefly review the epidemiology of CVD in PLWH highlighting disparities at the intersections of sex and gender, age, race/ethnicity, and the contributions of social determinants of health and psychosocial stress to increased CVD risk among individuals with marginalized identities. We then overview the pathophysiology of HIV and discuss the primary factors implicated as contributors to CVD risk among PLWH on antiretroviral therapy. Subsequently, we highlight the functional evidence of premature vascular dysfunction as an early pathophysiological determinant of CVD risk among PLWH, discuss several mechanisms underlying premature vascular dysfunction in PLWH, and synthesize current research on the pathophysiological mechanisms underlying accelerated vascular aging in PLWH, focusing on immune activation, chronic inflammation, and oxidative stress. We consider understudied aspects such as HIV-related changes to the gut microbiome and psychosocial stress, which may serve as mechanisms through which exercise can abrogate accelerated vascular aging. Emphasizing the significance of exercise, we review various modalities and their impacts on vascular health, proposing a holistic approach to managing CVD risks in PLWH. The discussion extends to critical future study areas related to vascular aging, CVD, and the efficacy of exercise interventions, with a call for more inclusive research that considers the diversity of the PLWH population.
Collapse
Affiliation(s)
- Raymond Jones
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | | | - Lauren B. Beach
- Department of Medical Social Sciences, Northwestern, Chicago, IL
- Department of Preventive Medicine, Northwestern, Chicago, IL
| | - Merry L. Lindsey
- School of Graduate Studies, Meharry Medical College, Nashville, TN
- Research Service, Nashville VA Medical Center, Nashville, TN
| | - Annet Kirabo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Center for Immunobiology, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
- Vanderbilt Institute for Global Health, Nashville, TN
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | | | - Nathaniel D.M. Jenkins
- Department of Health and Human Physiology, University of Iowa, Iowa City, IA
- Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
| |
Collapse
|
46
|
Reygner J, Delannoy J, Barba-Goudiaby MT, Gasc C, Levast B, Gaschet E, Ferraris L, Paul S, Kapel N, Waligora-Dupriet AJ, Barbut F, Thomas M, Schwintner C, Laperrousaz B, Corvaïa N. Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models. Appl Environ Microbiol 2024; 90:e0001624. [PMID: 38651930 PMCID: PMC11107171 DOI: 10.1128/aem.00016-24] [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] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a "good" donor as well as the intrinsic variability of donor-derived products' taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors' feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products' efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.IMPORTANCEGrowing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Stéphane Paul
- Team GIMAP, Centre International de Recherche en Infectiologie, Université Jean Monnet, Saint-Etienne, France
- Inserm, Université Claude Bernard Lyon, Lyon, France
- CIC 1408 Inserm Vaccinology, University Hospital of Saint-Etienne, Saint-Etienne, France
- Immunology Department, iBiothera Reference Center, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Nathalie Kapel
- UMR-S 1139, INSERM, Université Paris Cite, Paris, France
- Service de Coprologie fonctionnelle, Hôpital de la Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France
| | | | - Frederic Barbut
- UMR-S 1139, INSERM, Université Paris Cite, Paris, France
- National Reference Laboratory for Clostridioides difficile, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- The European Society of Clinical Microbiology and Infectious Diseases Study Group for Clostridioides difficile, Basel, Switzerland
| | - Muriel Thomas
- UMR1319, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | | |
Collapse
|
47
|
Pieczyńska-Zając JM, Malinowska A, Łagowska K, Leciejewska N, Bajerska J. The effects of time-restricted eating and Ramadan fasting on gut microbiota composition: a systematic review of human and animal studies. Nutr Rev 2024; 82:777-793. [PMID: 37528052 PMCID: PMC11082590 DOI: 10.1093/nutrit/nuad093] [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] [Indexed: 08/03/2023] Open
Abstract
CONTEXT It is well known that the microbiome undergoes cyclical diurnal rhythms. It has thus been hypothesized that meal timing may affect gut microbial composition, function, and host health. OBJECTIVE This review aims to examine the effects of time-restricted eating (TRE) and Ramadan fasting (RF) on the composition of the gut microbiota in animal and human studies. The associations between composition of microbiota and host metabolic parameters are also examined. DATA SOURCES A search was performed on the PubMed, Cochrane, Scopus, and Web of Science databases up to December 31, 2022. The search strategy was performed using the Medical Subject Heading (MeSH) terms "intermittent fasting" and "gastrointestinal microbiome" and the key words "Ramadan fasting" and "microbes." DATA EXTRACTION Seven human studies (4 TRE and 3 RF) and 9 animal studies (7 TRE, 2 RF-like) were retrieved. DATA ANALYSIS TRE and RF in human studies lead to an increase in gut microbial community alpha-diversity. In animal studies (both TRE and RF-like), fasting is not associated with improved alpha-diversity, but enhancement of microbial fluctuation is observed, compared with high-fat diet ad libitum groups. Within Firmicutes and Bacteroidetes phyla, no specific direction of changes resulting from fasting are observed in both animals and human. After TRE or RF, a greater abundance of the Faecalibacterium genus is observed in human studies; changes in Lactobacillus abundance are found in animal studies; and increases in Akkermansia are seen both in humans and in animals fed a feed-pellet diet. Only 2 human studies show a beneficial correlation between microbiota changes and host metabolic (HDL cholesterol) or anthropometric parameters (body mass index). CONCLUSIONS These findings support the importance of both regimens in improving the gut microbiota composition. However, based on results of animal studies, it can be suggested that diet remains the essential factor in forming the microbiota's environment. SYSTEMATIC REVIEW REGISTRATION PROSPERO registration no. CRD42021278918.
Collapse
Affiliation(s)
| | - Anna Malinowska
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Karolina Łagowska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, Poland
| | - Natalia Leciejewska
- Department of Physiology, Biochemistry, and Biostructure of Animals, Poznań University of Life Sciences, Poznań, Poland
| | - Joanna Bajerska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, Poland
| |
Collapse
|
48
|
Wei X, Wang J, Wang Y, Zhao Y, Long Y, Tan B, Li QX, Dong Z, Wan X. Dietary fiber and polyphenols from whole grains: effects on the gut and health improvements. Food Funct 2024; 15:4682-4702. [PMID: 38590246 DOI: 10.1039/d4fo00715h] [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: 04/10/2024]
Abstract
Cereals are the main source of energy in the human diet. Compared to refined grains, whole grains retain more beneficial components, including dietary fiber, polyphenols, proteins, vitamins, and minerals. Dietary fiber and bound polyphenols (biounavailable) in cereals are important active substances that can be metabolized by the gut microorganisms and affect the intestinal environment. There is a close relationship between the gut microbiota structures and various disease phenotypes, although the consistency of this link is affected by many factors, and the specific mechanisms are still unclear. Remodeling unfavorable microbiota is widely recognized as an important way to target the gut and improve diseases. This paper mainly reviews the interaction between the gut microbiota and cereal-derived dietary fiber and polyphenols, and also summarizes the changes to the gut microbiota and possible molecular mechanisms of related glycolipid metabolism. The exploration of single active ingredients in cereals and their synergistic health mechanisms will contribute to a better understanding of the health benefits of whole grains. It will further help promote healthier whole grain foods by cultivating new varieties with more potential and optimizing processing methods.
Collapse
Affiliation(s)
- Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
- Environmental Economics and Natural Resources Group, Wageningen University & Research, Wageningen 6706 KN, The Netherlands
| | - Jianhui Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Yaxuan Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Yilin Zhao
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Bin Tan
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| |
Collapse
|
49
|
Das R, Mishra P, Mishra B, Jha R. Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens. J Anim Sci Biotechnol 2024; 15:62. [PMID: 38702804 PMCID: PMC11069197 DOI: 10.1186/s40104-024-01022-7] [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: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17th embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21. RESULTS The results were considered significantly different at P < 0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21. CONCLUSION In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.
Collapse
Affiliation(s)
- Razib Das
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Pravin Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Birendra Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Rajesh Jha
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
| |
Collapse
|
50
|
Tanaka T, Sugiyama R, Sato Y, Kawaguchi M, Honda K, Iwaki H, Okano K. Precise microbiome engineering using natural and synthetic bacteriophages targeting an artificial bacterial consortium. Front Microbiol 2024; 15:1403903. [PMID: 38756723 PMCID: PMC11096457 DOI: 10.3389/fmicb.2024.1403903] [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: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising method to elucidate the functions of targeted bacteria in microbiomes. However, few methods to selectively kill target microorganisms in the microbiome without affecting the growth of nontarget microorganisms are available. In this study, we focused on the host-specific lytic ability of virulent phages and validated their potency for precise microbiome engineering. In an artificial microbiome consisting of Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Lactiplantibacillus plantarum, the addition of bacteriophages infecting their respective host strains specifically reduced the number of these bacteria more than 102 orders. Remarkably, the reduction in target bacteria did not affect the growth of nontarget bacteria, indicating that bacteriophages were effective tools for precise microbiome engineering. Moreover, a virulent derivative of the λ phage was synthesized from prophage DNA in the genome of λ lysogen by in vivo DNA assembly and phage-rebooting techniques, and E. coli-targeted microbiome engineering was achieved. These results propose a novel approach for precise microbiome engineering using bacteriophages, in which virulent phages are synthesized from prophage DNA in lysogenic strains without isolating phages from environmental samples.
Collapse
Affiliation(s)
- Tomoki Tanaka
- Department of Chemistry, Materials and Bioengineering, Graduate School of Science and Engineering, Kansai University, Osaka, Japan
| | - Ryoga Sugiyama
- Department of Chemistry, Materials and Bioengineering, Graduate School of Science and Engineering, Kansai University, Osaka, Japan
| | - Yu Sato
- Division of Life Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Manami Kawaguchi
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Osaka, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Hiroaki Iwaki
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Osaka, Japan
| | - Kenji Okano
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Osaka, Japan
| |
Collapse
|