1
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Chimileski S, Borisy GG, Dewhirst FE, Mark Welch JL. Tip extension and simultaneous multiple fission in a filamentous bacterium. Proc Natl Acad Sci U S A 2024; 121:e2408654121. [PMID: 39226354 DOI: 10.1073/pnas.2408654121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community-the human dental plaque biofilm-a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque.
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Affiliation(s)
- Scott Chimileski
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Gary G Borisy
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA 02142
| | - Floyd E Dewhirst
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA 02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115
| | - Jessica L Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA 02142
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2
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Molteni C, Forni D, Cagliani R, Sironi M. Comparative genomics reveal a novel phylotaxonomic order in the genus Fusobacterium. Commun Biol 2024; 7:1102. [PMID: 39244637 PMCID: PMC11380691 DOI: 10.1038/s42003-024-06825-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024] Open
Abstract
Fusobacteria have been associated to different diseases, including colorectal cancer (CRC), but knowledge of which taxonomic groups contribute to specific conditions is incomplete. We analyzed the genetic diversity and relationships within the Fusobacterium genus. We report recent and ancestral recombination in core genes, indicating that fusobacteria have mosaic genomes and emphasizing that taxonomic demarcation should not rely on single genes/gene regions. Across databases, we found ample evidence of species miss-classification and of undescribed species, which are both expected to complicate disease association. By focusing on a lineage that includes F. periodonticum/pseudoperiodonticum and F. nucleatum, we show that genomes belong to four modern populations, but most known species/subspecies emerged from individual ancestral populations. Of these, the F. periodonticum/pseudoperiodonticum population experienced the lowest drift and displays the highest genetic diversity, in line with the less specialized distribution of these bacteria in oral sites. A highly drifted ancestral population instead contributed genetic ancestry to a new species, which includes genomes classified within the F. nucleatum animalis diversity in a recent CRC study. Thus, evidence herein calls for a re-analysis of F. nucleatum animalis features associated to CRC. More generally, our data inform future molecular profiling approaches to investigate the epidemiology of Fusobacterium-associated diseases.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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3
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Costa LCMC, Carvalho MDG, Vale FF, Marques AT, Rasmussen LT, Chen T, Barros-Pinheiro M. Helicobacter pylori in oral cavity: current knowledge. Clin Exp Med 2024; 24:209. [PMID: 39230790 PMCID: PMC11374826 DOI: 10.1007/s10238-024-01474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
The oral cavity may play a role as a reservoir and in the transmission and colonization of Helicobacter pylori. The route of transmission for H. pylori is not fully understood. The prevalence of this pathogen varies globally, affecting half of the world's population, predominantly in developing countries. Here, we review the prevalence of H. pylori in the oral cavity, the characteristics that facilitate its colonization and dynamics in the oral microbiome, the heterogeneity and diversity of virulence of among strains, and noninvasive techniques for H. pylori detection in oral samples. The prevalence of H. pylori in the oral cavity varies greatly, being influenced by the characteristics of the population, regions where samples are collected in the oral cavity, and variations in detection methods. Although there is no direct association between the presence of H. pylori in oral samples and stomach infection, positive cases for gastric H. pylori frequently exhibit a higher prevalence of the bacterium in the oral cavity, suggesting that the stomach may not be the sole reservoir of H. pylori. In the oral cavity, H. pylori can cause microbiome imbalance and remodeling of the oral ecosystem. Detection of H. pylori in the oral cavity by a noninvasive method may provide a more accessible diagnostic tool as well as help prevent transmission and gastric re-colonization. Further research into this bacterium in the oral cavity will offer insights into the treatment of H. pylori infection, potentially developing new clinical approaches.
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Affiliation(s)
- Liana Cristina Melo Carneiro Costa
- Programa de Pós-graduação em Ciências da Saúde, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del-Rei (UFSJ), Divinópolis, Brazil.
- BioISI - BioSystems and Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisbon, Portugal.
| | - Maria das Graças Carvalho
- Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia da Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Filipa F Vale
- BioISI - BioSystems and Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisbon, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Andreia T Marques
- BioISI - BioSystems and Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisbon, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | | | - Tsute Chen
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Melina Barros-Pinheiro
- Programa de Pós-graduação em Ciências da Saúde, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del-Rei (UFSJ), Divinópolis, Brazil
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4
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Cornish AJ, Gruber AJ, Kinnersley B, Chubb D, Frangou A, Caravagna G, Noyvert B, Lakatos E, Wood HM, Thorn S, Culliford R, Arnedo-Pac C, Househam J, Cross W, Sud A, Law P, Leathlobhair MN, Hawari A, Woolley C, Sherwood K, Feeley N, Gül G, Fernandez-Tajes J, Zapata L, Alexandrov LB, Murugaesu N, Sosinsky A, Mitchell J, Lopez-Bigas N, Quirke P, Church DN, Tomlinson IPM, Sottoriva A, Graham TA, Wedge DC, Houlston RS. The genomic landscape of 2,023 colorectal cancers. Nature 2024; 633:127-136. [PMID: 39112709 PMCID: PMC11374690 DOI: 10.1038/s41586-024-07747-9] [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: 11/14/2022] [Accepted: 06/24/2024] [Indexed: 08/17/2024]
Abstract
Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.
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Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- University College London Cancer Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Frangou
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Boris Noyvert
- Cancer Research UK Centre and Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steve Thorn
- Department of Oncology, University of Oxford, Oxford, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jacob Househam
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - William Cross
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | | | - Aliah Hawari
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Connor Woolley
- Department of Oncology, University of Oxford, Oxford, UK
| | - Kitty Sherwood
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nathalie Feeley
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Güler Gül
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Luis Zapata
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Nirupa Murugaesu
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alona Sosinsky
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Jonathan Mitchell
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Philip Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
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5
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Kumar A, Casamassimo P, Kovalchin J, Claman D, Peng J, McDaniel J, Hunt WG, Wong CA. The changing profile of infective endocarditis: A multi-year retrospective study for dentists. Int J Paediatr Dent 2024; 34:673-679. [PMID: 38297423 DOI: 10.1111/ipd.13167] [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: 01/23/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Infective endocarditis (IE) has high morbidity and mortality and is often attributed to dental procedures. AIM This study characterized variables related to paediatric IE in a paediatric hospital cohort. DESIGN A retrospective review of medical records, from January 1, 2008, to January 1, 2020, to examine demographic, medical and dental history, and risk factors associated with children diagnosed with IE at Nationwide Children's Hospital. RESULTS Of the 242 patients who were admitted with tentative IE diagnoses, 67 met the inclusion criteria: 46 (69%) had underlying cardiac conditions and 21 (31%) had not. One-third had an infection with S. aureus and viridans streptococci. Age was significantly associated with intracardiac devices in children with IE. Mean hospitalization was 25 days, and the mortality was 6 (9%); 41(61%) required surgery for causative defects, and 24 (32%) had dental consultation during admission. CONCLUSION Although cardiac-related conditions were present in most cases, IE occurred in patients without cardiac factors.
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Affiliation(s)
- Ashok Kumar
- Division of Pediatric Dentistry, The Ohio State University College of Dentistry, and Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Paul Casamassimo
- Division of Pediatric Dentistry, The Ohio State University College of Dentistry, and Nationwide Children's Hospital, Columbus, Ohio, USA
| | - John Kovalchin
- Section of Cardiology, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Daniel Claman
- Division of Pediatric Dentistry, The Ohio State University College of Dentistry, and Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jin Peng
- Research Information Solutions and Innovation Research & Development, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jodee McDaniel
- Division of Pediatric Dentistry and Division of Dental Hygiene, The Ohio State University College of Dentistry, and Nationwide Children's Hospital, Columbus, Ohio, USA
| | - W Garrett Hunt
- Section of Infectious Diseases, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Chloe A Wong
- Division of Pediatric Dentistry, The Ohio State University College of Dentistry, and Nationwide Children's Hospital, Columbus, Ohio, USA
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6
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Li J, O’Toole PW. Disease-associated microbiome signature species in the gut. PNAS NEXUS 2024; 3:pgae352. [PMID: 39228810 PMCID: PMC11370893 DOI: 10.1093/pnasnexus/pgae352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
There is an accumulation of evidence that the human gut microbiota plays a role in maintaining health, and that an altered gut microbiota (sometimes called dysbiosis) associates with risk for many noncommunicable diseases. However, the dynamics of disease-linked bacteria in the gut and other body sites remain unclear. If microbiome alterations prove causative in particular diseases, therapeutic intervention may be possible. Furthermore, microbial signature taxa have been established for the diagnosis of some diseases like colon cancer. We identified 163 disease-enriched and 98 disease-depleted gut microbiome signature taxa at species-level resolution (signature species) from 10 meta-analyses of multiple diseases such as colorectal cancer, ulcerative colitis, Crohn's disease, irritable bowel syndrome, pancreatic cancer, and COVID-19 infection. Eight signature species were enriched and nine were depleted across at least half of the diseases studied. Compared with signature species depleted in diseases, a significantly higher proportion of disease-enriched signature species were identified as extra-intestinal (primarily oral) inhabitants, had been reported in bacteremia cases from the literature, and were aerotolerant anaerobes. These findings highlight the potential involvement of oral microbes, bacteremia isolates, and aerotolerant anaerobes in disease-associated gut microbiome alterations, and they have implications for patient care and disease management.
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Affiliation(s)
- Junhui Li
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
| | - Paul W O’Toole
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
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7
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Rodríguez-Varela R, Yaka R, Pochon Z, Sanchez-Pinto I, Solaun JL, Naidoo T, Guinet B, Pérez-Ramallo P, Lagerholm VK, de Anca Prado V, Valdiosera C, Krzewińska M, Herrasti L, Azkarate A, Götherström A. Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis. SCIENCE ADVANCES 2024; 10:eadp8625. [PMID: 39196943 PMCID: PMC11352919 DOI: 10.1126/sciadv.adp8625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/30/2024]
Abstract
Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Iban Sanchez-Pinto
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - José Luis Solaun
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
| | - Benjamin Guinet
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Lourdes Herrasti
- Departamento de Antropología, Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | - Agustín Azkarate
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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8
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Austin GI, Korem T. Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective. J Infect Dis 2024:jiae378. [PMID: 39189314 DOI: 10.1093/infdis/jiae378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Indexed: 08/28/2024] Open
Abstract
As investigations of low-biomass microbial communities have become more common, so too has the recognition of major challenges affecting these analyses. These challenges have been shown to compromise biological conclusions and have contributed to several controversies. Here, we review some of the most common and influential challenges in low-biomass microbiome research. We highlight key approaches to alleviate these potential pitfalls, combining experimental planning strategies and data analysis methods.
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Affiliation(s)
- George I Austin
- Department of Biomedical Informatics
- Program for Mathematical Genomics, Department of Systems Biology
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
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9
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Khan MW, Cruz de Jesus V, Mittermuller BA, Sareen S, Lee V, Schroth RJ, Hu P, Chelikani P. Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries. Cell Rep 2024; 43:114635. [PMID: 39154338 DOI: 10.1016/j.celrep.2024.114635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/04/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Early childhood caries (ECC) is influenced by microbial and host factors, including social, behavioral, and oral health. In this cross-sectional study, we analyze interkingdom dynamics in the dental plaque microbiome and its association with host variables. We use 16S rRNA and ITS1 amplicon sequencing on samples collected from preschool children and analyze questionnaire data to examine the social determinants of oral health. The results indicate a significant enrichment of Streptococcus mutans and Candida dubliniensis in ECC samples, in contrast to Neisseria oralis in caries-free children. Our interkingdom correlation analysis reveals that Candida dubliniensis is strongly correlated with both Neisseria bacilliformis and Prevotella veroralis in ECC. Additionally, ECC shows significant associations with host variables, including oral health status, age, place of residence, and mode of childbirth. This study provides empirical evidence associating the oral microbiome with socioeconomic and behavioral factors in relation to ECC, offering insights for developing targeted prevention strategies.
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Affiliation(s)
- Mohd Wasif Khan
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Vivianne Cruz de Jesus
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada; Department of Preventive Dental Science, University of Manitoba, Winnipeg, MB, Canada
| | - Betty-Anne Mittermuller
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada; Department of Preventive Dental Science, University of Manitoba, Winnipeg, MB, Canada
| | - Shaan Sareen
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada
| | - Victor Lee
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Department of Preventive Dental Science, University of Manitoba, Winnipeg, MB, Canada
| | - Robert J Schroth
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada; Department of Preventive Dental Science, University of Manitoba, Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Department of Biochemistry, Western University, London, ON, Canada.
| | - Prashen Chelikani
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada; Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada; Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB, Canada.
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10
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Khan MW, Fung DLX, Schroth RJ, Chelikani P, Hu P. A cross-cohort analysis of dental plaque microbiome in early childhood caries. iScience 2024; 27:110447. [PMID: 39104404 PMCID: PMC11298647 DOI: 10.1016/j.isci.2024.110447] [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: 11/10/2023] [Revised: 05/05/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Early childhood caries (ECC) is a multifactorial disease with a microbiome playing a significant role in caries progression. Understanding changes at the microbiome level in ECC is required to develop diagnostic and preventive strategies. In our study, we combined data from small independent cohorts to compare microbiome composition using a unified pipeline and applied a batch correction to avoid the pitfalls of batch effects. Our meta-analysis identified common biomarker species between different studies. We identified the best machine learning method for the classification of ECC versus caries-free samples and compared the performance of this method using a leave-one-dataset-out approach. Our random forest model was found to be generalizable when used in combination with other studies. While our results highlight the potential microbial species involved in ECC and disease classification, we also mentioned the limitations that can serve as a guide for future researchers to design and use appropriate tools for such analyses.
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Affiliation(s)
- Mohd Wasif Khan
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | | | - Robert J. Schroth
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Preventive Dental Science, University of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Prashen Chelikani
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry, Western University, London, ON, Canada
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11
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Tanwar H, Gnanasekaran JM, Allison D, Chuang LS, He X, Aimetti M, Baima G, Costalonga M, Cross RK, Sears C, Mehandru S, Cho J, Colombel JF, Raufman JP, Thumbigere-Math V. Unravelling the Oral-Gut Axis: Interconnection Between Periodontitis and Inflammatory Bowel Disease, Current Challenges, and Future Perspective. J Crohns Colitis 2024; 18:1319-1341. [PMID: 38417137 PMCID: PMC11324343 DOI: 10.1093/ecco-jcc/jjae028] [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: 08/21/2023] [Revised: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 03/01/2024]
Abstract
As the opposite ends of the orodigestive tract, the oral cavity and the intestine share anatomical, microbial, and immunological ties that have bidirectional health implications. A growing body of evidence suggests an interconnection between oral pathologies and inflammatory bowel disease [IBD], implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an 'oral-gut' axis, marked by a higher prevalence of periodontitis and other oral conditions in IBD patients and vice versa. We present an in-depth examination of the interconnection between oral pathologies and IBD, highlighting the shared microbiological and immunological pathways, and proposing a 'multi-hit' hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.
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Affiliation(s)
- Himanshi Tanwar
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | | | - Devon Allison
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Ling-shiang Chuang
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Massimo Costalonga
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Raymond K Cross
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cynthia Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saurabh Mehandru
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Pierre Raufman
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vivek Thumbigere-Math
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
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12
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Tanimoto H, Ogawa Y, Nambu T, Koi T, Ohashi H, Okinaga T, Yamamoto K. Microbial contamination of spittoons and germicidal effect of irradiation with krypton chloride excimer lamps (Far UV-C 222 nm). PLoS One 2024; 19:e0308404. [PMID: 39110743 PMCID: PMC11305547 DOI: 10.1371/journal.pone.0308404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND In dentistry, instruments, appliances, and body fluids such as saliva or blood are possible sources of infection. Although conventional antiseptic procedures effectively prevent infection, spittoons cannot be sanitized between each treated patient and are usually washed only with running water. However, there is currently no fast and efficient disinfection method that can be implemented between treatments. An optically filtered krypton chloride excimer lamp using ultraviolet light (Far UV-C) in the 200-230 nm wavelength range (innocuous to humans) has been recently used as a virus- and bacteria-inactivating technology. This study aimed to identify the bioburden of a dental spittoon and examine the susceptibility of two oral Streptococcus and two Enterococci to 222-nm Far UV-C by irradiating the spittoon with 222 nm Far UV-C for 5 min before evaluating the disinfection effect. METHODS Bacterial analysis and real-time polymerase-chain reaction testing was used to confirm the spittoon's biological contamination. Bacterial susceptibility to a 222-nm Far UV-C was determined with a graded dose irradiation test. After each treatment, the spittoon was irradiated with 222-nm Far UV-C for 5 min, and the disinfecting effect was evaluated. Microbial analysis of the spittoon's surface was performed using the Silva database. RESULTS We found that > 97% of the microbes consisted of six bacterial phyla, whereas no viruses were found. Pseudomonas aeruginosa was frequently detected. The 1-log reduction value of two oral-derived Streptococci and two Enterococci species at 222-nm Far UV-C was 4.5-7.3 mJ/cm2. Exposure of the spittoon to 222-nm Far UV-C at 3.6-13.5 mJ/cm2 significantly decreased bacterial counts (p < 0.001). CONCLUSIONS Irradiation with 222-nm Far UV-C at 3.6-13.5 mJ/cm2 significantly eliminates bacteria in spittoons, even when they are only rinsed with water. Hence, 222-nm Far UV-C irradiation may inhibit the risk of bacterial transmission from droplets in sink surfaces.
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Affiliation(s)
- Hiroaki Tanimoto
- Department of Operative Dentistry, Osaka Dental University, Osaka, Hirakata, Japan
| | | | - Takayuki Nambu
- Department of Microbiology, Osaka Dental University, Osaka, Hirakata, Japan
| | - Toru Koi
- Ushio Inc., Chiyoda-ku, Tokyo, Japan
| | | | - Toshinori Okinaga
- Department of Microbiology, Osaka Dental University, Osaka, Hirakata, Japan
| | - Kazuyo Yamamoto
- Department of Operative Dentistry, Osaka Dental University, Osaka, Hirakata, Japan
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13
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Lijia Z, Jia Chao Q, Li L, Shikun D, Peiyang G. Case report: A case of widespread soft tissue infection and multiple abscesses secondary to hidradenitis suppurativa inducing septic shock caused by Lawsonella clevelandensis in China. Front Med (Lausanne) 2024; 11:1392430. [PMID: 39165375 PMCID: PMC11333241 DOI: 10.3389/fmed.2024.1392430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024] Open
Abstract
Lawsonella clevelandensis is rare to associated with human infection, which may cause abscesses in abdominal cavity, liver, breast, and spine. Lawsonella clevelandensis is very difficult to be cultivated in regular manner; detection of 16S rRNA sequence is the main evidence for L. clevelandensis infection. The clinical manifestations of L. clevelandensis infection resemble other agents of Nocardia, Tuberculosis and non-tuberculous Mycobacterium (NTM) due to their morphologic similarities. Hidradenitis suppurativa (HS) is a chronic inflammatory disorder, which affects the intertriginous skin and is associated with numerous systemic comorbidities. HS eventually leads to severe pain, multiple abscesses, pus discharge, and irreversible tissue destruction. Lawsonella clevelandensis has not been reported to cause HS and systemic comorbidities. We presented the case of a 33-year-old male with widespread soft tissue infection and multiple abscesses secondary to HS (Hurley stage III) inducing septic shock caused by L. clevelandensis in China. He was diagnosed as HS and treated with intravenous antibiotic empirically. He developed multiple abscesses including lung and scrota. Bacterial and fungal cultures on blood and secretions from multiple skin lesions were all negative. Due to the misdiagnosis and progression of disease, the patient was transferred to intensive care unit, and he underwent drainage of the chest and right hemothorax removal under thoracoscopic. During the hospitalization, the patient developed septic shock and received mechanical ventilation. Computerized tomography (CT) scans revealed mediastinal emphysema, multiple subcutaneous emphysema, and severe pneumonia. Gene analysis of samples of incision and drainage of pus at the skin showed the rare infection of L. clevelandensis. Finally, the patients with recurrent soft tissue infections and multiple abscesses with negative microbiological culture results recovered after effective abscess drainage and antibiotic therapy. We suggested that NGS is a crucial supplementary diagnostic tool in individuals with recurrent skin infections and multiple abscesses, especially when conventional diagnostic methods are inconclusive.
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Affiliation(s)
- Zhi Lijia
- Department of Intensive Care Unit, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qi Jia Chao
- Department of Respiratory and Critical Care Medicine, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Li Li
- Department of Intensive Care Unit, Chengdu Integrated TCM and Western Medicine Hospital, Chengdu, China
| | - Deng Shikun
- Department of Intensive Care Unit, Chengdu Pidu District Hospital of Traditional Chinese Medicine, Chengdu, China
| | - Gao Peiyang
- Department of Intensive Care Unit, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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14
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Joo YB, Lee J, Park YJ, Bang SY, Kim K, Lee HS. Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity. PLoS One 2024; 19:e0308010. [PMID: 39106279 DOI: 10.1371/journal.pone.0308010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/16/2024] [Indexed: 08/09/2024] Open
Abstract
The lung is recognized as a site for initiating the formation of self-antigen and autoimmune responses in rheumatoid arthritis (RA). We aimed to investigate the association of upper respiratory microbiota with RA, autoantibody production, and disease activity. Forty-six patients with RA and 17 controls were examined. Nasopharyngeal swab samples were sequenced for microbiome profiling using the V3-V4 region of the 16S rRNA gene. The microbial diversity and relative abundance were compared between RA patients and controls. Correlation analyses were conducted to evaluate the relationship between microbial abundance and clinical markers such as autoantibodies and disease activity. Microbial diversity analysis revealed no major differences between RA patients and healthy controls. However, beta diversity analysis indicated a subtle distinction in microbial composition (unweighted UniFrac distance) between the two groups (P = 0.03), hinting at a minor subset of microbiota associated with disease status. Differential abundance analysis uncovered specific taxa at various taxonomic levels, including Saccharibacteria (TM7) [O-1] (PFDR = 2.53 × 10-2), TM7 [F-1] (PFDR = 5.20 × 10-3), Microbacterium (PFDR = 3.37 × 10-4), and Stenotrophomonas (PFDR = 2.57 × 10-3). The relative abundance of ten genera correlated significantly with anti-cyclic citrullinated peptide (anti-CCP) antibody levels (PFDR < 0.05) and 11 genera were significantly associated with disease activity markers, including ESR, CRP, DAS28-ESR, and DAS-CRP (PFDR < 0.05). In particular, Saccharibacteria TM7 [G-3] and Peptostreptococcaceae [XI] [G-1] were correlated with all disease activity biomarkers. Dysbiosis in the upper respiratory mucosa is associated with RA, anti-CCP antibody levels, and disease activity.
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Affiliation(s)
- Young Bin Joo
- Department of Internal Medicine, Division of Rheumatology, Hanyang University Guri Hospital, Guri, Republic of Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Republic of Korea
| | - Juho Lee
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Yune-Jung Park
- Department of Internal Medicine, Division of Rheumatology, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - So-Young Bang
- Department of Internal Medicine, Division of Rheumatology, Hanyang University Guri Hospital, Guri, Republic of Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Republic of Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Hye-Soon Lee
- Department of Internal Medicine, Division of Rheumatology, Hanyang University Guri Hospital, Guri, Republic of Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Republic of Korea
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15
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Wong MW, Lo IH, Wu WK, Liu PY, Yang YT, Chen CY, Wu MS, Wong SH, Lei WY, Yi CH, Liu TT, Hung JS, Liang SW, Gyawali CP, Chen CL. Impact of Esophageal Motility on Microbiome Alterations in Symptomatic Gastroesophageal Reflux Disease Patients With Negative Endoscopy: Exploring the Role of Ineffective Esophageal Motility and Contraction Reserve. J Neurogastroenterol Motil 2024; 30:332-342. [PMID: 38972868 PMCID: PMC11238106 DOI: 10.5056/jnm22191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/20/2023] [Accepted: 05/01/2023] [Indexed: 07/09/2024] Open
Abstract
Background/Aims Ineffective esophageal motility (IEM) is common in patients with gastroesophageal reflux disease (GERD) and can be associated with poor esophageal contraction reserve on multiple rapid swallows. Alterations in the esophageal microbiome have been reported in GERD, but the relationship to presence or absence of contraction reserve in IEM patients has not been evaluated. We aim to investigate whether contraction reserve influences esophageal microbiome alterations in patients with GERD and IEM. Methods We prospectively enrolled GERD patients with normal endoscopy and evaluated esophageal motility and contraction reserve with multiple rapid swallows during high-resolution manometry. The esophageal mucosa was biopsied for DNA extraction and 16S ribosomal RNA gene V3-V4 (Illumina)/full-length (Pacbio) amplicon sequencing analysis. Results Among the 56 recruited patients, 20 had normal motility (NM), 19 had IEM with contraction reserve (IEM-R), and 17 had IEM without contraction reserve (IEM-NR). Esophageal microbiome analysis showed a significant decrease in microbial richness in patients with IEM-NR when compared to NM. The beta diversity revealed different microbiome profiles between patients with NM or IEM-R and IEM-NR (P = 0.037). Several esophageal bacterial taxa were characteristic in patients with IEM-NR, including reduced Prevotella spp. and Veillonella dispar, and enriched Fusobacterium nucleatum. In a microbiome-based random forest model for predicting IEM-NR, an area under the receiver operating characteristic curve of 0.81 was yielded. Conclusions In symptomatic GERD patients with normal endoscopic findings, the esophageal microbiome differs based on contraction reserve among IEM. Absent contraction reserve appears to alter the physiology and microbiota of the esophagus.
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Affiliation(s)
- Ming-Wun Wong
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
- School of Post-Baccalaureate Chinese Medicine, Tzu Chi University, Hualien, Taiwan
| | - I-Hsuan Lo
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Kai Wu
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Departments of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Yu Liu
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tang Yang
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chun-Yao Chen
- Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Departments of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Sunny H Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Wei-Yi Lei
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Chih-Hsun Yi
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Tso-Tsai Liu
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Jui-Sheng Hung
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Shu-Wei Liang
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - C Prakash Gyawali
- Division of Gastroenterology, Washington University School of Medicine, St Louis, MI, USA
| | - Chien-Lin Chen
- Department of Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
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16
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Liu J, Spencer N, Utter DR, Grossman AS, Lei L, Dos Santos NC, Shi W, Baker JL, Hasturk H, He X, Bor B. Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation. MICROBIOME 2024; 12:132. [PMID: 39030586 PMCID: PMC11264962 DOI: 10.1186/s40168-024-01854-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/03/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear. RESULTS Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions. CONCLUSIONS Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella's enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts. Video Abstract.
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Affiliation(s)
- Jett Liu
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Nell Spencer
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Daniel R Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alex S Grossman
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Lei Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases &, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Nídia Castro Dos Santos
- Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
- Albert Einstein School of Dental Medicine, Albert Einstein Israelite Hospital, São Paulo, SP, Brazil
| | - Wenyuan Shi
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Hatice Hasturk
- Center for Clinical and Translational Research, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Xuesong He
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Batbileg Bor
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA.
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17
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Konkel JE, Cox JR, Wemyss K. Bite-sized immunology; damage and microbes educating immunity at the gingiva. Mucosal Immunol 2024:S1933-0219(24)00070-9. [PMID: 39038755 DOI: 10.1016/j.mucimm.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
Immune cells residing at the gingiva experience diverse and unique signals, tailoring their functions to enable them to appropriately respond to immunological challenges and maintain tissue integrity. The gingiva, defined as the mucosal barrier that surrounds and supports the teeth, is the only barrier site completely transected by a hard structure, the tooth. The tissue is damaged in early life during tooth eruption and chronically throughout life by the process of mastication. This occurs alongside challenges typical of barrier sites, including exposure to invading pathogens, the local commensal microbial community and environmental antigens. This review will focus on the immune network safeguarding gingival integrity, which is far less understood than that resident at other barrier sites. A detailed understanding of the gingiva-resident immune network is vital as it is the site of the inflammatory disease periodontitis, the most common chronic inflammatory condition in humans which has well-known detrimental systemic effects. Furthering our understanding of how the immune populations within the gingiva develop, are tailored in health, and how this is dysregulated in disease would further the development of effective therapies for periodontitis.
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Affiliation(s)
- Joanne E Konkel
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Joshua R Cox
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Kelly Wemyss
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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18
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Semmler F, Regis Belisário-Ferrari M, Kulosa M, Kaysser L. The Metabolic Potential of the Human Lung Microbiome. Microorganisms 2024; 12:1448. [PMID: 39065215 PMCID: PMC11278768 DOI: 10.3390/microorganisms12071448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
The human lung microbiome remains largely underexplored, despite its potential implications in the pharmacokinetics of inhaled drugs and its involvement in lung diseases. Interactions within these bacterial communities and with the host are complex processes which often involve microbial small molecules. In this study, we employed a computational approach to describe the metabolic potential of the human lung microbiome. By utilizing antiSMASH and BiG-SCAPE software, we identified 1831 biosynthetic gene clusters for the production of specialized metabolites in a carefully compiled genome database of lung-associated bacteria and fungi. It was shown that RiPPs represent the largest class of natural products within the bacteriome, while NRPs constitute the largest class of natural products in the lung mycobiome. All predicted BGCs were further categorized into 767 gene cluster families, and a subsequent network analysis highlighted that these families are widely distributed and contain many uncharacterized members. Moreover, in-depth annotation allowed the assignment of certain gene clusters to putative lung-specific functions within the microbiome, such as osmoadaptation or surfactant synthesis. This study establishes the lung microbiome as a prolific source for secondary metabolites and lays the groundwork for detailed investigation of this unique environment.
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Affiliation(s)
| | | | | | - Leonard Kaysser
- Department of Pharmaceutical Biology, Institute for Drug Discovery, University of Leipzig, 04317 Leipzig, Germany; (F.S.); (M.R.B.-F.); (M.K.)
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19
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Lundtorp-Olsen C, Nygaard N, Massarenti L, Constancias F, Damgaard C, Kahraman Gursoy U, van Splunter A, Bikker FJ, Gursoy M, Markvart M, Belstrøm D. Supragingival microbiota, cytokines, and proteins in individuals with different trajectories in experimental gingivitis. J Oral Microbiol 2024; 16:2372861. [PMID: 38979478 PMCID: PMC11229773 DOI: 10.1080/20002297.2024.2372861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/09/2024] [Indexed: 07/10/2024] Open
Abstract
Background Gingivitis in response to biofilm formation may exhibit different trajectories. The purposes of the present study were to characterize the composition of the supragingival microbiota and salivary cytokine and protein levels in healthy individuals with different gingivitis patterns, to test the hypothesis that manifestations of gingivitis associate with specific profiles in terms of supragingival microbiota, salivary cytokines, and proteins. Methods Forty orally and systemically healthy individuals refrained from all oral hygiene procedures for a period of 14 days, followed by a resolution period of 14 days with regular oral care. Supragingival plaque level and bleeding on probing (BOP) were recorded, and supragingival plaque as well as saliva samples were collected at baseline, day 14, and day 28. Based on change in BOP% from baseline to day 14, rapid (n = 15), moderate (n = 10), and slow (n = 15) responders were identified. Supragingival microbiota composition, salivary cytokine, and protein levels were compared between groups at baseline, day 14, and day 28. Results A significantly higher baseline abundance of Capnocytophaga, Eikenella, and Campylobacter species were recorded in rapid responders, whereas a significantly higher baseline abundance of Streptococcus species were detected in slow responders. Slow responders expressed a high degree of resilience, with minimal difference in microbial composition at baseline and after 14 days of resolution (day 28). On the contrary, significant differences in relative abundance of members of the core microbiota, Streptococcus, Actinomyces, and Rothia species, was noted in baseline samples versus day 28 samples in rapid responders. Comparable baseline cytokine and protein levels were recorded in all groups. Conclusion Supragingival microbiota composition, but not saliva cytokine and protein profiles, seems to influence the extent of the inflammatory response during development of gingivitis in systemically healthy individuals.
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Affiliation(s)
- Christine Lundtorp-Olsen
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikoline Nygaard
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Massarenti
- Department of Odontology, Section for Oral Biology and Immunopathology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Florentin Constancias
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Damgaard
- Department of Odontology, Section for Oral Biology and Immunopathology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulvi Kahraman Gursoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Annina van Splunter
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit, Amsterdam, Netherlands
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit, Amsterdam, Netherlands
| | - Mervi Gursoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Merete Markvart
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Belstrøm
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Iqbal NT, Chen RY, Griffin NW, Hibberd MC, Khalid A, Sadiq K, Jamil Z, Ahmed K, Iqbal J, Hotwani A, Kabir F, Rahman N, Rizvi A, Idress R, Ahmed Z, Ahmed S, Umrani F, Syed S, Moore SR, Ali A, Barratt MJ, Gordon JI. A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction. mSphere 2024; 9:e0019624. [PMID: 38742887 PMCID: PMC11332341 DOI: 10.1128/msphere.00196-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
Environmental enteric dysfunction (EED) is a subclinical syndrome of altered small intestinal function postulated to be an important contributor to childhood undernutrition. The role of small intestinal bacterial communities in the pathophysiology of EED is poorly defined due to a paucity of studies where there has been a direct collection of small intestinal samples from undernourished children. Sixty-three members of a Pakistani cohort identified as being acutely malnourished between 3 and 6 months of age and whose wasting (weight-for-length Z-score [WLZ]) failed to improve after a 2-month nutritional intervention underwent esophagogastroduodenoscopy (EGD). Paired duodenal luminal aspirates and duodenal mucosal biopsies were obtained from 43 children. Duodenal microbiota composition was characterized by sequencing bacterial 16S rRNA gene amplicons. Levels of bacterial taxa (amplicon sequence variants [ASVs]) were referenced to anthropometric indices, histopathologic severity in biopsies, expression of selected genes in the duodenal mucosa, and fecal levels of an immunoinflammatory biomarker (lipocalin-2). A "core" group of eight bacterial ASVs was present in the duodenal samples of 69% of participants. Streptococcus anginosus was the most prevalent, followed by Streptococcus sp., Gemella haemolysans, Streptococcus australis, Granulicatella elegans, Granulicatella adiacens, and Abiotrophia defectiva. At the time of EGD, none of the core taxa were significantly correlated with WLZ. Statistically significant correlations were documented between the abundances of Granulicatella elegans and Granulicatella adiacens and the expression of duodenal mucosal genes involved in immune responses (dual oxidase maturation factor 2, serum amyloid A, and granzyme H). These results suggest that a potential role for members of the oral microbiota in pathogenesis, notably Streptococcus, Gemella, and Granulicatella species, warrants further investigation.IMPORTANCEUndernutrition among women and children is a pressing global health problem. Environmental enteric dysfunction (EED) is a disease of the small intestine (SI) associated with impaired gut mucosal barrier function and reduced capacity for nutrient absorption. The cause of EED is ill-defined. One emerging hypothesis is that alterations in the SI microbiota contribute to EED. We performed a culture-independent analysis of the SI microbiota of a cohort of Pakistani children with undernutrition who had failed a standard nutritional intervention, underwent upper gastrointestinal tract endoscopy, and had histologic evidence of EED in their duodenal mucosal biopsies. The results revealed a shared group of bacterial taxa in their duodenums whose absolute abundances were correlated with levels of the expression of genes in the duodenal mucosa that are involved in inflammatory responses. A number of these bacterial taxa are more typically found in the oral microbiota, a finding that has potential physiologic and therapeutic implications.
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Affiliation(s)
- Najeeha T. Iqbal
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
| | - Robert Y. Chen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas W. Griffin
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthew C. Hibberd
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aqsa Khalid
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Zehra Jamil
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
| | - Kumail Ahmed
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Najeeb Rahman
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Arjumand Rizvi
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Romana Idress
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Zubair Ahmed
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Sana Syed
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Michael J. Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey I. Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
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Li H, Li J, Hu J, Chen J, Zhou W. High-performing cross-dataset machine learning reveals robust microbiota alteration in secondary apical periodontitis. Front Cell Infect Microbiol 2024; 14:1393108. [PMID: 38975327 PMCID: PMC11224960 DOI: 10.3389/fcimb.2024.1393108] [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: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
Multiple research groups have consistently underscored the intricate interplay between the microbiome and apical periodontitis. However, the presence of variability in experimental design and quantitative assessment have added a layer of complexity, making it challenging to comprehensively assess the relationship. Through an unbiased methodological refinement analysis, we re-analyzed 4 microbiota studies including 120 apical samples from infected teeth (with/without root canal treatment), healthy teeth, using meta-analysis and machine learning. With high-performing machine-learning models, we discover disease signatures of related species and enriched metabolic pathways, expanded understanding of apical periodontitis with potential therapeutic implications. Our approach employs uniform computational tools across datasets to leverage statistical power and define a reproducible signal potentially linked to the development of secondary apical periodontitis (SAP).
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Affiliation(s)
- Hao Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiehang Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiani Hu
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
- School of Chemistry Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jionglin Chen
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
| | - Wei Zhou
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
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22
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Braz SHG, Monteiro MF, Matumoto EK, Corrêa MG, Casarin RCV, Ribeiro FV, Cirano FR, Casati MZ, Pimentel SP. Microbial colonization in the partially exposed nonabsorbable membrane during alveolar ridge preservation. Clin Oral Investig 2024; 28:373. [PMID: 38874776 DOI: 10.1007/s00784-024-05763-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
AIM This study evaluated the impact of the partial exposition of the nonabsorbable membrane (dPTFE) on microbial colonization during bone healing. MATERIALS AND METHODS Patients indicated for tooth extraction were randomized to dPTFE group (n = 22) - tooth extraction and alveolar ridge preservation (ARP) using an intentionally exposed dPTFE membrane and USH group (n = 22) - tooth extraction and unassisted socket healing. Biofilm samples were collected at the barrier in the dPTFE and on the natural healing site in the USH after 3 and 28 days. Samples from the inner surface of the dPTFE barrier were also collected (n = 13). The microbiome was evaluated using the Illumina MiSeq system. RESULTS Beta diversity was different from 3 to 28 days in both groups, and at 28 days, different microbial communities were identified between therapies. The dPTFE was characterized by a higher prevalence and abundance of gram-negative and anaerobic species than USH. Furthermore, the inner surface of the dPTFE membrane was colonized by a different community than the one observed on the outer surface. CONCLUSION Intentionally exposed dPTFE membrane modulates microbial colonization in the ARP site, creating a more homogeneous and anaerobic community on the inner and outer surfaces of the membrane. CLINICAL RELEVANCE DPTFE promoted faster biofilm colonization and enrichment of gram-negative and anaerobes close to the regenerated site in the membrane's inner and outer surfaces. dPTFE membrane can be used exposed to the oral site, but approaches for biofilm control should still be considered. The study was retrospectively registered at Clinicaltrials.gov (NCT04329351).
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Affiliation(s)
- Silvia Helena Garcia Braz
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
| | - Mabelle Freitas Monteiro
- Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Av. Limeira, 901, Areião, Piracicaba, 13414-903, SP, Brazil.
| | - Edson Ken Matumoto
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
| | - Mônica Grazieli Corrêa
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
| | - Renato Corrêa Viana Casarin
- Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Av. Limeira, 901, Areião, Piracicaba, 13414-903, SP, Brazil
| | - Fernanda Vieira Ribeiro
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
| | - Fabiano Ribeiro Cirano
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
| | - Marcio Zaffalon Casati
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
| | - Suzana Peres Pimentel
- Dental Research Division, School of Dentistry, Paulista University, Av. Dr. Bacelar, 1212, 4° andar, Vila Clementino, São Paulo, 04026-002, SP, Brazil
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Zhu J, Sun C, Li M, Hu G, Zhao XM, Chen WH. Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial. Gut 2024; 73:1087-1097. [PMID: 38050061 PMCID: PMC11187400 DOI: 10.1136/gutjnl-2023-330168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
OBJECTIVE We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis. DESIGN Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups. RESULTS Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users. CONCLUSION Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use. TRIAL REGISTRATION NUMBER ChiCTR2300072310.
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Affiliation(s)
- Jiaying Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Min Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guoru Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Henan, China
- Medical Artificial Intelligence Research Institute, Binzhou Medical University, Yantai, China
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24
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Powell AM, Ali Khan FZ, Ravel J, Elovitz MA. Untangling Associations of Microbiomes of Pregnancy and Preterm Birth. Clin Perinatol 2024; 51:425-439. [PMID: 38705650 PMCID: PMC11070640 DOI: 10.1016/j.clp.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
This review illuminates the complex interplay between various maternal microbiomes and their influence on preterm birth (PTB), a driving and persistent contributor to neonatal morbidity and mortality. Here, we examine the dynamics of oral, gastrointestinal (gut), placental, and vaginal microbiomes, dissecting their roles in the pathogenesis of PTB. Importantly, focusing on the vaginal microbiome and PTB, the review highlights (1) a protective role of Lactobacillus species; (2) an increased risk with select anaerobes; and (3) the influence of social health determinants on the composition of vaginal microbial communities.
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Affiliation(s)
- Anna Maya Powell
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Phipps 249, Baltimore, MD 21287, USA
| | - Fouzia Zahid Ali Khan
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Phipps 249, Baltimore, MD 21287, USA
| | - Jacques Ravel
- Department of Microbiology and Immunology, Institute for Genome Sciences, 670 West Baltimore Street, 3rd Floor, Room 3173, Baltimore, MD 21201, USA
| | - Michal A Elovitz
- Department of Obstetrics and Gynecology, Women's Health Research, Icahn School of Medicine at Mount Sinai, Women's Biomedical Research Institute, 1468 Madison Avenue, New York, NY 10029, USA.
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Guan Y, Zhu Z, Peng Q, Li M, Li X, Yang JW, Lu YH, Wang M, Xie BB. Genomic and Metagenomic Insights into the Distribution of Nicotine-degrading Enzymes in Human Microbiota. Curr Genomics 2024; 25:226-235. [PMID: 39086996 PMCID: PMC11288164 DOI: 10.2174/0113892029302230240319042208] [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: 01/03/2024] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Nicotine degradation is a new strategy to block nicotine-induced pathology. The potential of human microbiota to degrade nicotine has not been explored. Aims This study aimed to uncover the genomic potentials of human microbiota to degrade nicotine. Methods To address this issue, we performed a systematic annotation of Nicotine-Degrading Enzymes (NDEs) from genomes and metagenomes of human microbiota. A total of 26,295 genomes and 1,596 metagenomes for human microbiota were downloaded from public databases and five types of NDEs were annotated with a custom pipeline. We found 959 NdhB, 785 NdhL, 987 NicX, three NicA1, and three NicA2 homologs. Results Genomic classification revealed that six phylum-level taxa, including Proteobacteria, Firmicutes, Firmicutes_A, Bacteroidota, Actinobacteriota, and Chloroflexota, can produce NDEs, with Proteobacteria encoding all five types of NDEs studied. Analysis of NicX prevalence revealed differences among body sites. NicX homologs were found in gut and oral samples with a high prevalence but not found in lung samples. NicX was found in samples from both smokers and non-smokers, though the prevalence might be different. Conclusion This study represents the first systematic investigation of NDEs from the human microbiota, providing new insights into the physiology and ecological functions of human microbiota and shedding new light on the development of nicotine-degrading probiotics for the treatment of smoking-related diseases.
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Affiliation(s)
- Ying Guan
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Zhouhai Zhu
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Qiyuan Peng
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Meng Li
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Xuan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jia-Wei Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yan-Hong Lu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
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26
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Lundtorp-Olsen C, Markvart M, Twetman S, Belstrøm D. Effect of Probiotic Supplements on the Oral Microbiota-A Narrative Review. Pathogens 2024; 13:419. [PMID: 38787271 PMCID: PMC11124442 DOI: 10.3390/pathogens13050419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Data from systematic reviews and meta-analyses show that probiotics positively impact clinical parameters of oral diseases such as gingivitis, dental caries, and periodontitis. However, the working mechanism of probiotics is not fully understood, but is hypothesized to be mediated by direct and indirect interactions with the oral microbiota and the human host. In the present narrative review, we focused on the microbiological effect of probiotic supplements based on data retrieved from randomized clinical trials (RCTs). In addition, we assessed to what extent contemporary molecular methods have been employed in clinical trials in the field of oral probiotics. Multiple RCTs have been performed studying the potential effect of probiotics on gingivitis, dental caries, and periodontitis, as evaluated by microbial endpoints. In general, results are conflicting, with some studies reporting a positive effect, whereas others are not able to record any effect. Major differences in terms of study designs and sample size, as well as delivery route, frequency, and duration of probiotic consumption, hamper comparison across studies. In addition, most RCTs have been performed with a limited sample size using relatively simple methods for microbial identification, such as culturing, qPCR, and DNA-DNA checkerboard, while high-throughput methods such as 16S sequencing have only been employed in a few studies. Currently, state-of-the-art molecular methods such as metagenomics, metatranscriptomics, and metaproteomics have not yet been used in RCTs in the field of probiotics. The present narrative review revealed that the effect of probiotic supplements on the oral microbiota remains largely uncovered. One important reason is that most RCTs are performed without studying the microbiological effect. To facilitate future systematic reviews and meta-analyses, an internationally agreed core outcome set for the reporting of microbial endpoints in clinical trials would be desirable. Such a standardized collection of outcomes would most likely improve the quality of probiotic research in the oral context.
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Affiliation(s)
| | | | | | - Daniel Belstrøm
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (C.L.-O.); (M.M.); (S.T.)
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Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.14.589416. [PMID: 38645133 PMCID: PMC11030450 DOI: 10.1101/2024.04.14.589416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations. Results We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. Conclusions In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.
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Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy C. Davenport
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Selvaraj K, Venkatesan LS, Ganapathy D, Sathishkumar P. Treatment of dental biofilm-forming bacterium Streptococcus mutans using tannic acid-mediated gold nanoparticles. Microb Pathog 2024; 189:106568. [PMID: 38354988 DOI: 10.1016/j.micpath.2024.106568] [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: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Biosynthesized gold nanoparticles (AuNPs) are highly attracted as a biocompatible nanodrug to treat various diseased conditions in humans. In this study, phytochemical tannic acid-mediated AuNPs (TA-AuNPs) are successfully synthesized and tested for antibacterial and antibiofilm activity against dental biofilm-forming Streptococcus mutans biofilm. The synthesized TA-AuNPs are appeared as spherical in shape with an average size of 19 nm. The antibacterial potential of TA-AuNPs was evaluated using ZOI and MIC measurements; while, antibiofilm efficacy was measured by checking the eradication of preformed biofilm on the tooth model. The ZOI and MIC values for TA-AuNPs are 25 mm in diameter and 4 μg/mL, respectively. The MTT assay, CLSM, and SEM results demonstrate that the preformed S. mutans biofilm is completely eradicated at 4xMIC (16 μg/mL) of TA-AuNPs. Finally, the present study reveals that the synthesized TA-AuNPs might be a great therapeutic drug to treat dental biofilm-forming bacterium S. mutans.
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Affiliation(s)
- Kaviya Selvaraj
- Green Lab, Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, Tamil Nadu, India
| | - Lekha Sree Venkatesan
- Green Lab, Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, Tamil Nadu, India
| | - Dhanraj Ganapathy
- Green Lab, Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, Tamil Nadu, India
| | - Palanivel Sathishkumar
- Green Lab, Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, Tamil Nadu, India.
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Hernandez-Nicols BF, Robledo-Pulido JJ, Alvarado-Navarro A. Etiopathogenesis of Psoriasis: Integration of Proposed Theories. Immunol Invest 2024; 53:348-415. [PMID: 38240030 DOI: 10.1080/08820139.2024.2302823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Psoriasis is a chronic inflammatory disease characterized by squamous and erythematous plaques on the skin and the involvement of the immune system. Global prevalence for psoriasis has been reported around 1-3% with a higher incidence in adults and similar proportions between men and women. The risk factors associated with psoriasis are both extrinsic and intrinsic, out of which a polygenic predisposition is a highlight out of the latter. Psoriasis etiology is not yet fully described, but several hypothesis have been proposed: 1) the autoimmunity hypothesis is based on the over-expression of antimicrobial peptides such as LL-37, the proteins ADAMTSL5, K17, and hsp27, or lipids synthesized by the PLA2G4D enzyme, all of which may serve as autoantigens to promote the differentiation of autoreactive lymphocytes T and unleash a chronic inflammatory response; 2) dysbiosis of skin microbiota hypothesis in psoriasis has gained relevance due to the observations of a loss of diversity and the participation of pathogenic bacteria such as Streptococcus spp. or Staphylococcus spp. the fungi Malassezia spp. or Candida spp. and the virus HPV, HCV, or HIV in psoriatic plaques; 3) the oxidative stress hypothesis, the most recent one, describes that the cell injury and the release of proinflammatory mediators and antimicrobial peptides that leads to activate of the Th1/Th17 axis observed in psoriasis is caused by a higher release of reactive oxygen species and the imbalance between oxidant and antioxidant mechanisms. This review aims to describe the mechanisms involved in the three hypotheses on the etiopathogeneses of psoriasis.
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Affiliation(s)
- Brenda Fernanda Hernandez-Nicols
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Juan José Robledo-Pulido
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Anabell Alvarado-Navarro
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Hernández-Cabanyero C, Vonaesch P. Ectopic colonization by oral bacteria as an emerging theme in health and disease. FEMS Microbiol Rev 2024; 48:fuae012. [PMID: 38650052 PMCID: PMC11065354 DOI: 10.1093/femsre/fuae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/23/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024] Open
Abstract
The number of research papers published on the involvement of the oral microbiota in systemic diseases has grown exponentially over the last 4 years clearly demonstrating the growing interest in this field. Indeed, accumulating evidence highlights the central role of ectopic colonization by oral bacteria in numerous noncommunicable diseases including inflammatory bowel diseases (IBDs), undernutrition, preterm birth, neurological diseases, liver diseases, lung diseases, heart diseases, or colonic cancer. There is thus much interest in understanding the molecular mechanisms that lead to the colonization and maintenance of ectopic oral bacteria. The aim of this review is to summarize and conceptualize the current knowledge about ectopic colonization by oral bacteria, highlight wherever possible the underlying molecular mechanisms and describe its implication in health and disease. The focus lies on the newly discovered molecular mechanisms, showcasing shared pathophysiological mechanisms across different body sites and syndromes and highlighting open questions in the field regarding the pathway from oral microbiota dysbiosis to noncommunicable diseases.
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Affiliation(s)
- Carla Hernández-Cabanyero
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, UNIL-Sorge, 1015 Lausanne, Switzerland
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Demusaj D, Toma R, Khan T, Hu L, Banavar G, Vuyisich M. A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study. Biotechniques 2024; 76:83-93. [PMID: 38319053 DOI: 10.2144/btn-2023-0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples. We sampled and metatranscriptomically analyzed subgingival and subgingival-P samples of three different teeth in 20 individuals. The subgingival-P samples were comparable to the subgingival samples in the relative abundances of microorganisms and microbial gene expression levels. Our data demonstrate that the novel method of collecting and analyzing the subgingival-P samples can act as a proxy for the subgingiva, paving the way for large and diverse studies investigating the role of the subgingival microbiome in health and disease.
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Affiliation(s)
- Diana Demusaj
- Viome Life Sciences, Inc., Bothell, WA 98011 and Bellevue, WA 98004, New York, NY 10018, USA
| | - Ryan Toma
- Viome Life Sciences, Inc., Bothell, WA 98011 and Bellevue, WA 98004, New York, NY 10018, USA
| | - Tanveer Khan
- Viome Life Sciences, Inc., Bothell, WA 98011 and Bellevue, WA 98004, New York, NY 10018, USA
| | - Lan Hu
- Viome Life Sciences, Inc., Bothell, WA 98011 and Bellevue, WA 98004, New York, NY 10018, USA
| | - Guruduth Banavar
- Viome Life Sciences, Inc., Bothell, WA 98011 and Bellevue, WA 98004, New York, NY 10018, USA
| | - Momchilo Vuyisich
- Viome Life Sciences, Inc., Bothell, WA 98011 and Bellevue, WA 98004, New York, NY 10018, USA
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33
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Ekwudo MN, Gubert C, Hannan AJ. The microbiota-gut-brain axis in Huntington's disease: pathogenic mechanisms and therapeutic targets. FEBS J 2024. [PMID: 38426291 DOI: 10.1111/febs.17102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/08/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Huntington's disease (HD) is a currently incurable neurogenerative disorder and is typically characterized by progressive movement disorder (including chorea), cognitive deficits (culminating in dementia), psychiatric abnormalities (the most common of which is depression), and peripheral symptoms (including gastrointestinal dysfunction). There are currently no approved disease-modifying therapies available for HD, with death usually occurring approximately 10-25 years after onset, but some therapies hold promising potential. HD subjects are often burdened by chronic diarrhea, constipation, esophageal and gastric inflammation, and a susceptibility to diabetes. Our understanding of the microbiota-gut-brain axis in HD is in its infancy and growing evidence from preclinical and clinical studies suggests a role of gut microbial population imbalance (gut dysbiosis) in HD pathophysiology. The gut and the brain can communicate through the enteric nervous system, immune system, vagus nerve, and microbiota-derived-metabolites including short-chain fatty acids, bile acids, and branched-chain amino acids. This review summarizes supporting evidence demonstrating the alterations in bacterial and fungal composition that may be associated with HD. We focus on mechanisms through which gut dysbiosis may compromise brain and gut health, thus triggering neuroinflammatory responses, and further highlight outcomes of attempts to modulate the gut microbiota as promising therapeutic strategies for HD. Ultimately, we discuss the dearth of data and the need for more longitudinal and translational studies in this nascent field. We suggest future directions to improve our understanding of the association between gut microbes and the pathogenesis of HD, and other 'brain and body disorders'.
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Affiliation(s)
- Millicent N Ekwudo
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
| | - Carolina Gubert
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
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Ge Y, Bamashmous S, Mancinelli-Lyle D, Zadeh M, Mohamadzadeh M, Kotsakis GA. Interdental oral hygiene interventions elicit varying compositional microbiome changes in naturally occurring gingivitis: Secondary data analysis from a clinical trial. J Clin Periodontol 2024; 51:309-318. [PMID: 38088457 DOI: 10.1111/jcpe.13899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 09/27/2023] [Accepted: 10/22/2023] [Indexed: 02/17/2024]
Abstract
AIM To evaluate the effect of different oral irrigators on the sub-gingival microbiome composition in patients with naturally occurring plaque-induced gingivitis. MATERIALS AND METHODS Sub-gingival plaque was collected from adults participating in a clinical trial assessing the efficacy of oral hygiene with two different oral irrigators (Waterpik Water Flosser [Group 1] and Oral-B Water Flosser [Group 2]) versus dental flossing (Group 3) for microbiome analysis. Plaque samples were reflective of naturally occurring plaque-induced gingivitis at baseline and of gingival health at the endpoint (4 weeks). Clinical measures of gingival inflammation were collected, and the sub-gingival microbiome was analysed by 16S rRNA sequencing to identify amplicon sequence variants. RESULTS Oral hygiene instruction with self-performed manual toothbrushing and water-jet irrigation led to significant reductions in inflammation for all groups; both oral irrigators outperformed flossing in bleeding-on-probing reduction (p < .001). Microbiome diversity of sub-gingival plaque remained relatively stable over time, but significant changes were noted in certain taxa, consistent with increases in the relative abundance of commensals and reductions in late colonizers and periodontal pathogens in the water-jet groups. CONCLUSIONS Reduction in gingival inflammation at 4 weeks within the water-jet groups is accompanied by slight but critical changes in microbiome composition. Although biodiversity does not substantially change within 4 weeks during the resolution of naturally induced gingivitis, significant relative increases in commensal early colonizers such as Streptococcus, Veillonella and Fusobacterium were accompanied by a shift towards a less anaerobic microbiota associated with return to health. These changes were contingent upon the type of interdental hygiene, with Group 1 exhibiting more significant alterations in microbiome composition towards a periodontal-health-compatible community.
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Affiliation(s)
- Yong Ge
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, Texas, USA
| | - Shatha Bamashmous
- Department of Periodontology, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Deborah Mancinelli-Lyle
- Department of Periodontology, Academic Center for Dentistry, University of Amsterdam, Amsterdam, The Netherlands
| | - Mojgan Zadeh
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, Texas, USA
| | - Mansour Mohamadzadeh
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, Texas, USA
| | - Georgios A Kotsakis
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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Hernández-Ruiz P, Escalona Montaño AR, Amezcua-Guerra LM, González-Pacheco H, Niccolai E, Amedei A, Aguirre-García MM. Potential Association of the Oral Microbiome with Trimethylamine N-Oxide Quantification in Mexican Patients with Myocardial Infarction. Mediators Inflamm 2024; 2024:3985731. [PMID: 38415052 PMCID: PMC10898950 DOI: 10.1155/2024/3985731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024] Open
Abstract
Many attempts have been proposed to evaluate the linkage between the oral-gut-liver axis and the mechanisms related to the diseases' establishment. One of them is the oral microbiota translocation into the bloodstream, liver, and gut, promoting a host dysbiosis and triggering the presence of some metabolites such as trimethylamine N-oxide (TMAO), known as a risk marker for cardiovascular disease, and especially the myocardial infarction (MI). In the present pilot study, the involvement of oral dysbiosis related to the presence of TMAO has been considered an independent component of the standard risk factors (SRs) in the development of MI, which has not been previously described in human cohorts. A positive and significant correlation of TMAO levels with Porphyromonas was identified; likewise, the increase of the genus Peptidiphaga in patients without SRs was observed. We determined that the presence of SRs does not influence the TMAO concentration in these patients. This report is the first study where the relationship between oral dysbiosis and TMAO is specified in the Mexican population. Our findings provide information on the possible contribution of the oral pathogens associated with gut dysbiosis in the development of MI, although further analysis should be performed.
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Affiliation(s)
- Paulina Hernández-Ruiz
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Alma R Escalona Montaño
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Luis M Amezcua-Guerra
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Héctor González-Pacheco
- Unidad de Cuidados Coronarios, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
- Interdisciplinary Internal Medicine Unit, Careggi University Hospital, Florence 50134, Italy
| | - María M Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
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Wu T, Bai Y, Jing Y, Chen F. What can we learn from treatments of oral lichen planus? Front Cell Infect Microbiol 2024; 14:1279220. [PMID: 38426013 PMCID: PMC10902003 DOI: 10.3389/fcimb.2024.1279220] [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: 08/19/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024] Open
Abstract
Oral lichen planus (OLP), a T-lymphocyte-mediated disease of the oral mucosa, has a complex pathogenesis that involves a number of factors. The disease is characterized by recurrent episodes and requires continuous follow up, and there is no curative treatment available. Erosive lichen planus, among others, has a risk of malignant transformation and requires standardized treatment to control its progression. Different clinical subtypes of oral lichen planus require appropriate treatment. Pharmacological treatments are the most widely available and have the greatest variety of options and a number of novel pharmacological treatments are presented as highlights, including JAK enzyme inhibitors. The second is photodynamic therapy, which is the leading physiological treatment. In addition, periodontal treatment and psychological treatment should not be neglected. In this review, we briefly discuss the most recent developments in therapies for oral lichen planus after summarizing the most widely used clinical treatments, aiming to provide different proposals for future clinical treatment.
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Affiliation(s)
- Tingting Wu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Yang Bai
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Yin Jing
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Fangchun Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
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Luo S, Shao R, Hong Y, Zhang T, Zhou Q, Zhou Q, Rao F, Zhao X, Dong Y, Zhu R, Ling P, Cui G, Guan Z, Luo P, He Y, Qi X, Liao J, Hong W. Identifying the oral microbiome of adolescents with and without dental fluorosis based on full-length 16S rRNA gene sequencing. Front Microbiol 2024; 15:1296753. [PMID: 38380100 PMCID: PMC10876846 DOI: 10.3389/fmicb.2024.1296753] [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: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024] Open
Abstract
Dental fluorosis, resulting from long-term environmental exposure to fluoride, is prevalent among diverse populations worldwide. Severe fluorosis not only compromises the aesthetic appeal of teeth but also impairs their functionality. This study aims to investigate the oral microbiome in dental fluorosis and the health individuals of adolescents living in the endemic fluorosis area of Guizhou, China through full-length 16S rDNA sequencing. Fourty-six individuals meet the sampling criteria, and we divided these samples into the following groups: a healthy group (H = 23) and a dental fluorosis group (F = 23), and two subgroups of Miao ethnicity: a healthy Miao group (Hm = 13) and a dental fluorosis Miao group (Fm = 15). A total of 660,389 high-quality sequences were obtained, and 12,007 Amplicon Sequence Variants (ASVs) were identified, revealing significant variations in oral microbiome between Fm and Hm groups. The composition of oral microbiota was similar between the H and F groups. At the genus level, Pseudopropionibacterium and at the species level, Streptococcus oralis_subsp.dentisani_clade_058 were less abundant in group F than in group H (P < 0.05). Further analysis revealed that the abundance of Capnocytophaga gingivalis and Kingella denitrificans was significantly lower in Fm fluorosis patients than in the Hm group (P < 0.05). Based on the LEfSe analysis, the potential core biomarkers in the oral of Fm fluorosis patients were identified at different taxonomic levels, ranging from phylum to species. These include Gammaproteobacteria, Prevotella sp_HMT_304, Gemella sanguinis, and Gracilibacteria_(GN02). Network analysis revealed that the microbiota in the fluorosis group exhibited more complex interactions with each other than the healthy group. Notably, within the Hm group, the potential biomarkers Capnocytophaga gingivalis and Kingella denitrificans exhibited a positive correlation. Finally, we employed PICRUSt2 analysis to explore the abundance clustering of the top 30 functional units in each sample, and we found that the metabolic pathway compositions of the four groups were similar. In summary, our findings suggest that the microbial composition of plaque in Hm patients with dental fluorosis is significantly altered, and we identified the potential marker microorganisms that contribute to these changes.
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Affiliation(s)
- Shanshan Luo
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Ruirui Shao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Yue Hong
- He Guantun Town Health Center in Qixingguan District, Bijie, Guizhou, China
| | - Ting Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
- Collaborative Innovation Center for Preventionand Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guiyang, Guizhou, China
| | - Qingshuai Zhou
- Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Qian Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Fengqing Rao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Xingxing Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangting Dong
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Ruiyu Zhu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ping Ling
- Pediatric Intensive Care Unit, Guiyang Maternal and Child Health Care Hospital, Guiyang, Guizhou, China
| | - Guzhen Cui
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhizhong Guan
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Peng Luo
- Collaborative Innovation Center for Preventionand Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guiyang, Guizhou, China
| | - Yan He
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
- Collaborative Innovation Center for Preventionand Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guiyang, Guizhou, China
| | - Jian Liao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
| | - Wei Hong
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and School/Hospital of Stomatology Guizhou Medical University, Guiyang, Guizhou, China
- Collaborative Innovation Center for Preventionand Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guiyang, Guizhou, China
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Liu J, Jiang J, Lan Y, Li C, Han R, Wang J, Wang T, Zhao Z, Fan Z, He L, Fang J. Metagenomic analysis of oral and intestinal microbiome of patients during the initial stage of orthodontic treatment. Am J Orthod Dentofacial Orthop 2024; 165:161-172.e3. [PMID: 37966405 DOI: 10.1016/j.ajodo.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/01/2023] [Accepted: 07/01/2023] [Indexed: 11/16/2023]
Abstract
INTRODUCTION This prospective study analyzed changes in the oral and intestinal microbiomes in patients before and after fixed orthodontic treatment, elucidating the impacts of fixed orthodontic treatment on patient health and metabolism. METHODS Metagenomic analysis was conducted on stool, dental plaque, and saliva samples from 10 fixed orthodontic patients. All the samples were sequenced with Illumina NovaSeq 6000 with a paired-end sequencing length of 150 bp. Identification of taxa in metagenomes and functional annotation of genes of the microbiota were performed using the data after quality control. Clinical periodontal parameters, including the gingiva index, plaque index, and pocket probing depth, were examined at each time point in triplicates. Patients also received a table to record their oral hygiene habits of brushing, flossing, and dessert consumption frequency over 1 month. RESULTS The brushing and flossing times per day of patients were significantly increased after treatment compared with baseline. The number of times a patient ate dessert daily was also fewer after treatment than at baseline. In addition, the plaque index decreased significantly, whereas the pH value of saliva, gingiva index, and pocket probing depth did not change. No significant differences were observed between the participants before and after orthodontic treatment regarding alpha-diversity analysis of the gut, dental plaque, or saliva microbiota. However, on closer analysis, periodontal disease-associated bacteria levels in the oral cavity remain elevated. Alterations in gut microbiota were also observed after orthodontic treatment. CONCLUSIONS The richness and diversity of the microbiome did not change significantly during the initial stage of fixed orthodontic treatment. However, the levels of periodontal disease-associated bacteria increased.
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Affiliation(s)
- Jialing Liu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiyang Jiang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chengyan Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ruiying Han
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiao Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Tianyi Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Libang He
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
| | - Jie Fang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
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Stubbendieck RM, Hurst JH, Kelly MS. Dolosigranulum pigrum: A promising nasal probiotic candidate. PLoS Pathog 2024; 20:e1011955. [PMID: 38300905 PMCID: PMC10833571 DOI: 10.1371/journal.ppat.1011955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Affiliation(s)
- Reed M. Stubbendieck
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Jillian H. Hurst
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America
- Children’s Health and Discovery Institute, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Matthew S. Kelly
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
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Drigot ZG, Clark SE. Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia. Curr Opin Microbiol 2024; 77:102428. [PMID: 38277901 PMCID: PMC10922932 DOI: 10.1016/j.mib.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.
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Affiliation(s)
- Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA.
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Baker JL, Mark Welch JL, Kauffman KM, McLean JS, He X. The oral microbiome: diversity, biogeography and human health. Nat Rev Microbiol 2024; 22:89-104. [PMID: 37700024 PMCID: PMC11084736 DOI: 10.1038/s41579-023-00963-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 09/14/2023]
Abstract
The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.
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Affiliation(s)
- Jonathon L Baker
- Oregon Health & Science University, Portland, OR, USA
- J. Craig Venter Institute, La Jolla, CA, USA
- UC San Diego School of Medicine, La Jolla, CA, USA
| | - Jessica L Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | | | - Xuesong He
- The Forsyth Institute, Cambridge, MA, USA.
- Harvard School of Dental Medicine, Boston, MA, USA.
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Huffines JT, Boone RL, Kiedrowski MR. Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model. mSphere 2024; 9:e0058923. [PMID: 38179905 PMCID: PMC10826359 DOI: 10.1128/msphere.00589-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024] Open
Abstract
Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression. Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where S. aureus-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include S. aureus and several species belonging to the genus Corynebacterium, including Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and S. aureus, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal C. propinquum and C. pseudodiphtheriticum, reduce S. aureus growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between Corynebacterium species and S. aureus dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.IMPORTANCEChronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of S. aureus and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on S. aureus interactions with the nasal epithelium and the dominant genus of the healthy URT, Corynebacterium. Interactions between Corynebacterium species and S. aureus have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of S. aureus and clinical isolates of Corynebacterium from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.
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Affiliation(s)
- Joshua T. Huffines
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - RaNashia L. Boone
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Megan R. Kiedrowski
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
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Liu K, Guo Q, Ding Y, Luo L, Huang J, Zhang Q. Alterations in nasal microbiota of patients with amyotrophic lateral sclerosis. Chin Med J (Engl) 2024; 137:162-171. [PMID: 37482646 PMCID: PMC10798702 DOI: 10.1097/cm9.0000000000002701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Links between alterations in gut microbiota composition and amyotrophic lateral sclerosis (ALS) have previously been reported. This study aimed to examine the microbiota in the nasal cavity of ALS. METHODS Sixty-six ALS patients and 40 healthy caregivers who live in close proximity with patients were enrolled. High throughput metagenomic sequencing of the 16S ribosomal deoxyribonucleic acid (rDNA) gene V3-V4 region of nasal microbiota was used to characterize the alpha and beta diversity and relative abundance of bacterial taxa, predict function, and conduct correlation analysis between specific taxa and clinical features. RESULTS The nasal microbiome of ALS patients showed lower alpha diversity than that of corresponding healthy family members. Genera Gaiella , Sphingomonas , Polaribacter _1, Lachnospiraceae _NK4A136_group, Klebsiella , and Alistipes were differentially enriched in ALS patients compared to controls. Nasal microbiota composition in ALS patients significantly differed from that in healthy subjects (unweighted UniFrac P = 0.001), while Linear discriminant analysis Effect Size (LEfSe) analysis indicated that Bacteroidetes and Firmicutes dominated healthy nasal communities at the phylum level, whereas Actinobacteria was the predominant phylum and Thermoleophilia was the predominant class in ALS patients. Genus Faecalibacterium and Alistipes were positively correlated with ALS functional rating scale revised (ALSFRS-R; rs = 0.349, P = 0.020 and rs = 0.393, P = 0.008), while Prevotella -9 and Bacteroides operational taxonomic units (OTUs) were positively associated with lung function (FVC) in ALS patients ( rs = 0.304, P = 0.045, and rs = 0.300, P = 0.048, respectively). Prevotella -1 was positively correlated with white blood cell counts (WBC, rs = 0.347, P = 0.021), neutrophil percentage (Neu%, rs = 0.428, P = 0.004), and neutrophil-to-lymphocyte ratio (NLR, rs = 0.411, P = 0.006), but negatively correlated with lymphocyte percentage (Lym%, rs = -0.408, P = 0.006). In contrast, Streptococcus was negatively associated with Neu% ( rs = -0.445, P = 0.003) and NLR ( rs = -0.436, P = 0.003), while positively associated with Lym% ( rs = 0.437, P = 0.003). No significant differences in nasal microbiota richness and evenness were detected among the severe and mild ALS patients. CONCLUSIONS ALS is accompanied by altered nasal microbial community composition and diversity. The findings presented here highlight the need to understand how dysbiosis of nasal microbiota may contribute to the development of ALS.
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Affiliation(s)
- Kaixiong Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Qifu Guo
- Department of Neurology, Fujian Institute of Neurology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Ying Ding
- Department of Neurology, Fujian Institute of Neurology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Li Luo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Jianchai Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Qijie Zhang
- Department of Neurology, Fujian Institute of Neurology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
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Wang B, Deng J, Donati V, Merali N, Frampton AE, Giovannetti E, Deng D. The Roles and Interactions of Porphyromonas gingivalis and Fusobacterium nucleatum in Oral and Gastrointestinal Carcinogenesis: A Narrative Review. Pathogens 2024; 13:93. [PMID: 38276166 PMCID: PMC10820765 DOI: 10.3390/pathogens13010093] [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: 12/03/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Epidemiological studies have spotlighted the intricate relationship between individual oral bacteria and tumor occurrence. Porphyromonas gingivalis and Fusobacteria nucleatum, which are known periodontal pathogens, have emerged as extensively studied participants with potential pathogenic abilities in carcinogenesis. However, the complex dynamics arising from interactions between these two pathogens were less addressed. This narrative review aims to summarize the current knowledge on the prevalence and mechanism implications of P. gingivalis and F. nucleatum in the carcinogenesis of oral squamous cell carcinoma (OSCC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). In particular, it explores the clinical and experimental evidence on the interplay between P. gingivalis and F. nucleatum in affecting oral and gastrointestinal carcinogenesis. P. gingivalis and F. nucleatum, which are recognized as keystone or bridging bacteria, were identified in multiple clinical studies simultaneously. The prevalence of both bacteria species correlated with cancer development progression, emphasizing the potential impact of the collaboration. Regrettably, there was insufficient experimental evidence to demonstrate the synergistic function. We further propose a hypothesis to elucidate the underlying mechanisms, offering a promising avenue for future research in this dynamic and evolving field.
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Affiliation(s)
- Bing Wang
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
| | - Juan Deng
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
| | - Valentina Donati
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
- Unit of Pathological Anatomy 2, Azienda Ospedaliero-Universitaria Pisana, 56100 Pisa, Italy
| | - Nabeel Merali
- Minimal Access Therapy Training Unit (MATTU), Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; (N.M.); (A.E.F.)
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK
- Section of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Medical Science, University of Surrey, Guilford GU2 7WG, UK
| | - Adam E. Frampton
- Minimal Access Therapy Training Unit (MATTU), Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; (N.M.); (A.E.F.)
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK
- Section of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Medical Science, University of Surrey, Guilford GU2 7WG, UK
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
- Fondazione Pisana per la Scienza, 56100 Pisa, Italy
| | - Dongmei Deng
- Department of Prevention Dentistry, Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universitreit Amsterdam, 1081 LA Amsterdam, The Netherlands
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Kırdök E, Kashuba N, Damlien H, Manninen MA, Nordqvist B, Kjellström A, Jakobsson M, Lindberg AM, Storå J, Persson P, Andersson B, Aravena A, Götherström A. Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. Sci Rep 2024; 13:22125. [PMID: 38238372 PMCID: PMC10796427 DOI: 10.1038/s41598-023-48762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/30/2023] [Indexed: 01/22/2024] Open
Abstract
Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
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Affiliation(s)
- Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin, Turkey.
| | - Natalija Kashuba
- Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H Box 626, 751 26, Uppsala, Sweden
| | - Hege Damlien
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Mikael A Manninen
- PAES, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science, University of Helsinki, Viikinkaari 1, P.O. Box 65, Helsinki, Finland
| | - Bengt Nordqvist
- Foundation War-Booty Site Finnestorp, Klarinettvägen 75, 434 75, Kungsbacka, Sweden
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Evolutionsbiologiskt Centrum EBC Norbyvägen 18 A, Uppsala, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Hus Vita, 44018, Kalmar, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Per Persson
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Insitutet, P.O. Box 285, 171 77, Stockholm, Sweden
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
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46
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Aguirre-García MM, Amedei A, Hernández-Ruiz P, Gómez-García AP, Niccolai E, Moreno-Rodríguez AM, Pinto-Cardoso S, Alviter-Plata A, Escalona-Montaño AR, Ordaz-Robles ER, González-Salazar MDC, Springall Del Villar R, Berrios-Bárcenas EA, Ávila-Vanzzini N. Cytokine and microbiota profiles in obesity-related hypertension patients. Front Cell Infect Microbiol 2024; 13:1325261. [PMID: 38292856 PMCID: PMC10824975 DOI: 10.3389/fcimb.2023.1325261] [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: 10/20/2023] [Accepted: 12/30/2023] [Indexed: 02/01/2024] Open
Abstract
Background Systemic arterial hypertension is linked to a heightened risk of cardiovascular diseases on a global scale. In Mexico, nearly half of adults in vulnerable conditions experience hypertension. Imbalance in the oral and intestinal microbiota composition has been observed in patients with hypertension, documented by a decrease of bacteria producing short-chain fatty acids, which play a critical role in blood pressure regulation. Aim To examine the cytokines' profile and assess the characteristics of oral and gut microbiota in obesity-related hypertension in Mexican patients. Methods A cross-sectional, observational, and analytical study was carried out. Twenty-two patients were categorized by their body mass index (BMI) as overweight and obese, and the diagnosis of primary hypertension. DNA from supragingival dental plaque and feces samples was used to carry out 16S rRNA sequencing. Additionally, 13 cytokines were quantified. Results In the oral microbiota, Kluyvera was found to be significantly enriched in obese compared to overweight patients. Instead, the gut microbiota was dominated by Firmicutes. However, the correlation between certain genera and proinflammatory cytokines was noted. Conclusion This exploratory study provides insights into the complex relationship between the oral and gut microbiota and their association with systemic inflammation in obesity-related hypertension.
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Affiliation(s)
- María Magdalena Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Interdisciplinary Internal Medicine Unit, Careggi University Hospital, Florence, Italy
| | - Paulina Hernández-Ruiz
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Ana Pamela Gómez-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Aura M. Moreno-Rodríguez
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Ciudad de México, Mexico
| | - Adriana Alviter-Plata
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Alma R. Escalona-Montaño
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Erick R. Ordaz-Robles
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - María del C. González-Salazar
- Outpatient Clinic, Cardiovascular Risk Factors Clinic, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, Mexico
| | | | - Enrique A. Berrios-Bárcenas
- Outpatient Clinic, Cardiovascular Risk Factors Clinic, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, Mexico
| | - Nydia Ávila-Vanzzini
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
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Lin Y, Liang X, Li Z, Gong T, Ren B, Li Y, Peng X. Omics for deciphering oral microecology. Int J Oral Sci 2024; 16:2. [PMID: 38195684 PMCID: PMC10776764 DOI: 10.1038/s41368-023-00264-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
The human oral microbiome harbors one of the most diverse microbial communities in the human body, playing critical roles in oral and systemic health. Recent technological innovations are propelling the characterization and manipulation of oral microbiota. High-throughput sequencing enables comprehensive taxonomic and functional profiling of oral microbiomes. New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. Advanced imaging modalities including fluorescence, mass spectrometry, and Raman spectroscopy have enabled the visualization of the spatial organization and interactions of oral microbes with increasing resolution. Fluorescence techniques link phylogenetic identity with localization. Mass spectrometry imaging reveals metabolic niches and activities while Raman spectroscopy generates rapid biomolecular fingerprints for classification. Culturomics facilitates the isolation and cultivation of novel fastidious oral taxa using high-throughput approaches. Ongoing integration of these technologies holds the promise of transforming our understanding of oral microbiome assembly, gene expression, metabolites, microenvironments, virulence mechanisms, and microbe-host interfaces in the context of health and disease. However, significant knowledge gaps persist regarding community origins, developmental trajectories, homeostasis versus dysbiosis triggers, functional biomarkers, and strategies to deliberately reshape the oral microbiome for therapeutic benefit. The convergence of sequencing, imaging, cultureomics, synthetic systems, and biomimetic models will provide unprecedented insights into the oral microbiome and offer opportunities to predict, prevent, diagnose, and treat associated oral diseases.
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Affiliation(s)
- Yongwang Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyue Liang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhengyi Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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48
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Chen J, Sun Y, Li J, Lyu M, Yuan L, Sun J, Chen S, Hu C, Wei Q, Xu Z, Guo T, Cheng X. In-depth metaproteomics analysis of tongue coating for gastric cancer: a multicenter diagnostic research study. MICROBIOME 2024; 12:6. [PMID: 38191439 PMCID: PMC10773145 DOI: 10.1186/s40168-023-01730-8] [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: 08/06/2023] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Our previous study revealed marked differences in tongue images between individuals with gastric cancer and those without gastric cancer. However, the biological mechanism of tongue images as a disease indicator remains unclear. Tongue coating, a major factor in tongue appearance, is the visible layer on the tongue dorsum that provides a vital environment for oral microorganisms. While oral microorganisms are associated with gastric and intestinal diseases, the comprehensive function profiles of oral microbiota remain incompletely understood. Metaproteomics has unique strength in revealing functional profiles of microbiota that aid in comprehending the mechanism behind specific tongue coating formation and its role as an indicator of gastric cancer. METHODS We employed pressure cycling technology and data-independent acquisition (PCT-DIA) mass spectrometry to extract and identify tongue-coating proteins from 180 gastric cancer patients and 185 non-gastric cancer patients across 5 independent research centers in China. Additionally, we investigated the temporal stability of tongue-coating proteins based on a time-series cohort. Finally, we constructed a machine learning model using the stochastic gradient boosting algorithm to identify individuals at high risk of gastric cancer based on tongue-coating microbial proteins. RESULTS We measured 1432 human-derived proteins and 13,780 microbial proteins from 345 tongue-coating samples. The abundance of tongue-coating proteins exhibited high temporal stability within an individual. Notably, we observed the downregulation of human keratins KRT2 and KRT9 on the tongue surface, as well as the downregulation of ABC transporter COG1136 in microbiota, in gastric cancer patients. This suggests a decline in the defense capacity of the lingual mucosa. Finally, we established a machine learning model that employs 50 microbial proteins of tongue coating to identify individuals at a high risk of gastric cancer, achieving an area under the curve (AUC) of 0.91 in the independent validation cohort. CONCLUSIONS We characterized the alterations in tongue-coating proteins among gastric cancer patients and constructed a gastric cancer screening model based on microbial-derived tongue-coating proteins. Tongue-coating proteins are shown as a promising indicator for identifying high-risk groups for gastric cancer. Video Abstract.
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Affiliation(s)
- Jiahui Chen
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
| | - Yingying Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Jie Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Mengge Lyu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Li Yuan
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
| | - Jiancheng Sun
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shangqi Chen
- Department of General Surgery, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Can Hu
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
| | - Qing Wei
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
| | - Zhiyuan Xu
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China.
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China.
- Research Center for Industries of the Future, Westlake University, Hangzhou, China.
| | - Xiangdong Cheng
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China.
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Yu KM, Cho HS, Lee AM, Lee JW, Lim SK. Analysis of the influence of host lifestyle (coffee consumption, drinking, and smoking) on Korean oral microbiome. Forensic Sci Int Genet 2024; 68:102942. [PMID: 37862769 DOI: 10.1016/j.fsigen.2023.102942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/24/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
If a DNA sample collected in the field is old or degraded, short tandem repeat analysis is difficult to perform, a representative analysis method currently used for individual identification. Given that microorganisms exist everywhere and within the human body, in similar amounts to human cells, microbial analysis could be used to identify individuals even in cases in which human DNA-based identification is difficult. Research has demonstrated that the types of microorganisms within the human body differ depending on various internal or external factors, such as body part or bodily fluid type, lifestyle, geographical area of residence, sex, and age. In this study, we aimed to examine the relationship between lifestyle factors and the composition and diversity of the oral microbiome in individuals living in Korea. We collected 43 saliva samples from Korean individuals and analyzed the oral microbiome and its variations due to external factors, such as coffee consumption, drinking, and smoking. Linear discriminant analysis effect size revealed that Oribacterium, Campylobacter, and Megasphaera were abundant in coffee consumers, whereas Saccharimonadales, Clostridia, and Catonella were abundant in alcohol non-drinkers. We found increased levels of Stomatobaculum in the saliva of smokers, compared with that of non-smokers. Thus, our analysis revealed characteristic microorganisms for each parameter that was evaluated (coffee consumption, smoking, drinking). Consequently, our study provides insight into the oral microbiome in the Korean population and lays the foundation for developing the Korean Forensic Microbiome Database.
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Affiliation(s)
- Kyeong-Min Yu
- Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Hye-Seon Cho
- Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - A-Mi Lee
- Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Ji-Woo Lee
- Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Si-Keun Lim
- Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea.
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50
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Guo Y, Kitamoto S, Caballero-Flores G, Kim Y, Watanabe D, Sugihara K, Núñez G, Alteri CJ, Inohara N, Kamada N. Oral pathobiont Klebsiella chaperon usher pili provide site-specific adaptation for the inflamed gut mucosa. Gut Microbes 2024; 16:2333463. [PMID: 38545880 PMCID: PMC10984132 DOI: 10.1080/19490976.2024.2333463] [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: 12/20/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
The ectopic gut colonization by orally derived pathobionts has been implicated in the pathogenesis of various gastrointestinal diseases, including inflammatory bowel disease (IBD). For example, gut colonization by orally derived Klebsiella spp. has been linked to IBD in mice and humans. However, the mechanisms whereby oral pathobionts colonize extra-oral niches, such as the gut mucosa, remain largely unknown. Here, we performed a high-density transposon (Tn) screening to identify genes required for the adaptation of an oral Klebsiella strain to different mucosal sites - the oral and gut mucosae - at the steady state and during inflammation. We find that K. aerogenes, an oral pathobiont associated with both oral and gut inflammation in mice, harbors a newly identified genomic locus named "locus of colonization in the inflamed gut (LIG)" that encodes genes related to iron acquisition (Sit and Chu) and host adhesion (chaperon usher pili [CUP] system). The LIG locus is highly conserved among K. aerogenes strains, and these genes are also present in several other Klebsiella species. The Tn screening revealed that the LIG locus is required for the adaptation of K. aerogenes in its ectopic niche. In particular, we determined K. aerogenes employs a CUP system (CUP1) present in the LIG locus for colonization in the inflamed gut, but not in the oral mucosa. Thus, oral pathobionts likely exploit distinct adaptation mechanisms in their ectopically colonized intestinal niche compared to their native niche.
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Affiliation(s)
- Yijie Guo
- Department of Psychiatry and Center for Brain Science, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Gustavo Caballero-Flores
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Yeji Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daisuke Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kohei Sugihara
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Gabriel Núñez
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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