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Govender P, Ghai M. Population-specific differences in the human microbiome: Factors defining the diversity. Gene 2024; 933:148923. [PMID: 39244168 DOI: 10.1016/j.gene.2024.148923] [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: 05/24/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
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2
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Gilbert JA, Hartmann EM. The indoors microbiome and human health. Nat Rev Microbiol 2024:10.1038/s41579-024-01077-3. [PMID: 39030408 DOI: 10.1038/s41579-024-01077-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/21/2024]
Abstract
Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.
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Affiliation(s)
- Jack A Gilbert
- Department of Paediatrics, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
- Department of Medicine, Division of Pulmonary Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
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3
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Alahdal H, Almuneef G, Alkhulaifi MM, Aldibasi O, Aljouie A, Alharbi O, Almohawes ZN, Basingab F, Rejili M. Gut microbiota composition in patients with Crohn's disease in Saudi Arabia. PLoS One 2024; 19:e0299749. [PMID: 38656971 PMCID: PMC11042705 DOI: 10.1371/journal.pone.0299749] [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: 09/07/2023] [Accepted: 02/14/2024] [Indexed: 04/26/2024] Open
Abstract
Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.
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Affiliation(s)
- Hadil Alahdal
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ghaida Almuneef
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Manal Muhammed Alkhulaifi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Omar Aldibasi
- Biostatistics Section, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Aljouie
- Artificial Intelligence and Bioinformatics Department, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- Department of Health Informatics, College of Public Health and Health Informatics, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Othman Alharbi
- Department of Medicine, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Zakiah Naser Almohawes
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mokhtar Rejili
- Department of Life Sciences, College of Sciences, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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4
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Herman C, Barker BM, Bartelli TF, Chandra V, Krajmalnik-Brown R, Jewell M, Li L, Liao C, McAllister F, Nirmalkar K, Xavier JB, Gregory Caporaso J. Assessing Engraftment Following Fecal Microbiota Transplant. ARXIV 2024:arXiv:2404.07325v1. [PMID: 38659636 PMCID: PMC11042410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent Clostridium difficile infections, and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to priming the microbiome for cancer treatment, and restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in determining if a recipient didn't respond because the engrafted microbiome didn't produce the desired outcomes (a successful FMT, but negative treatment outcome), or the microbiome didn't engraft (an unsuccessful FMT and negative treatment outcome). The lack of a consistent methodology for quantifying FMT engraftment extent hinders the assessment of FMT success and its relation to clinical outcomes, and presents challenges for comparing FMT results and protocols across studies. Here we review 46 studies of FMT in humans and model organisms and group their approaches for assessing the extent to which an FMT engrafts into three criteria: 1) Chimeric Asymmetric Community Coalescence investigates microbiome shifts following FMT engraftment using methods such as alpha diversity comparisons, beta diversity comparisons, and microbiome source tracking. 2) Donated Microbiome Indicator Features tracks donated microbiome features (e.g., amplicon sequence variants or species of interest) as a signal of engraftment with methods such as differential abundance testing based on the current sample collection, or tracking changes in feature abundances that have been previously identified (e.g., from FMT or disease-relevant literature). 3) Temporal Stability examines how resistant post-FMT recipient's microbiomes are to reverting back to their baseline microbiome. Individually, these criteria each highlight a critical aspect of microbiome engraftment; investigated together, however, they provide a clearer assessment of microbiome engraftment. We discuss the pros and cons of each of these criteria, providing illustrative examples of their application. We also introduce key terminology and recommendations on how FMT studies can be analyzed for rigorous engraftment extent assessment.
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Affiliation(s)
- Chloe Herman
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Thais F Bartelli
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vidhi Chandra
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, U.S.A
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, U.S.A
| | | | - Le Li
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khemlal Nirmalkar
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, U.S.A
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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5
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Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med 2024; 5:101426. [PMID: 38366600 PMCID: PMC10982974 DOI: 10.1016/j.xcrm.2024.101426] [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: 04/12/2023] [Revised: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
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Affiliation(s)
- Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Romulo de Oliveira
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; Department of Medicine and Life Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Isabel Ruf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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6
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Liu Q, Yang Y, Pan M, Yang F, Yu Y, Qian Z. Role of the gut microbiota in tumorigenesis and treatment. Theranostics 2024; 14:2304-2328. [PMID: 38646653 PMCID: PMC11024857 DOI: 10.7150/thno.91700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/01/2024] [Indexed: 04/23/2024] Open
Abstract
The gut microbiota is a crucial component of the intricate microecosystem within the human body that engages in interactions with the host and influences various physiological processes and pathological conditions. In recent years, the association between dysbiosis of the gut microbiota and tumorigenesis has garnered increasing attention, as it is recognized as a hallmark of cancer within the scientific community. However, only a few microorganisms have been identified as potential drivers of tumorigenesis, and enhancing the molecular understanding of this process has substantial scientific importance and clinical relevance for cancer treatment. In this review, we delineate the impact of the gut microbiota on tumorigenesis and treatment in multiple types of cancer while also analyzing the associated molecular mechanisms. Moreover, we discuss the utility of gut microbiota data in cancer diagnosis and patient stratification. We further outline current research on harnessing microorganisms for cancer treatment while also analyzing the prospects and challenges associated with this approach.
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Affiliation(s)
- Qingya Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yun Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meng Pan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fan Yang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Qian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
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7
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Jardou M, Brossier C, Marquet P, Picard N, Druilhe A, Lawson R. Solid organ transplantation and gut microbiota: a review of the potential immunomodulatory properties of short-chain fatty acids in graft maintenance. Front Cell Infect Microbiol 2024; 14:1342354. [PMID: 38476165 PMCID: PMC10927761 DOI: 10.3389/fcimb.2024.1342354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Transplantation is the treatment of choice for several end-stage organ defects: it considerably improves patient survival and quality of life. However, post-transplant recipients may experience episodes of rejection that can favor or ultimately lead to graft loss. Graft maintenance requires a complex and life-long immunosuppressive treatment. Different immunosuppressive drugs (i.e., calcineurin inhibitors, glucocorticoids, biological immunosuppressive agents, mammalian target of rapamycin inhibitors, and antiproliferative or antimetabolic agents) are used in combination to mitigate the immune response against the allograft. Unfortunately, the use of these antirejection agents may lead to opportunistic infections, metabolic (e.g., post-transplant diabetes mellitus) or cardiovascular (e.g., arterial hypertension) disorders, cancer (e.g., non-Hodgkin lymphoma) and other adverse effects. Lately, immunosuppressive drugs have also been associated with gut microbiome alterations, known as dysbiosis, and were shown to affect gut microbiota-derived short-chain fatty acids (SCFA) production. SCFA play a key immunomodulatory role in physiological conditions, and their impairment in transplant patients could partly counterbalance the effect of immunosuppressive drugs leading to the activation of deleterious pathways and graft rejection. In this review, we will first present an overview of the mechanisms of graft rejection that are prevented by the immunosuppressive protocol. Next, we will explain the dynamic changes of the gut microbiota during transplantation, focusing on SCFA. Finally, we will describe the known functions of SCFA in regulating immune-inflammatory reactions and discuss the impact of SCFA impairment in immunosuppressive drug treated patients.
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Affiliation(s)
| | | | | | | | | | - Roland Lawson
- National Institute of Health and Medical Research (FRANCE) (INSERM), Univ. Limoges, Pharmacology & Transplantation, U1248, Limoges, France
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [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: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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9
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Aliwa B, Horvath A, Traub J, Feldbacher N, Habisch H, Fauler G, Madl T, Stadlbauer V. Altered gut microbiome, bile acid composition and metabolome in sarcopenia in liver cirrhosis. J Cachexia Sarcopenia Muscle 2023; 14:2676-2691. [PMID: 37767786 PMCID: PMC10751428 DOI: 10.1002/jcsm.13342] [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: 03/12/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Sarcopenia in liver cirrhosis is associated with low quality of life and high mortality risk. The pathogenesis has yet to be fully understood. We hypothesized that gut microbiome, bile acid (BA) composition and metabolites differ between cirrhotic patients with and without sarcopenia and contribute to pathogenesis. METHODS Cirrhotic patients with (n = 78) and without (n = 38) sarcopenia and non-cirrhotic controls with (n = 39) and without (n = 20) sarcopenia were included in this study. Faecal microbiome composition was studied by 16S rDNA sequencing, serum and faecal BA composition by ultra-high-performance liquid chromatography-tandem mass spectrometry, and metabolite composition in serum, faeces and urine by nuclear magnetic resonance. RESULTS Bacteroides fragilis, Blautia marseille, Sutterella spp. and Veillonella parvula were associated with cirrhotic patients with sarcopenia, whereas Bacteroides ovatus was more abundant in cirrhotic patients without sarcopenia. We observed significantly elevated secondary BAs, deoxycholic acid (DCA; P = 0.01) and lithocholic acid (LCA; P = 0.02), and the ratios of deoxycholic acid to cholic acid (DCA:CA; P = 0.04), lithocholic acid to chenodeoxycholic acid (LCA:CDCA; P = 0.03) and 12 alpha-hydroxylated to non-12 alpha-hydroxylated BAs (12-α-OH:non-12-α-OH BAs; P = 0.04) in serum of cirrhotic patients with sarcopenia compared with cirrhotic patients without sarcopenia, indicating an enhanced transformation of primary to secondary BAs by the gut microbiome. CA (P = 0.02) and the ratios of CA:CDCA (P = 0.03) and total ursodeoxycholic acid to total secondary BAs (T-UDCA:total-sec-BAs, P = 0.03) were significantly reduced in the stool of cirrhotic patients with sarcopenia compared with cirrhotic patients without sarcopenia. Also, valine and acetate were significantly reduced in the serum of cirrhotic patients with sarcopenia compared with cirrhotic patients without sarcopenia (P = 0.01 and P = 0.03, respectively). Multivariate logistic regression further confirmed the association of B. ovatus (P = 0.01, odds ratio [OR]: 12.8, 95% confidence interval [CI]: 168.1; 2.2), the ratios of 12-α-OH:non-12-α-OH BAs (P = 0.03, OR: 2.54, 95% CI: 0.99; 6.55) and T-UDCA:total-sec-BAs (P = 0.04, OR: 0.25, 95% CI: 0.06; 0.98) in serum and stool CA:CDCA (P = 0.04, OR: 0.79, 95% CI: 0.62; 0.99), and serum valine (P = 0.04, OR: 1.00, 95% CI: 1.02; 1.00) with sarcopenia in cirrhosis after correcting for the severity of liver disease and sex. CONCLUSIONS Our study suggests a potential functional gut microbiome-host interaction linking sarcopenia with the altered gut microbiomes, BA profiles and amino acids pointing towards a potential mechanistic interplay in understanding sarcopenia pathogenesis.
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Affiliation(s)
- Benard Aliwa
- Division of Gastroenterology and Hepatology, Department of Internal MedicineMedical University of GrazGrazAustria
- Department of Food Science, Nutrition and TechnologyUniversity of NairobiNairobiKenya
| | - Angela Horvath
- Division of Gastroenterology and Hepatology, Department of Internal MedicineMedical University of GrazGrazAustria
- Centre for Biomarker Research in Medicine (CBmed)GrazAustria
| | - Julia Traub
- Department of Clinical Medical NutritionUniversity Hospital GrazGrazAustria
| | - Nicole Feldbacher
- Division of Gastroenterology and Hepatology, Department of Internal MedicineMedical University of GrazGrazAustria
- Centre for Biomarker Research in Medicine (CBmed)GrazAustria
| | - Hansjörg Habisch
- Gottfried Schatz Research Center, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
| | - Günter Fauler
- Clinical Institute for Medical and Chemical Laboratory DiagnosticsGrazAustria
| | - Tobias Madl
- Gottfried Schatz Research Center, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Vanessa Stadlbauer
- Division of Gastroenterology and Hepatology, Department of Internal MedicineMedical University of GrazGrazAustria
- Centre for Biomarker Research in Medicine (CBmed)GrazAustria
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10
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Tomofuji Y, Kishikawa T, Sonehara K, Maeda Y, Ogawa K, Kawabata S, Oguro-Igashira E, Okuno T, Nii T, Kinoshita M, Takagaki M, Yamamoto K, Arase N, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Fujimoto M, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population. Cell Rep 2023; 42:113324. [PMID: 37935197 DOI: 10.1016/j.celrep.2023.113324] [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: 06/05/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Interaction between the gut microbiome and host plays a key role in human health. Here, we perform a metagenome shotgun-sequencing-based analysis of Japanese participants to reveal associations between the gut microbiome, host genetics, and plasma metabolome. A genome-wide association study (GWAS) for microbial species (n = 524) identifies associations between the PDE1C gene locus and Bacteroides intestinalis and between TGIF2 and TGIF2-RAB5IF gene loci and Bacteroides acidifiaciens. In a microbial gene ortholog GWAS, agaE and agaS, which are related to the metabolism of carbohydrates forming the blood group A antigen, are associated with blood group A in a manner depending on the secretor status determined by the East Asian-specific FUT2 variant. A microbiome-metabolome association analysis (n = 261) identifies associations between bile acids and microbial features such as bile acid metabolism gene orthologs including bai and 7β-hydroxysteroid dehydrogenase. Our publicly available data will be a useful resource for understanding gut microbiome-host interactions in an underrepresented population.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
| | - Noriko Arase
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Akiko Hosokawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Neurology, Suita Municipal Hospital, Suita 564-8567, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita 565-0871, Japan.
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11
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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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12
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Angthong P, Chaiyapechara S, Rungrassamee W. Shrimp microbiome and immune development in the early life stages. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104765. [PMID: 37380117 DOI: 10.1016/j.dci.2023.104765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
With its contribution to nutrition, development, and disease resistance, gut microbiome has been recognized as a crucial component of the animal's health and well-being. Microbiome in the gastrointestinal tract constantly interacts with the host animal's immune systems as part of the normal function of the intestines. Interactions between the microbiome and the immune system are complex and dynamic, with the microbiome shaping immune development and function. In contrast, the immune system modulates the composition and activity of the microbiome. In shrimp, as with all other aquatic animals, the interaction between the microbiome and the animals occurs at the early developmental stages. This early interaction is likely essential to the development of immune responses of the animal as well as many key physiological developments that further contribute to the health of shrimp. This review provides background knowledge on the early developmental stage of shrimp and its microbiome, examines the interaction between the microbiome and the immune system in the early life stage of shrimp, and discusses potential pitfalls and challenges associated with microbiome research. Understanding the interaction between the microbiome and shrimp immune system at this crucial developmental stage could have the potential to aid in the establishment of a healthy microbiome, improve shrimp survival, and provide ways to shape the microbiome with feed supplements or other strategies.
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Affiliation(s)
- Pacharaporn Angthong
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sage Chaiyapechara
- Aquaculture Service Development Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand.
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13
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Lima IS, da Silva TM, Weiss S, Homuth G, Lerch MM, Figueiredo CA, Alcantara-Neves NM, Barreto ML, Marques CR. Genome-wide association study of Helicobacter pylori serological status in Latin American children. Helicobacter 2023; 28:e13008. [PMID: 37497783 DOI: 10.1111/hel.13008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/07/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Few genome-wide association studies (GWAS) on Helicobacter pylori infection susceptibility have been conducted for admixed populations from developing countries. Here, we performed a GWAS to identify genetic factors associated with H. pylori serostatus in a cohort of admixed children from a large Latin American urban center. METHODS A cross-sectional study involving 1161 children from 4 to 11 years old living in poor areas of Salvador, in northeastern Brazil. Logistic regression analysis was performed to detect associations between single-nucleotide variants (SNVs) and H. pylori seropositivity, assuming an additive genetic model. Enrichment analyses were conducted using the MAGMA v1.10 software. RESULTS We found 22 SNVs to be suggestively associated (p < 10-5 ) with H. pylori seropositivity. The most suggestive SNV was the rs77955022 (p = 4.83e-07) located in an intronic region of EXOC3 at 5p15.33. The second most suggestively associated SNV was rs10914996 (p = 8.97e-07), located in an intergenic region at 1p34.3. Furthermore, we were able to replicate three SNVs (p < 0.05) in the Study of Health in Pomerania (SHIP) cohort: the rs2339212 and rs4795970, both located at 17q12 near TMEM132E, as well as the rs6595814, an intronic variant of FBN2 at 5q23.3. The enrichment analysis indicated the participation of genes and metabolic pathways related to the regulation of the digestive system and gastric acid secretion in the risk of seropositivity for H. pylori. CONCLUSIONS Additional studies are required to validate these association findings in larger population samples and to get insight into the underlying physiological mechanisms.
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Affiliation(s)
- Iasmin Souza Lima
- Multidisciplinary Institute in Health, Federal University of Bahia, Vitória da Conquista, Brazil
| | | | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Maurício Lima Barreto
- Center of Data and Knowledge Integration for Health, Instituto Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil
| | - Cintia Rodrigues Marques
- Multidisciplinary Institute in Health, Federal University of Bahia, Vitória da Conquista, Brazil
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14
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Rodenes-Gavidia A, Lamelas A, Bloor S, Hobson A, Treadway S, Haworth J, Vijayakumar V, Naghibi M, Day R, Chenoll E. An insight into the functional alterations in the gut microbiome of healthy adults in response to a multi-strain probiotic intake: a single arm open label trial. Front Cell Infect Microbiol 2023; 13:1240267. [PMID: 37841999 PMCID: PMC10570534 DOI: 10.3389/fcimb.2023.1240267] [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: 06/14/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Background Probiotic supplements, by definition, provide a benefit to the host, but few studies have investigated the effect of probiotic supplements in healthy adult populations. Purpose The present, single arm, open label clinical trial, evaluated compositional and functional changes in the fecal microbiome of healthy adults after supplementation with a 14-strain probiotic. Methods We analysed the effect of a 14-strain probiotic blend (Bacillus subtilis NCIMB 30223, Bifidobacterium bifidum NCIMB 30179, B. breve NCIMB 30180, B. infantis NCIMB 30181, B. longum NCIMB 30182, Lactobacillus helveticus NCIMB 30184, L. delbrueckii subsp. bulgaricus NCIMB 30186, Lacticaseibacillus paracasei NCIMB 30185, Lactiplantibacillus plantarum NCIMB 30187, Lacticaseibacillus rhamnosus NCIMB 30188, L. helveticus NCIMB 30224, Lactobacillus salivarius NCIMB 30225, Lactococcus lactis subsp. lactis NCIMB 30222, and Streptococcus thermophilus NCIMB 30189), on the faecal microbiota of healthy young adults (n=41) in a single arm study. The adults consumed 4 capsules daily of the 14 strain blend(8 billion colony forming units/day) for 8 weeks. Compositional and functional changes in faecal microbiota before and after supplementation were assessed using shotgun metagenomic sequencing. Fasting breath analysis, faecal biochemistry and bowel habits were also assessed. Results In healthy adult participants, no significant changes to the overall alpha- or beta-diversity was observed after 8 weeks of multi-strain probiotic supplementation. However, in a simplified model that considered only time and individual differences, significant decreases (p < 0.05) in family Odoribacteraceae and Bacteroidaceae abundance and a significant increase (p < 0.05) in genus Megamonas abundance were observed. At a functional level, there were significant changes in functional gene abundance related to several functional pathways, including phenylalanine metabolism, O-antigen nucleotide sugar biosynthesis, bacterial chemotaxis, and flagellar assembly. No significant changes in stool form or frequency, fecal biochemistry, or methane and hydrogen breath tests were observed. Conclusion In healthy young adults, overall alpha- and beta-diversity did not change in response to probiotic intake even though modest compositional changes at the family and genus level were observed. However, at functional level, results identified changes in gene abundance for several functional pathways.
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Affiliation(s)
- Andrea Rodenes-Gavidia
- ADM BIOPOLIS, University of Valencia Science Park (Parc Científic de la Universitat de València), Valencia, Spain
| | - Araceli Lamelas
- ADM BIOPOLIS, University of Valencia Science Park (Parc Científic de la Universitat de València), Valencia, Spain
| | - Sarah Bloor
- Functional Gut Clinic, Manchester, United Kingdom
- Anglia Ruskin University, Essex, Norwich, United Kingdom
| | - Anthony Hobson
- Functional Gut Clinic, Manchester, United Kingdom
- Anglia Ruskin University, Essex, Norwich, United Kingdom
| | - Sam Treadway
- Functional Gut Clinic, Manchester, United Kingdom
| | | | | | - Malwina Naghibi
- Medical Department, ADM Health & Wellness, Somerset, United Kingdom
| | - Richard Day
- Medical Department, ADM Health & Wellness, Somerset, United Kingdom
| | - Empar Chenoll
- ADM BIOPOLIS, University of Valencia Science Park (Parc Científic de la Universitat de València), Valencia, Spain
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15
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Ren Y, Wu J, Wang Y, Zhang L, Ren J, Zhang Z, Chen B, Zhang K, Zhu B, Liu W, Li S, Li X. Lifestyle patterns influence the composition of the gut microbiome in a healthy Chinese population. Sci Rep 2023; 13:14425. [PMID: 37660184 PMCID: PMC10475076 DOI: 10.1038/s41598-023-41532-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
High-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and lifestyle differences in the Chinese population are limited. Here, we carried out an independent cohort study-the Chinese Healthy Gut Project (n = 483)-where correlations between the gut microbiota and dietary and lifestyle variables in a healthy Chinese population are defined. We collected both questionnaire data, including basic information and lifestyle and dietary variables, and fecal stools from the enrolled volunteers. We then performed 16S rRNA sequencing on the microbial DNA isolated from the stools to assess the composition of the intestinal microbiota. We found that Prevotella and Bacteroides were the most abundant genera in the healthy Chinese gut microbiome. Additionally, 9 out of 29 clinical and questionnaire-based phenotype covariates were found to be associated with the variation in the composition of the gut microbiota. Among these lifestyle phenotypes, sleep procrastination, negative mood, and drinking habits had the largest effect size. Additionally, an appreciable effect of urbanization was observed, resulting in decreased intra-individual diversity, increased inter-individual diversity, and an increased abundance of the Bacteroides enterotype. The results of this study provide a foundation for assessing the healthy Chinese gut microbiota community structure at baseline in a healthy Chinese population. Furthermore, this study also provides insights into understanding how distinctive living habits influence the relationships between the Chinese gut microbiome and systemic health state.
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Affiliation(s)
- Yi Ren
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Jiawei Wu
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Yilin Wang
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Lanying Zhang
- Coyote Diagnostics Lab (Beijing) Co., Ltd., Beijing, China
| | - Jing Ren
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Zhiming Zhang
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Binghan Chen
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Kejian Zhang
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Baoli Zhu
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Sabrina Li
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China.
- Coyote Diagnostics Lab (Beijing) Co., Ltd., Beijing, China.
| | - Xu Li
- Coyote Bioscience (Beijing) Co., Ltd., Beijing, China.
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16
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Cickovski T, Mathee K, Aguirre G, Tatke G, Hermida A, Narasimhan G, Stollstorff M. Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective. PLoS One 2023; 18:e0273890. [PMID: 37594987 PMCID: PMC10437823 DOI: 10.1371/journal.pone.0273890] [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: 08/16/2022] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Attention Deficit Hyperactivity Disorder (ADHD) is an increasingly prevalent neuropsychiatric disorder characterized by hyperactivity, inattention, and impulsivity. Symptoms emerge from underlying deficiencies in neurocircuitry, and recent research has suggested a role played by the gut microbiome. The gut microbiome is an ecosystem of interdependent taxa involved in an exponentially complex web of interactions, plus host gene and reaction pathways, some of which involve neurotransmitters with roles in ADHD neurocircuitry. Studies have analyzed the ADHD gut microbiome using macroscale metrics such as diversity and differential abundance, and have proposed several taxa as elevated or reduced in ADHD compared to Control. Few studies have delved into the complex underlying dynamics ultimately responsible for the emergence of such metrics, leaving a largely incomplete, sometimes contradictory, and ultimately inconclusive picture. We aim to help complete this picture by venturing beyond taxa abundances and into taxa relationships (i.e. cooperation and competition), using a publicly available gut microbiome dataset (targeted 16S, v3-4 region, qPCR) from an observational, case-control study of 30 Control (15 female, 15 male) and 28 ADHD (15 female, 13 male) undergraduate students. We first perform the same macroscale analyses prevalent in ADHD gut microbiome literature (diversity, differential abundance, and composition) to observe the degree of correspondence, or any new trends. We then estimate two-way ecological relationships by producing Control and ADHD Microbial Co-occurrence Networks (MCNs), using SparCC correlations (p ≤ 0.01). We perform community detection to find clusters of taxa estimated to mutually cooperate along with their centroids, and centrality calculations to estimate taxa most vital to overall gut ecology. We finally summarize our results, providing conjectures on how they can guide future experiments, some methods for improving our experiments, and general implications for the field.
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Affiliation(s)
- Trevor Cickovski
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, United States of America
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, FL, United States of America
| | - Gloria Aguirre
- Department of Biological Sciences, College of Arts, Sciences and Education, Florida International University, Miami, FL, United States of America
| | - Gorakh Tatke
- Department of Biological Sciences, College of Arts, Sciences and Education, Florida International University, Miami, FL, United States of America
| | - Alejandro Hermida
- Cognitive Neuroscience Laboratory, Department of Psychology, Florida International University, Miami, FL, United States of America
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, United States of America
| | - Melanie Stollstorff
- Cognitive Neuroscience Laboratory, Department of Psychology, Florida International University, Miami, FL, United States of America
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17
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Blackmer-Raynolds L, Sampson TR. Overview of the Gut Microbiome. Semin Neurol 2023; 43:518-529. [PMID: 37562449 DOI: 10.1055/s-0043-1771463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The human gastrointestinal tract is home to trillions of microorganisms-collectively referred to as the gut microbiome-that maintain a symbiotic relationship with their host. This diverse community of microbes grows and changes as we do, with developmental, lifestyle, and environmental factors all shaping microbiome community structure. Increasing evidence suggests this relationship is bidirectional, with the microbiome also influencing host physiological processes. For example, changes in the gut microbiome have been shown to alter neurodevelopment and have lifelong effects on the brain and behavior. Age-related changes in gut microbiome composition have also been linked to inflammatory changes in the brain, perhaps increasing susceptibility to neurological disease. Indeed, associations between gut dysbiosis and many age-related neurological diseases-including Parkinson's disease, Alzheimer's disease, multiple sclerosis, and amyotrophic lateral sclerosis-have been reported. Further, microbiome manipulation in animal models of disease highlights a potential role for the gut microbiome in disease development and progression. Although much remains unknown, these associations open up an exciting new world of therapeutic targets, potentially allowing for improved quality of life for a wide range of patient populations.
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Affiliation(s)
| | - Timothy R Sampson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia
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18
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Nagarajan A, Scoggin K, Gupta J, Threadgill DW, Andrews-Polymenis HL. Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome. MICROBIOME 2023; 11:149. [PMID: 37420306 PMCID: PMC10329326 DOI: 10.1186/s40168-023-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/18/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice. CC mice are a panel of mice that are genetically diverse across strains, but genetically identical within a given strain allowing repetition and deeper analysis than is possible with other collections of genetically diverse mice. RESULTS 16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed a large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 17 significant Quantitative Trait Loci (QTL) linked to 14 genera on 9 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr analysis and Genecards database. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. A subset of these CC mice was infected with Salmonella Typhimurium. Using infection outcome data, an increase in abundance of genus Lachnospiraceae and decrease in genus Parasutterella correlated with positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces. CONCLUSION Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection. Video Abstract.
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Affiliation(s)
- Aravindh Nagarajan
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - Kristin Scoggin
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
| | - Jyotsana Gupta
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - David W. Threadgill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX USA
- Department of Biochemistry & Biophysics and Department of Nutrition, Texas A&M University, College Station, TX USA
| | - Helene L. Andrews-Polymenis
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
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19
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Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. Nat Commun 2023; 14:3510. [PMID: 37316519 PMCID: PMC10267222 DOI: 10.1038/s41467-023-39121-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.
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Affiliation(s)
- Xiaofan Jin
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Jia Yan
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Xiandong Meng
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- University of California San Francisco, San Francisco, CA, USA.
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20
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Abstract
Cardiometabolic disease comprises cardiovascular and metabolic dysfunction and underlies the leading causes of morbidity and mortality, both within the United States and worldwide. Commensal microbiota are implicated in the development of cardiometabolic disease. Evidence suggests that the microbiome is relatively variable during infancy and early childhood, becoming more fixed in later childhood and adulthood. Effects of microbiota, both during early development, and in later life, may induce changes in host metabolism that modulate risk mechanisms and predispose toward the development of cardiometabolic disease. In this review, we summarize the factors that influence gut microbiome composition and function during early life and explore how changes in microbiota and microbial metabolism influence host metabolism and cardiometabolic risk throughout life. We highlight limitations in current methodology and approaches and outline state-of-the-art advances, which are improving research and building toward refined diagnosis and treatment options in microbiome-targeted therapies.
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Affiliation(s)
- Curtis L Gabriel
- Division of Gastroenterology, Hepatology and Nutrition (C.L.G.), Vanderbilt University Medical Center, Nashville
- Tennessee Center for AIDS Research (C.L.G.), Vanderbilt University Medical Center, Nashville
| | - Jane F Ferguson
- Division of Cardiovascular Medicine (J.F.F.), Vanderbilt University Medical Center, Nashville
- Vanderbilt Microbiome Innovation Center (J.F.F.), Vanderbilt University Medical Center, Nashville
- Vanderbilt Institute for Infection, Immunology, and Inflammation (J.F.F.), Vanderbilt University Medical Center, Nashville
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21
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Amin N, Liu J, Bonnechere B, MahmoudianDehkordi S, Arnold M, Batra R, Chiou YJ, Fernandes M, Ikram MA, Kraaij R, Krumsiek J, Newby D, Nho K, Radjabzadeh D, Saykin AJ, Shi L, Sproviero W, Winchester L, Yang Y, Nevado-Holgado AJ, Kastenmüller G, Kaddurah-Daouk R, van Duijn CM. Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals. JAMA Psychiatry 2023; 80:597-609. [PMID: 37074710 PMCID: PMC10116384 DOI: 10.1001/jamapsychiatry.2023.0685] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/07/2023] [Indexed: 04/20/2023]
Abstract
Importance Metabolomics reflect the net effect of genetic and environmental influences and thus provide a comprehensive approach to evaluating the pathogenesis of complex diseases, such as depression. Objective To identify the metabolic signatures of major depressive disorder (MDD), elucidate the direction of associations using mendelian randomization, and evaluate the interplay of the human gut microbiome and metabolome in the development of MDD. Design, Setting and Participants This cohort study used data from participants in the UK Biobank cohort (n = 500 000; aged 37 to 73 years; recruited from 2006 to 2010) whose blood was profiled for metabolomics. Replication was sought in the PREDICT and BBMRI-NL studies. Publicly available summary statistics from a 2019 genome-wide association study of depression were used for the mendelian randomization (individuals with MDD = 59 851; control individuals = 113 154). Summary statistics for the metabolites were obtained from OpenGWAS in MRbase (n = 118 000). To evaluate the interplay of the metabolome and the gut microbiome in the pathogenesis of depression, metabolic signatures of the gut microbiome were obtained from a 2019 study performed in Dutch cohorts. Data were analyzed from March to December 2021. Main Outcomes and Measures Outcomes were lifetime and recurrent MDD, with 249 metabolites profiled with nuclear magnetic resonance spectroscopy with the Nightingale platform. Results The study included 6811 individuals with lifetime MDD compared with 51 446 control individuals and 4370 individuals with recurrent MDD compared with 62 508 control individuals. Individuals with lifetime MDD were younger (median [IQR] age, 56 [49-62] years vs 58 [51-64] years) and more often female (4447 [65%] vs 2364 [35%]) than control individuals. Metabolic signatures of MDD consisted of 124 metabolites spanning the energy and lipid metabolism pathways. Novel findings included 49 metabolites, including those involved in the tricarboxylic acid cycle (ie, citrate and pyruvate). Citrate was significantly decreased (β [SE], -0.07 [0.02]; FDR = 4 × 10-04) and pyruvate was significantly increased (β [SE], 0.04 [0.02]; FDR = 0.02) in individuals with MDD. Changes observed in these metabolites, particularly lipoproteins, were consistent with the differential composition of gut microbiota belonging to the order Clostridiales and the phyla Proteobacteria/Pseudomonadota and Bacteroidetes/Bacteroidota. Mendelian randomization suggested that fatty acids and intermediate and very large density lipoproteins changed in association with the disease process but high-density lipoproteins and the metabolites in the tricarboxylic acid cycle did not. Conclusions and Relevance The study findings showed that energy metabolism was disturbed in individuals with MDD and that the interplay of the gut microbiome and blood metabolome may play a role in lipid metabolism in individuals with MDD.
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Affiliation(s)
- Najaf Amin
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Bruno Bonnechere
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- REVAL Rehabilitation Research Center, Faculty of Rehabilitation Sciences, Hasselt University, Hasselt, Belgium
- Technology-Supported and Data-Driven Rehabilitation, Data Sciences Institute, Hasselt University, Hasselt, Belgium
| | | | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Richa Batra
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Yu-Jie Chiou
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Marco Fernandes
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jan Krumsiek
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Danielle Newby
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences and Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Andrew J. Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences and Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis
| | - Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - William Sproviero
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Laura Winchester
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Yang Yang
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | | | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina
| | - Cornelia M. van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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22
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Salazar J, Durán P, Díaz MP, Chacín M, Santeliz R, Mengual E, Gutiérrez E, León X, Díaz A, Bernal M, Escalona D, Hernández LAP, Bermúdez V. Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:5845. [PMID: 37239571 PMCID: PMC10218639 DOI: 10.3390/ijerph20105845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/20/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023]
Abstract
The gut microbiota (GM) has been the subject of intense research in recent years. Therefore, numerous factors affecting its composition have been thoroughly examined, and with them, their function and role in the individual's systems. The gut microbiota's taxonomical composition dramatically impacts older adults' health status. In this regard, it could either extend their life expectancy via the modulation of metabolic processes and the immune system or, in the case of dysbiosis, predispose them to age-related diseases, including bowel inflammatory and musculoskeletal diseases and metabolic and neurological disorders. In general, the microbiome of the elderly tends to present taxonomic and functional changes, which can function as a target to modulate the microbiota and improve the health of this population. The GM of centenarians is unique, with the faculty-promoting metabolic pathways capable of preventing and counteracting the different processes associated with age-related diseases. The molecular mechanisms by which the microbiota can exhibit anti-ageing properties are mainly based on anti-inflammatory and antioxidant actions. This review focuses on analysing the current knowledge of gut microbiota characteristics and modifiers, its relationship with ageing, and the GM-modulating approaches to increase life expectancy.
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Affiliation(s)
- Juan Salazar
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Pablo Durán
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - María P. Díaz
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Maricarmen Chacín
- Centro de Investigaciones en Ciencias de la Vida, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Sociedad Internacional de Rejuvenecimiento Facial No Quirúrgico (SIRF), Barranquilla 080002, Colombia
| | - Raquel Santeliz
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Edgardo Mengual
- Biological Research Institute “Doctors Orlando Castejon and Haydee V Castejon”, Faculty of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Emma Gutiérrez
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Xavier León
- Instituto Ecuatoriano de Seguridad Social, Cuenca 010101, Ecuador
| | - Andrea Díaz
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Marycarlota Bernal
- Facultad de Ingenierias, Universidad Simón Bolívar, Cúcuta 540001, Colombia
| | - Daniel Escalona
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | | | - Valmore Bermúdez
- Centro de Investigaciones en Ciencias de la Vida, Universidad Simón Bolívar, Barranquilla 080002, Colombia
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23
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Liu F, Lu H, Dong B, Huang X, Cheng H, Qu R, Hu Y, Zhong L, Guo Z, You Y, Xu ZZ. Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/– Bacteria. mSystems 2023; 8:e0073822. [PMID: 36971593 PMCID: PMC10134872 DOI: 10.1128/msystems.00738-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes.
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24
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Kilic O, Kaya HI, Secme M, Ki Li Nc M, Sevgican CI, Buber I, Dodurga Y, Si Msek O, Ergin C, Kilic ID. The effect of heart failure on gut microbial richness and diversity. Rev Port Cardiol 2023:S0870-2551(23)00120-8. [PMID: 36893840 DOI: 10.1016/j.repc.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/29/2022] [Accepted: 06/08/2022] [Indexed: 03/09/2023] Open
Abstract
INTRODUCTION With recent advances in genome sequencing technology, a large body of evidence has accumulated over the last few years linking alterations in microbiota with cardiovascular disease. In this study, we aimed to compare gut microbial composition using 16S ribosomal DNA (rDNA) sequencing techniques in patients with coronary artery disease (CAD) and stable heart failure (HF) with reduced ejection fraction and patients with CAD but with normal ejection fraction. We also studied the relationship between systemic inflammatory markers and microbial richness and diversity. METHODS A total of 40 patients (19 with HF and CAD, 21 with CAD but without HF) were included in the study. HF was defined as left ventricular ejection fraction <40%. Only stable ambulatory patients were included in the study. Gut microbiota were assessed from the participants' fecal samples. The diversity and richness of microbial populations in each sample were assessed by the Chao1-estimated OTU number and the Shannon index. RESULTS The Chao1-estimated OTU number and Shannon index were similar between HF and control groups. There was no statistically significant relationship between inflammatory marker levels (tumor necrosis factor-alpha, interleukin 1-beta, endotoxin, C-reactive protein, galectin-3, interleukin 6, and lipopolysaccharide-binding protein) and microbial richness and diversity when analyzed at the phylum level. CONCLUSION In the current study, compared to patients with CAD but without HF, stable HF patients with CAD did not show changes in gut microbial richness and diversity. At the genus level Enterococcus sp. was more commonly identified in HF patients, in addition to certain changes in species levels, including increased Lactobacillus letivazi.
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Affiliation(s)
- Oguz Kilic
- Department of Cardiology, Karaman Training and Research Hospital, Karaman, Turkey; Department of Cardiology, Pamukkale University Hospitals, Denizli, Turkey.
| | - Halil Ibrahim Kaya
- Department of Food Engineering, University of Bayburt University, Bayburt, Turkey
| | - Mucahit Secme
- Department of Medical Biology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Mehmet Ki Li Nc
- Department of Cardiology, Konya City Hospital, Konya, Turkey; Department of Cardiology, Pamukkale University Hospitals, Denizli, Turkey
| | | | - Ipek Buber
- Department of Cardiology, Pamukkale University Hospitals, Denizli, Turkey
| | - Yavuz Dodurga
- Department of Medical Biology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Omer Si Msek
- Department of Food Engineering, University of Pamukkale University, Denizli, Turkey
| | - Cagrı Ergin
- Department of Medical Microbiology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Ismail Dogu Kilic
- Department of Cardiology, Pamukkale University Hospitals, Denizli, Turkey
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25
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van Praagh J, Havenga K. What Is the Microbiome? A Description of a Social Network. Clin Colon Rectal Surg 2023; 36:91-97. [PMID: 36844706 PMCID: PMC9946720 DOI: 10.1055/s-0043-1760863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The gut microbiome has coevolved with its hosts over the years, forming a complex and symbiotic relationship. It is formed by what we do, what we eat, where we live, and with whom we live. The microbiome is known to influence our health by training our immune system and providing nutrients for the human body. However, when the microbiome becomes out of balance and dysbiosis occurs, the microorganisms within can cause or contribute to diseases. This major influencer on our health is studied intensively, but it is unfortunately often overlooked by the surgeon and in surgical practice. Because of that, there is not much literature about the microbiome and its influence on surgical patients or procedures. However, there is evidence that it plays a major role, showing that it needs to be a topic of interest for the surgeon. This review is written to show the surgeon the importance of the microbiome and why it should be taken into consideration when preparing or treating patients.
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Affiliation(s)
- J.B. van Praagh
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Klaas Havenga
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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26
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Hoque MN, Rahman MS, Sarkar MMH, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Hossain MA, Khan MS, Islam T. Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients. PLoS One 2023; 18:e0278134. [PMID: 36656835 PMCID: PMC9851516 DOI: 10.1371/journal.pone.0278134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/09/2022] [Indexed: 01/20/2023] Open
Abstract
We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.
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Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - M. Anwar Hossain
- Jashore Unive rsity of Science and Technology, Jashore, Bangladesh
| | - M. Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, Bangladesh
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27
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McKay I, van Dorst J, Katz T, Doumit M, Prentice B, Owens L, Belessis Y, Chuang S, Jaffe A, Thomas T, Coffey M, Ooi CY. Diet and the gut-lung axis in cystic fibrosis - direct & indirect links. Gut Microbes 2023; 15:2156254. [PMID: 36573804 PMCID: PMC9809969 DOI: 10.1080/19490976.2022.2156254] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Cystic fibrosis (CF) is a multisystem, autosomal, recessive disease primarily affecting the lungs, pancreas, gastrointestinal tract, and liver. Whilst there is increasing evidence of a microbial 'gut-lung axis' in chronic respiratory conditions, there has been limited analysis of such a concept in CF. We performed a comprehensive dietary and microbiota analysis to explore the interactions between diet, gastrointestinal microbiota, respiratory microbiota, and clinical outcomes in children with CF. Our results demonstrate significant alterations in intestinal inflammation and respiratory and gastrointestinal microbiota when compared to age and gender matched children without CF. We identified correlations between the gastrointestinal and respiratory microbiota, lung function, CF pulmonary exacerbations and anthropometrics, supporting the concept of an altered gut-lung axis in children with CF. We also identified significant differences in dietary quality with CF children consuming greater relative proportions of total, saturated and trans fats, and less relative proportions of carbohydrates, wholegrains, fiber, insoluble fiber, starch, and resistant starch. Our findings position the CF diet as a potential modulator in gastrointestinal inflammation and the proposed gut-lung axial relationship in CF. The dietary intake of wholegrains, fiber and resistant starch may be protective against intestinal inflammation and should be explored as potential therapeutic adjuvants for children with CF.
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Affiliation(s)
- Isabelle McKay
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Josie van Dorst
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Tamarah Katz
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Nutrition and Dietetics, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Michael Doumit
- Department of Physiotherapy, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Bernadette Prentice
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Louisa Owens
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Yvonne Belessis
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Sandra Chuang
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Torsten Thomas
- Biological, Earth and Environmental Sciences, University of New South Wales, Randwick, Australia
- University of New South Wales, Centre for Marine Science and Innovation, Randwick, Australia
| | - Michael Coffey
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
| | - Chee Y. Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
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Salazar C, Giménez M, Riera N, Parada A, Puig J, Galiana A, Grill F, Vieytes M, Mason CE, Antelo V, D'Alessandro B, Risso J, Iraola G. Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates. MICROBIOME 2022; 10:208. [PMID: 36457116 PMCID: PMC9715416 DOI: 10.1186/s40168-022-01407-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/21/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood. RESULTS In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure. CONCLUSIONS We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.
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Affiliation(s)
- Cecilia Salazar
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Matias Giménez
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
- Molecular Microbiology Laboratory, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Nadia Riera
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Andrés Parada
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Josefina Puig
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | | | | | | | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Verónica Antelo
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Bruno D'Alessandro
- Servicio de Evaluación de la Calidad y Control Ambiental, Intendencia de Montevideo, Montevideo, Uruguay
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jimena Risso
- Servicio de Evaluación de la Calidad y Control Ambiental, Intendencia de Montevideo, Montevideo, Uruguay
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay.
- Wellcome Sanger Institute, Hinxton, UK.
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile.
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Westlake Gut Project: A consortium of microbiome epidemiology for the gut microbiome and health research in China. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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30
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Terry SM, Barnett JA, Gibson DL. A critical analysis of eating disorders and the gut microbiome. J Eat Disord 2022; 10:154. [PMID: 36329546 PMCID: PMC9635068 DOI: 10.1186/s40337-022-00681-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
The gut microbiota, also known as our "second brain" is an exciting frontier of research across a multitude of health domains. Gut microbes have been implicated in feeding behaviour and obesity, as well as mental health disorders including anxiety and depression, however their role in the development and maintenance of eating disorders (EDs) has only recently been considered. EDs are complex mental health conditions, shaped by a complicated interplay of factors. Perhaps due to an incomplete understanding of the etiology of EDs, treatment remains inadequate with affected individuals likely to face many relapses. The gut microbiota may be a missing piece in understanding the etiology of eating disorders, however more robust scientific inquiry is needed in the field before concrete conclusions can be made. In this spotlight paper, we critically evaluate what is known about the bi-directional relationship between gut microbes and biological processes that are implicated in the development and maintenance of EDs, including physiological functioning, hormones, neurotransmitters, the central nervous system, and the immune system. We outline limitations of current research, propose concrete steps to move the field forward and, hypothesize potential clinical implications of this research. Our gut is inhabited by millions of bacteria which have more recently been referred to as "our second brain". In fact, these microbes are thought to play a role in ED behaviour, associated anxiety and depression, and even affect our weight. Recent research has dove into this field with promising findings that have the potential to be applied clinically to improve ED recovery. The present paper discusses what is known about the gut microbiome in relation to EDs and the promising implications that leveraging this knowledge, through fecal microbiome transplants, probiotics, and microbiome-directed supplemental foods, could have on ED treatment.
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Affiliation(s)
- Sydney M Terry
- Department of Medicine, Faculty of Medicine, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | - Jacqueline A Barnett
- Department of Biology, I.K. Barber Faculty of Science, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Deanna L Gibson
- Department of Medicine, Faculty of Medicine, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada. .,Department of Biology, I.K. Barber Faculty of Science, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada.
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31
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Berthelot JM, Darrieutort-Laffite C, Le Goff B. Contribution of HLA DRB1, PTPN22, and CTLA4, to RA dysbiosis. Joint Bone Spine 2022; 89:105446. [PMID: 35940545 DOI: 10.1016/j.jbspin.2022.105446] [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: 05/30/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
This narrative review gathers current evidence for a contribution of rheumatoid arthritis (RA) HLA-DRB1, PTPN22 and CTLA4 polymorphisms to the gut dysbiosis observed in RA, especially at its onset (transient excess of Prevotella). The gut microbiome contains elements which are 30% heritable, including genera like Bacteroides and Veillonella, and to a lesser extent Prevotella. The first months/year seems a critical period for the selection of a core of microbiota, that should be considered as a second self by the immune system, and tolerized by regulatory T and B cells. Imperfect tolerization may increase the risk of RA following further repeated silent translocations of various gut microorganisms, including Prevotella copri, from gut to joints (fostered by a concurrent loss in gut mucosa of protective bacteria like Faecalibacterium prausnitzii). Genetics studies confirmed that Prevotella copri was partly heritable, and strong associations were observed between the overall microbial composition of stools and the HLA-DRB1 RA risk allele, either in a US cohort (P=0.00001), or the Twins UK cohort (P=0.033). This finding also stands for persons still free from RA, and was replicated in the Swiss SCREEN-RA cohort. Gene variants of PTPN22 also modify intestinal microbiota composition, compromise granulocyte-mediated antibacterial defence in gut, and reduce the suppressive effect of gut regulatory B cells. CTLA4 variants may similarly contribute to RA dysbiosis, since immunotherapy by CTLA-4 blockade depends on microbiota, and CTLA4 activates T follicular regulatory cells to reduce immune responses to segmented filamentous bacteria. Suggestions for future works are made.
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Affiliation(s)
- Jean-Marie Berthelot
- Rheumatology Unit, Nantes University Hospital, Hôtel-Dieu, CHU Nantes, Place Alexis Ricordeau, 44093 Nantes Cedex 01, France.
| | - Christelle Darrieutort-Laffite
- Rheumatology Unit, Nantes University Hospital, Hôtel-Dieu, CHU Nantes, Place Alexis Ricordeau, 44093 Nantes Cedex 01, France
| | - Benoît Le Goff
- Rheumatology Unit, Nantes University Hospital, Hôtel-Dieu, CHU Nantes, Place Alexis Ricordeau, 44093 Nantes Cedex 01, France
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32
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Wojciechowski S, Majchrzak-Górecka M, Biernat P, Odrzywołek K, Pruss Ł, Zych K, Jan Majta, Milanowska-Zabel K. Machine learning on the road to unlocking microbiota's potential for boosting immune checkpoint therapy. Int J Med Microbiol 2022; 312:151560. [PMID: 36113358 DOI: 10.1016/j.ijmm.2022.151560] [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: 08/30/2021] [Revised: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022] Open
Abstract
The intestinal microbiota is a complex and diverse ecological community that fulfills multiple functions and substantially impacts human health. Despite its plasticity, unfavorable conditions can cause perturbations leading to so-called dysbiosis, which have been connected to multiple diseases. Unfortunately, understanding the mechanisms underlying the crosstalk between those microorganisms and their host is proving to be difficult. Traditionally used bioinformatic tools have difficulties to fully exploit big data generated for this purpose by modern high throughput screens. Machine Learning (ML) may be a potential means of solving such problems, but it requires diligent application to allow for drawing valid conclusions. This is especially crucial as gaining insight into the mechanistic basis of microbial impact on human health is highly anticipated in numerous fields of study. This includes oncology, where growing amounts of studies implicate the gut ecosystems in both cancerogenesis and antineoplastic treatment outcomes. Based on these reports and first signs of clinical benefits related to microbiota modulation in human trials, hopes are rising for the development of microbiome-derived diagnostics and therapeutics. In this mini-review, we're inspecting analytical approaches used to uncover the role of gut microbiome in immune checkpoint therapy (ICT) with the use of shotgun metagenomic sequencing (SMS) data.
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Affiliation(s)
| | | | | | - Krzysztof Odrzywołek
- Ardigen, Podole 76, 30-394 Kraków, Poland; Institute of Computer Science, Faculty of Computer Science, Electronics and Telecommunications, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków, Poland
| | - Łukasz Pruss
- Ardigen, Podole 76, 30-394 Kraków, Poland; Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-373 Wroclaw, Poland
| | | | - Jan Majta
- Ardigen, Podole 76, 30-394 Kraków, Poland; Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae. Nat Commun 2022; 13:5617. [PMID: 36153315 PMCID: PMC9509339 DOI: 10.1038/s41467-022-33313-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients. Multidrug-resistant Enterobacteriaceae (MRE) represent a major threat for patients’ health. Here, the authors describe how cooperation between gut commensal bacteria (Lactobacillus spp. And Clostridiales) restrict MRE colonization in mice and patients
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34
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Vieira AR, Modesto A. Oral microbiome-dental caries associated genotypes analysis of 6- to 19-year-old individuals shows novel associations. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2022.875953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The need to determine risk factors for complex diseases continues to drive efforts of identification of etiological factors of common conditions. Molecular tools have created new opportunities to identify risk factors that may act interactively. The goal of this work was exploring potential interactions between oral microbial species and common genetic variants. Ninety-two 6- to 19-year-old individuals recruited through the University of Pittsburgh Dental Registry and DNA Repository project that had oral microbiome and genotyping of 44 single nucleotide polymorphism (SNP) data available were studied. Over-representation of alleles between individuals with or without particular microorganisms was determined using chi-square or Fisher's exact tests. Alpha of 0.001, to account for multiple testing (0.05/44), was considered statistically significant. Associations were found between Candida albicans and enamelin rs3796704 (p = 0.0006), and Staphylococcus epidermidis and tuftelin rs3828054 (p = 0.001). Microbiota and their metabolites might predispose oral disease when interacting with the host genetic variation and future studies should address their causal roles in oral disease.
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35
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Boulund U, Bastos DM, Ferwerda B, van den Born BJ, Pinto-Sietsma SJ, Galenkamp H, Levin E, Groen AK, Zwinderman AH, Nieuwdorp M. Gut microbiome associations with host genotype vary across ethnicities and potentially influence cardiometabolic traits. Cell Host Microbe 2022; 30:1464-1480.e6. [PMID: 36099924 DOI: 10.1016/j.chom.2022.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022]
Abstract
Previous studies in mainly European populations have reported that the gut microbiome composition is associated with the human genome. However, the genotype-microbiome interaction in different ethnicities is largely unknown. We performed a large fecal microbiome genome-wide association study of a single multiethnic cohort, the Healthy Life in an Urban Setting (HELIUS) cohort (N = 4,117). Mendelian randomization was performed using the multiethnic Pan-UK Biobank (N = 460,000) to dissect potential causality. We identified ethnicity-specific associations between host genomes and gut microbiota. Certain microbes were associated with genotype in multiple ethnicities. Several of the microbe-associated loci were found to be related to immune functions, interact with glutamate and the mucus layer, or be expressed in the gut or brain. Additionally, we found that gut microbes potentially influence cardiometabolic health factors such as BMI, cholesterol, and blood pressure. This provides insight into the relationship of ethnicity and gut microbiota and into the possible causal effects of gut microbes on cardiometabolic traits.
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Affiliation(s)
- Ulrika Boulund
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Diogo M Bastos
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Bert-Jan van den Born
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; Department of Public and Occupational Health, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; HorAIzon BV, 2645 LT Delfgauw, the Netherlands
| | - Albert K Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands.
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36
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Gut Microbiota Composition in Undernourished Children Associated with Diet and Sociodemographic Factors: A Case–Control Study in Indonesia. Microorganisms 2022; 10:microorganisms10091748. [PMID: 36144350 PMCID: PMC9502830 DOI: 10.3390/microorganisms10091748] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 12/16/2022] Open
Abstract
Malnutrition, which consists of undernutrition and overnutrition, is associated with gut microbiota composition, diet, and sociodemographic factors. Undernutrition is a nutrient deficiency that that should be identified to prevent other diseases. In this study, we evaluate the gut microbiota composition in undernourished children in association with diet and sociodemographic factors. We observed normal children (n= 20) and undernourished children (n= 20) for ten days in Lombok and Yogyakarta. Diet, sociodemographic factors, and medical records were recorded using food records, screening forms, and standard household questionnaires. Gut microbiota analysis was performed using 16S rRNA gene sequencing targeting the V3–V4 region. The result showed that the undernourished group had lower energy intake. In addition, the undernourished group had lower quality of medical records, parent knowledge, education, and exclusive breastfeeding. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia were significantly different between normal and undernourished children. Based on LefSe, we determined that Akkermansia is a biomarker for undernourished children. In conclusion, diet and sociodemographic factors affect the gut microbiota composition of undernourished children.
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37
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [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: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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38
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Jacobs JP, Goudarzi M, Lagishetty V, Li D, Mak T, Tong M, Ruegger P, Haritunians T, Landers C, Fleshner P, Vasiliauskas E, Ippoliti A, Melmed G, Shih D, Targan S, Borneman J, Fornace AJ, McGovern DPB, Braun J. Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome. Genome Med 2022; 14:91. [PMID: 35971134 PMCID: PMC9377146 DOI: 10.1186/s13073-022-01099-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Crohn's disease (CD) patients demonstrate distinct intestinal microbial compositions and metabolic characteristics compared to unaffected controls. However, the impact of inflammation and underlying genetic risk on these microbial profiles and their relationship to disease phenotype are unclear. We used lavage sampling to characterize the colonic mucosal-luminal interface (MLI) microbiome of CD patients in endoscopic remission and unaffected controls relative to obesity, disease genetics, and phenotype. METHODS Cecum and sigmoid colon were sampled from 110 non-CD controls undergoing screening colonoscopy who were stratified by body mass index and 88 CD patients in endoscopic remission (396 total samples). CD polygenic risk score (GRS) was calculated using 186 known CD variants. MLI pellets were analyzed by 16S ribosomal RNA gene sequencing, and supernatants by untargeted liquid chromatography-mass spectrometry. RESULTS CD and obesity were each associated with decreased cecal and sigmoid MLI bacterial diversity and distinct bacterial composition compared to controls, including expansion of Escherichia/Shigella. Cecal and sigmoid dysbiosis indices for CD were significantly greater in obese controls than non-overweight controls. CD, but not obesity, was characterized by altered biogeographic relationship between the sigmoid and cecum. GRS was associated with select taxonomic shifts that overlapped with changes seen in CD compared to controls including Fusobacterium enrichment. Stricturing or penetrating Crohn's disease behavior was characterized by lower MLI bacterial diversity and altered composition, including reduced Faecalibacterium, compared to uncomplicated CD. Taxonomic profiles including reduced Parasutterella were associated with clinical disease progression over a mean follow-up of 3.7 years. Random forest classifiers using MLI bacterial abundances could distinguish disease state (area under the curve (AUC) 0.93), stricturing or penetrating Crohn's disease behavior (AUC 0.82), and future clinical disease progression (AUC 0.74). CD patients showed alterations in the MLI metabolome including increased cholate:deoxycholate ratio compared to controls. CONCLUSIONS Obesity, CD in endoscopic remission, and high CD genetic risk have overlapping colonic mucosal-luminal interface (MLI) microbiome features, suggesting a shared microbiome contribution to CD and obesity which may be influenced by genetic factors. Microbial profiling during endoscopic remission predicted Crohn's disease behavior and progression, supporting that MLI sampling could offer unique insight into CD pathogenesis and provide novel prognostic biomarkers.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA.
| | | | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Tytus Mak
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Maomeng Tong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Paul Ruegger
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Carol Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Philip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Eric Vasiliauskas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Andrew Ippoliti
- Department of Medicine, Keck School of Medicine of USC, Los Angeles, USA
| | - Gil Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - David Shih
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
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Payami H. The many genomes of Parkinson's disease. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2022; 167:59-80. [PMID: 36427959 DOI: 10.1016/bs.irn.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genetic component of Parkinson's disease, once firmly believed non-existent, involves the human genome, mitochondrial genome, and the microbiome. Understanding the genomics of PD requires identification of PD-relevant genes and learning how they interact within the hologenome and with their environment. This chapter is an evidence-based perspective of a geneticist on how far we have come in this endeavor. The contemporary scientific society started with a naive and simplistic view of PD, evolved to accept that Parkinson's disease is probably the most complex disease there is, the progress we have made in discovering the genes and elucidating their functions, and now assembling the parts to create the whole.
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Affiliation(s)
- Haydeh Payami
- Professor of Genetics and Neurology, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
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Cao X, Dong A, Kang G, Wang X, Duan L, Hou H, Zhao T, Wu S, Liu X, Huang H, Wu R. Modeling spatial interaction networks of the gut microbiota. Gut Microbes 2022; 14:2106103. [PMID: 35921525 PMCID: PMC9351588 DOI: 10.1080/19490976.2022.2106103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
How the gut microbiota is organized across space is postulated to influence microbial succession and its mutualistic relationships with the host. The lack of dynamic or perturbed abundance data poses considerable challenges for characterizing the spatial pattern of microbial interactions. We integrate allometric scaling theory, evolutionary game theory, and prey-predator theory into a unified framework under which quasi-dynamic microbial networks can be inferred from static abundance data. We illustrate that such networks can capture the full properties of microbial interactions, including causality, the sign of the causality, strength, and feedback loop, and are dynamically adaptive along spatial gradients, and context-specific, characterizing variability between individuals and within the same individual across time and space. We design and conduct a gut microbiota study to validate the model, characterizing key spatial determinants of the microbial differences between ulcerative colitis and healthy controls. Our model provides a sophisticated means of unraveling a complete atlas of how microbial interactions vary across space and quantifying causal relationships between such spatial variability and change in health state.
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Affiliation(s)
- Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China,Xiaocang Cao Department of Gastroenterology and Hepatology Tianjin Medical University General Hospital, Tianjin Medical UniversityGeneral Hospital, Tianjin Medical University, TianjinHebeiChina
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Xiaoli Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Liyun Duan
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Huixing Hou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Tianming Zhao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Shuang Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinjuan Liu
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China,Xinjuan Liu Department of Gastroenterology Beijing Chaoyang Hospital, Capital Medical University, BeijingHebeiChina
| | - He Huang
- School of Chemical Engineering and Technology, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China,He Huang School of Chemical Engineering and Technology Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, TianjinHebeiChina
| | - Rongling Wu
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA, USA,CONTACT Rongling Wu Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, the Pennsylvania State University, Hershey, PA17033, USA
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Ahmad S, Ashktorab H, Brim H, Housseau F. Inflammation, microbiome and colorectal cancer disparity in African-Americans: Are there bugs in the genetics? World J Gastroenterol 2022; 28:2782-2801. [PMID: 35978869 PMCID: PMC9280725 DOI: 10.3748/wjg.v28.i25.2782] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/27/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Dysregulated interactions between host inflammation and gut microbiota over the course of life increase the risk of colorectal cancer (CRC). While environmental factors and socio-economic realities of race remain predominant contributors to CRC disparities in African-Americans (AAs), this review focuses on the biological mediators of CRC disparity, namely the under-appreciated influence of inherited ancestral genetic regulation on mucosal innate immunity and its interaction with the microbiome. There remains a poor understanding of mechanisms linking immune-related genetic polymorphisms and microbiome diversity that could influence chronic inflammation and exacerbate CRC disparities in AAs. A better understanding of the relationship between host genetics, bacteria, and CRC pathogenesis will improve the prediction of cancer risk across race/ethnicity groups overall.
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Affiliation(s)
- Sami Ahmad
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, DC 20060, United States
| | - Hassan Brim
- Department of Pathology, Howard University, Washington, DC 20060, United States
| | - Franck Housseau
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
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Chu Y, Zhao Z, Cai L, Zhang G. Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis. ENVIRONMENTAL RESEARCH 2022; 210:112901. [PMID: 35227678 DOI: 10.1016/j.envres.2022.112901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.
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Affiliation(s)
- Yunmeng Chu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China
| | - Zelong Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, 201800, China
| | - Lixi Cai
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China; Faculty of Basic Medicine, Putian University, Putian, 351100, Fujian, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China.
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Markowitz RHG, LaBella AL, Shi M, Rokas A, Capra JA, Ferguson JF, Mosley JD, Bordenstein SR. Microbiome-associated human genetic variants impact phenome-wide disease risk. Proc Natl Acad Sci U S A 2022; 119:e2200551119. [PMID: 35749358 PMCID: PMC9245617 DOI: 10.1073/pnas.2200551119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/29/2022] [Indexed: 12/26/2022] Open
Abstract
Human genetic variation associates with the composition of the gut microbiome, yet its influence on clinical traits remains largely unknown. We analyzed the consequences of nearly a thousand gut microbiome-associated variants (MAVs) on phenotypes reported in electronic health records from tens of thousands of individuals. We discovered and replicated associations of MAVs with neurological, metabolic, digestive, and circulatory diseases. Five significant MAVs in these categories correlate with the relative abundance of microbes down to the strain level. We also demonstrate that these relationships are independently observed and concordant with microbe by disease associations reported in case-control studies. Moreover, a selective sweep and population differentiation impacted some disease-linked MAVs. Combined, these findings establish triad relationships among the human genome, microbiome, and disease. Consequently, human genetic influences may offer opportunities for precision diagnostics of microbiome-associated diseases but also highlight the relevance of genetic background for microbiome modulation and therapeutics.
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Affiliation(s)
- Robert H. George Markowitz
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, TN 37232
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
| | | | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
| | - John A. Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143
| | - Jane F. Ferguson
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, TN 37232
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jonathan D. Mosley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Seth R. Bordenstein
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, TN 37232
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
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Grego S, Welling CM, Miller GH, Coggan PF, Sellgren KL, Hawkins BT, Ginsburg GS, Ruiz JR, Fisher DA, Stoner BR. A hands-free stool sampling system for monitoring intestinal health and disease. Sci Rep 2022; 12:10859. [PMID: 35760855 PMCID: PMC9237014 DOI: 10.1038/s41598-022-14803-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
Analysis of stool offers simple, non-invasive monitoring for many gastrointestinal (GI) diseases and access to the gut microbiome, however adherence to stool sampling protocols remains a major challenge because of the prevalent dislike of handling one's feces. We present a technology that enables individual stool specimen collection from toilet wastewater for fecal protein and molecular assay. Human stool specimens and a benchtop test platform integrated with a commercial toilet were used to demonstrate reliable specimen collection over a wide range of stool consistencies by solid/liquid separation followed by spray-erosion. The obtained fecal suspensions were used to perform occult blood tests for GI cancer screening and for microbiome 16S rRNA analysis. Using occult blood home test kits, we found overall 90% agreement with standard sampling, 96% sensitivity and 86% specificity. Microbiome analysis revealed no significant difference in within-sample species diversity compared to standard sampling and specimen cross-contamination was below the detection limit of the assay. Furthermore, we report on the use of an analogue turbidity sensor to assess in real time loose stools for tracking of diarrhea. Implementation of this technology in residential settings will improve the quality of GI healthcare by facilitating increased adherence to routine stool monitoring.
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Affiliation(s)
- Sonia Grego
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA.
| | - Claire M Welling
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Graham H Miller
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Peter F Coggan
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Katelyn L Sellgren
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Brian T Hawkins
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Jose R Ruiz
- Division of Gastroenterology, School of Medicine, Duke University, Durham, NC, USA
| | - Deborah A Fisher
- Division of Gastroenterology, School of Medicine, Duke University, Durham, NC, USA
| | - Brian R Stoner
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
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Horigome A, Hashikura N, Yoshida K, Xiao JZ, Odamaki T. 2'-Fucosyllactose Increases the Abundance of Blautia in the Presence of Extracellular Fucosidase-Possessing Bacteria. Front Microbiol 2022; 13:913624. [PMID: 35722280 PMCID: PMC9201481 DOI: 10.3389/fmicb.2022.913624] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Blautia is a genus of anaerobic bacteria that is widely distributed in the mammalian gut. Recently, an increasing body of research has demonstrated a link between this genus and human health, suggesting applications as a novel probiotic strain. Moreover, we have previously shown that 2'-fucosyllactose (2'-FL), a major component of human milk oligosaccharides, increases the relative abundance of Blautia sp., particularly Blautia wexlerae, in the cultured fecal microbiota of healthy adults using a pH-controlled single-batch fermenter. However, the effects of 2'-FL on Blautia proliferation vary among individuals. In this study, we assessed the impact of the intrinsic gut microbiota on the prebiotic effects of 2'-FL. Metagenomic analysis of feces collected from all donors showed that the homolog of the intracellular GH95 α-l-fucosidase gene was considerably enriched in two non-responders (individuals who showed no increase in Blautia proliferation), whereas the homologous genes encoding extracellular α-l-fucosidase were more abundant in responders, suggesting that lactose and fucose released into the environment could be substrates mediating the growth of Blautia. In vitro assays confirmed the ability of B. wexlerae to utilize the two carbohydrates but not 2'-FL. We also observed that B. wexlerae utilized fucose released from 2'-FL by Bifidobacterium bifidum, which possessed extracellular GH95 α-l-fucosidase, in co-cultures of these two organisms. Finally, increasing the proportion of extracellular GH95 by the addition of a B. bifidum strain led to Blautia proliferation by 2'-FL in fecal cultures of the two non-responders. These findings provided valuable perspectives on individualized nutritional approaches to properly control the gut microbiota. Future clinical trials are needed to obtain further insights into the characteristics of responders vs. non-responders.
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Affiliation(s)
- Ayako Horigome
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Nanami Hashikura
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Keisuke Yoshida
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
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Chen SS, Liao XM, Wei QZ, Zhou YY, Su MY, Hu Y, Song YY, Zhang ZQ, Liang JJ. Associations of the Gut Microbiota Composition and Fecal Short-Chain Fatty Acids with Leukocyte Telomere Length in Children Aged 6 to 9 Years in Guangzhou, China: A Cross-sectional Study. J Nutr 2022; 152:1549-1559. [PMID: 35278080 DOI: 10.1093/jn/nxac063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/13/2022] [Accepted: 03/08/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Telomere length (TL) serves as a marker of cellular senescence and appears to plateau between the age of 4 y and young adulthood, after which the gut microbiota are supposed to be established. However, scarce data are available regarding the correlation between gut microbiota composition and TL in the pediatric population. OBJECTIVES We aimed to investigate whether the gut microbiota and the concentrations of SCFAs in feces are associated with leukocyte TL in children. METHODS In total, 401 children aged 6-9 y from Guangzhou were enrolled in this cross-sectional study. qPCR was used to determine relative TL in peripheral blood leukocytes. The gut microbiota was characterized by 16S ribosomal RNA amplicon sequencing and the fecal concentrations of total SCFAs and SCFA subtypes were determined using HPLC. The multivariate methods with an unbiased variable selection (MUVR) algorithm and partial least square models were used to select predictable operational taxonomic units (OTUs). Further correlation analyses were performed based on multiple linear regression models with adjustment for covariates and false discovery rate. RESULTS With the use of MUVR, 35 relevant and minimal optimal OTUs were finally selected. Multiple linear regression analysis showed that the abundance of several OTUs, including OTU334 (belonging to the genus Family XIII AD3011 group), OTU726 (belonging to the species Lachnoclostridium phocaeense), OTU1441 (belonging to the genus Ruminococcus torques group), OTU2553 (belonging to the genus Lachnospiraceae UCG-010), and OTU3375 (belonging to the family Lachnospiraceae), was negatively associated with leukocyte TL (β: -0.187 to -0.142; false discovery rate (FDR)-corrected P value (PFDR) = 0.009-0.035]. However, neither SCFA subtype nor total SCFA content in feces exhibited significant associations with TL (β: -0.032 to 0.048; PFDR = 0.915-0.969). CONCLUSIONS The gut microbiota, but not fecal SCFA concentration, was significantly associated with TL in this pediatric population.
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Affiliation(s)
- Shan-Shan Chen
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xue-Mei Liao
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qin-Zhi Wei
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ying-Yu Zhou
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Meng-Yang Su
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yan Hu
- Department of Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan-Yan Song
- Department of Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhe-Qing Zhang
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jing-Jing Liang
- Department of Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System. J Neuroimmune Pharmacol 2022; 17:76-93. [PMID: 34993905 DOI: 10.1007/s11481-021-10046-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022]
Abstract
Opioid use disorder (OUD) is defined as the chronic use or misuse of prescribed or illicitly obtained opioids and is characterized by clinically significant impairment. The etiology of OUD is multifactorial as it is influenced by genetics, environmental factors, stress response and behavior. Given the profound role of the gut microbiome in health and disease states, in recent years there has been a growing interest to explore interactions between the gut microbiome and the central nervous system as a causal link and potential therapeutic source for OUD. This review describes the role of the gut microbiome and opioid-induced immunopathological disturbances at the gut epithelial surface, which collectively contribute to OUD and perpetuate the vicious cycle of addiction and relapse.
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Gut–Skin Axis: Unravelling the Connection between the Gut Microbiome and Psoriasis. Biomedicines 2022; 10:biomedicines10051037. [PMID: 35625774 PMCID: PMC9138548 DOI: 10.3390/biomedicines10051037] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
Evidence has shown that gut microbiome plays a role in modulating the development of diseases beyond the gastrointestinal tract, including skin disorders such as psoriasis. The gut–skin axis refers to the bidirectional relationship between the gut microbiome and skin health. This is regulated through several mechanisms such as inflammatory mediators and the immune system. Dysregulation of microbiota has been seen in numerous inflammatory skin conditions such as atopic dermatitis, rosacea, and psoriasis. Understanding how gut microbiome are involved in regulating skin health may lead to development of novel therapies for these skin disorders through microbiome modulation, in particularly psoriasis. In this review, we will compare the microbiota between psoriasis patients and healthy control, explain the concept of gut–skin axis and the effects of gut dysbiosis on skin physiology. We will also review the current evidence on modulating gut microbiome using probiotics in psoriasis.
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Joyce SA, O'Malley D. Bile acids, bioactive signalling molecules in interoceptive gut-to-brain communication. J Physiol 2022; 600:2565-2578. [PMID: 35413130 PMCID: PMC9325455 DOI: 10.1113/jp281727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022] Open
Abstract
Aside from facilitating solubilisation and absorption of dietary lipids and lipid-soluble vitamins, amphipathic bile acids (BAs) also act as bioactive signalling molecules. A plethora of conjugated or un-conjugated primary and bacterially-modified secondary BA moieties have been identified, with significant divergence between species. These molecules are excreted into the external environment of the intestinal lumen, yet nuclear and membrane receptors that are sensitive to BAs are expressed internally in the liver, intestinal and neural tissues, amongst others. The diversity of BAs and receptors underpins the multitude of distinct bioactive functions attributed to BAs, but also hampers elucidation of the physiological mechanisms underpinning these actions. In this topical review, we have considered the potential of BAs as cross-barrier signalling molecules that contribute to interoceptive pathways informing the central nervous system of environmental changes in the gut lumen. Activation of BAs on FGF19 -secreting enterocytes, enteroendocrine cells coupled to sensory nerves or intestinal immune cells would facilitate indirect signalling, whereas direct activation of BA receptors in the brain are likely to occur primarily under pathophysiological conditions when concentrations of BAs are elevated. Abstract figure legend The figure illustrates the microbial modification of hepatic primary bile acids into secondary bile acids. In addition to facilitating lipid digestion and absorption, bile acids act as bioactive signalling molecules by binding to bile acid receptors expressed on enterocytes, neural afferent-coupled enteroendocrine cells and immune cells. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Dervla O'Malley
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Physiology, College of Medicine and Health, University College Cork, Cork, Ireland
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50
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Caron B, Patin E, Rotival M, Charbit B, Albert ML, Quintana-Murci L, Duffy D, Rausell A. Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes. Genome Med 2022; 14:28. [PMID: 35264221 PMCID: PMC8905727 DOI: 10.1186/s13073-022-01032-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Blood plasma proteins play an important role in immune defense against pathogens, including cytokine signaling, the complement system, and the acute-phase response. Recent large-scale studies have reported genetic (i.e., protein quantitative trait loci, pQTLs) and non-genetic factors, such as age and sex, as major determinants to inter-individual variability in immune response variation. However, the contribution of blood-cell composition to plasma protein heterogeneity has not been fully characterized and may act as a mediating factor in association studies. METHODS Here, we evaluated plasma protein levels from 400 unrelated healthy individuals of western European ancestry, who were stratified by sex and two decades of life (20-29 and 60-69 years), from the Milieu Intérieur cohort. We quantified 229 proteins by Luminex in a clinically certified laboratory and their levels of variation were analyzed together with 5.2 million single-nucleotide polymorphisms. With respect to non-genetic variables, we included 254 lifestyle and biochemical factors, as well as counts of seven circulating immune cell populations measured by hemogram and standardized flow cytometry. RESULTS Collectively, we found 152 significant associations involving 49 proteins and 20 non-genetic variables. Consistent with previous studies, age and sex showed a global, pervasive impact on plasma protein heterogeneity, while body mass index and other health status variables were among the non-genetic factors with the highest number of associations. After controlling for these covariates, we identified 100 and 12 pQTLs acting in cis and trans, respectively, collectively associated with 87 plasma proteins and including 19 novel genetic associations. Genetic factors explained the largest fraction of the variability of plasma protein levels, as compared to non-genetic factors. In addition, blood-cell fractions, including leukocytes, lymphocytes, monocytes, neutrophils, eosinophils, basophils, and platelets, had a larger contribution to inter-individual variability than age and sex and appeared as confounders of specific genetic associations. Finally, we identified new genetic associations with plasma protein levels of five monogenic Mendelian disease genes including two primary immunodeficiency genes (Ficolin-3 and FAS). CONCLUSIONS Our study identified novel genetic and non-genetic factors associated to plasma protein levels which may inform health status and disease management.
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Affiliation(s)
- Barthelemy Caron
- Université de Paris, INSERM UMR1163, Imagine Institute, Clinical Bioinformatics Laboratory, F-75006, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Université de Paris, F-75015, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Université de Paris, F-75015, Paris, France
| | - Bruno Charbit
- Cytometry and Biomarkers UTechS, CRT, Institut Pasteur, Université de Paris, F-75015, Paris, France
| | | | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Université de Paris, F-75015, Paris, France
- Human Genomics and Evolution, Collège de France, F-75005, Paris, France
| | - Darragh Duffy
- Cytometry and Biomarkers UTechS, CRT, Institut Pasteur, Université de Paris, F-75015, Paris, France.
- Translational Immunology Unit, Institut Pasteur, Université de Paris, F-75015, Paris, France.
| | - Antonio Rausell
- Université de Paris, INSERM UMR1163, Imagine Institute, Clinical Bioinformatics Laboratory, F-75006, Paris, France.
- Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, F-75015, Paris, France.
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