1
|
Sun X, Zhou X, Shi X, Abed OA, An X, Lei YL, Moon JJ. Strategies for the development of metalloimmunotherapies. Nat Biomed Eng 2024:10.1038/s41551-024-01221-7. [PMID: 38914800 DOI: 10.1038/s41551-024-01221-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/30/2024] [Indexed: 06/26/2024]
Abstract
Metal ions play crucial roles in the regulation of immune pathways. In fact, metallodrugs have a long record of accomplishment as effective treatments for a wide range of diseases. Here we argue that the modulation of interactions of metal ions with molecules and cells involved in the immune system forms the basis of a new class of immunotherapies. By examining how metal ions modulate the innate and adaptive immune systems, as well as host-microbiota interactions, we discuss strategies for the development of such metalloimmunotherapies for the treatment of cancer and other immune-related diseases.
Collapse
Affiliation(s)
- Xiaoqi Sun
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Editas Medicine, Cambridge, MA, USA.
| | - Xingwu Zhou
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoyue Shi
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Omar A Abed
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xinran An
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Yu Leo Lei
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
2
|
Diddeniya G, Ghaffari MH, Hernandez-Sanabria E, Guan LL, Malmuthuge N. INVITED REVIEW: Impact of Maternal Health and Nutrition on the Microbiome and Immune Development of Neonatal Calves. J Dairy Sci 2024:S0022-0302(24)00869-5. [PMID: 38825126 DOI: 10.3168/jds.2024-24835] [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: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024]
Abstract
This comprehensive review highlights the intricate interplay between maternal factors and the co-development of the microbiome and immune system in neonatal calves. Based on human and mouse studies, multiple prenatal and postnatal factors influence this process by altering the host-associated microbiomes (gut, respiratory tract, skin), microbial colonization trajectories, and priming of the immune systems (mucosal and systemic). This review emphasizes the importance of early life exposure, highlighting postnatal factors that work in synergy with maternal factors in further finetuning the co-development of the neonatal microbiome and immunity. In cattle, there is a general lack of research to identify the maternal effect on the early colonization process of neonatal calves (gut, respiratory tract) and its impact on the priming of the immune system. Past studies have primarily investigated the maternal effects on the passive transfer of immunity at birth. The co-development process of the microbiome and immune system is vital for lifelong health and production in cattle. Therefore, comprehensive research beyond the traditional focus on passive immunity is an essential step in this endeavor. Calf microbiome research reports the colonization of diverse bacterial communities in newborns, which is affected by the colostrum feeding method immediately after birth. In contrast to human studies reporting a strong link between maternal and infant bacterial communities, there is a lack of evidence to clearly define cow-to-calf transmission in cattle. Maternal exposure has been shown to promote the colonization of beneficial bacteria in neonatal calves. Nonetheless, calf microbiome research lacks links to early development of the immune system. An in-depth understanding of the impact of maternal factors on microbiomes and immunity will improve the management of pregnant cows to raise immune-fit neonatal calves. It is essential to investigate the diverse effects of maternal health conditions and nutrition during pregnancy on the gut microbiome and immunity of neonatal calves through collaboration among researchers from diverse fields such as microbiology, immunology, nutrition, veterinary science, and epidemiology.
Collapse
Affiliation(s)
| | | | - Emma Hernandez-Sanabria
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven 3000, Belgium
| | - Le Luo Guan
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, Canada
| | - Nilusha Malmuthuge
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, Canada.
| |
Collapse
|
3
|
Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation. Nat Med 2024:10.1038/s41591-024-02999-4. [PMID: 38783139 DOI: 10.1038/s41591-024-02999-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Hematopoietic cell transplantation (HCT) uses cytotoxic chemotherapy and/or radiation followed by intravenous infusion of stem cells to cure malignancies, bone marrow failure and inborn errors of immunity, hemoglobin and metabolism. Lung injury is a known complication of the process, due in part to disruption in the pulmonary microenvironment by insults such as infection, alloreactive inflammation and cellular toxicity. How microorganisms, immunity and the respiratory epithelium interact to contribute to lung injury is uncertain, limiting the development of prevention and treatment strategies. Here we used 278 bronchoalveolar lavage (BAL) fluid samples to study the lung microenvironment in 229 pediatric patients who have undergone HCT treated at 32 children's hospitals between 2014 and 2022. By leveraging paired microbiome and human gene expression data, we identified high-risk BAL compositions associated with in-hospital mortality (P = 0.007). Disadvantageous profiles included bacterial overgrowth with neutrophilic inflammation, microbiome contraction with epithelial fibroproliferation and profound commensal depletion with viral and staphylococcal enrichment, lymphocytic activation and cellular injury, and were replicated in an independent cohort from the Netherlands (P = 0.022). In addition, a broad array of previously occult pathogens was identified, as well as a strong link between antibiotic exposure, commensal bacterial depletion and enrichment of viruses and fungi. Together these lung-immune system-microorganism interactions clarify the important drivers of fatal lung injury in pediatric patients who have undergone HCT. Further investigation is needed to determine how personalized interpretation of heterogeneous pulmonary microenvironments may be used to improve pediatric HCT outcomes.
Collapse
Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Courtney M Rowan
- Department of Pediatrics, Division of Critical Care Medicine, Indiana University, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Division of Pediatric Oncology Harvard Medical School Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, Benioff Children's Hospital Oakland, University of California, San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- Department of Pediatrics, Division of Critical Care Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Department of Pediatric Medicine, Division of Critical Care, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Division of Pediatric Oncology Harvard Medical School Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Department of Pediatrics, Division of Pediatric Critical Care, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Department of Pediatrics, Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Columbia University, New York, NY, USA
| | - Paul Castillo
- UF Health Shands Children's Hospital, University of Florida, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, Division of Critical Care Medicine, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Department of Pediatrics, Division of Infectious Diseases, Children's National Hospital, Washington DC, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Department of Pediatrics, Division of Pediatric Hematology/Oncology/BMT, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
4
|
Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Murga-Garrido SM, Ting-Chun Pan J, Bhanap P, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Rep 2024; 43:114029. [PMID: 38573852 PMCID: PMC11102039 DOI: 10.1016/j.celrep.2024.114029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T cell-deficient mice is strikingly and similarly altered. Our findings demonstrate that microbial- and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations.
Collapse
Affiliation(s)
- Jordan C Harris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bruktawit Goshu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuichi Yokoyama
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lenka Dohnalová
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen K White
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adele Harman
- Transgenic Core, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sofía M Murga-Garrido
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Preeti Bhanap
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
5
|
Mann ER, Lam YK, Uhlig HH. Short-chain fatty acids: linking diet, the microbiome and immunity. Nat Rev Immunol 2024:10.1038/s41577-024-01014-8. [PMID: 38565643 DOI: 10.1038/s41577-024-01014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
The short-chain fatty acids (SCFAs) butyrate, propionate and acetate are microbial metabolites and their availability in the gut and other organs is determined by environmental factors, such as diet and use of antibiotics, that shape the diversity and metabolism of the microbiota. SCFAs regulate epithelial barrier function as well as mucosal and systemic immunity via evolutionary conserved processes that involve G protein-coupled receptor signalling or histone deacetylase activity. Indicatively, the anti-inflammatory role of butyrate is mediated through direct effects on the differentiation of intestinal epithelial cells, phagocytes, B cells and plasma cells, and regulatory and effector T cells. Intestinally derived SCFAs also directly and indirectly affect immunity at extra-intestinal sites, such as the liver, the lungs, the reproductive tract and the brain, and have been implicated in a range of disorders, including infections, intestinal inflammation, autoimmunity, food allergies, asthma and responses to cancer therapies. An ecological understanding of microbial communities and their interrelated metabolic states, as well as the engineering of butyrogenic bacteria may support SCFA-focused interventions for the prevention and treatment of immune-mediated diseases.
Collapse
Affiliation(s)
- Elizabeth R Mann
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ying Ka Lam
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| |
Collapse
|
6
|
Yuan F, Yang L, Hsiao SH, Herndon NL, Gaulke CA, Fang Y. A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis. Virology 2024; 592:109996. [PMID: 38301448 DOI: 10.1016/j.virol.2024.109996] [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: 09/12/2023] [Revised: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
While vaccination and therapeutics for prevention/treatment of influenza are available, new strategies are needed to combat influenza disease in susceptible populations, particularly young children and newborns. Host associated microbiota play an important role in modulating the virulence of numerous pathogens, including the influenza A virus. In this study, we examined microbiome-influenza interactions in a neonatal piglet model system. The nasal microbiome of newborn piglets was longitudinally sampled before and after intranasal infection with recombinant viruses expressing hemagglutinins (HAs) derived from distinct zoonotic H1 subtypes. We found that viruses expressing different parental HAs manifested unique patterns of pathogenicity, and varied impacts on microbial community diversity. Despite these virus specific differences, a consistent microbial signature of viral infection was detected. Our results indicate that influenza A virus infection associates with the restructuring of nasal microbiome and such shifts in microbial diversity may contribute to outcomes of viral infection in neonatal piglets.
Collapse
Affiliation(s)
- Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA
| | - Lufan Yang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA
| | - Shih-Hsuan Hsiao
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Nicole L Herndon
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Christopher A Gaulke
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Personalized Nutrition Initiative, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Cancer Center at Illinois, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA.
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA.
| |
Collapse
|
7
|
Kemnitz N, Fuchs P, Remy R, Ruehrmund L, Bartels J, Klemenz AC, Trefz P, Miekisch W, Schubert JK, Sukul P. Effects of Contagious Respiratory Pathogens on Breath Biomarkers. Antioxidants (Basel) 2024; 13:172. [PMID: 38397770 PMCID: PMC10886173 DOI: 10.3390/antiox13020172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Due to their immediate exhalation after generation at the cellular/microbiome levels, exhaled volatile organic compounds (VOCs) may provide real-time information on pathophysiological mechanisms and the host response to infection. In recent years, the metabolic profiling of the most frequent respiratory infections has gained interest as it holds potential for the early, non-invasive detection of pathogens and the monitoring of disease progression and the response to therapy. Using previously unpublished data, randomly selected individuals from a COVID-19 test center were included in the study. Based on multiplex PCR results (non-SARS-CoV-2 respiratory pathogens), the breath profiles of 479 subjects with the presence or absence of flu-like symptoms were obtained using proton-transfer-reaction time-of-flight mass spectrometry. Among 223 individuals, one respiratory pathogen was detected in 171 cases, and more than one pathogen in 52 cases. A total of 256 subjects had negative PCR test results and had no symptoms. The exhaled VOC profiles were affected by the presence of Haemophilus influenzae, Streptococcus pneumoniae, and Rhinovirus. The endogenous ketone, short-chain fatty acid, organosulfur, aldehyde, and terpene concentrations changed, but only a few compounds exhibited concentration changes above inter-individual physiological variations. Based on the VOC origins, the observed concentration changes may be attributed to oxidative stress and antioxidative defense, energy metabolism, systemic microbial immune homeostasis, and inflammation. In contrast to previous studies with pre-selected patient groups, the results of this study demonstrate the broad inter-individual variations in VOC profiles in real-life screening conditions. As no unique infection markers exist, only concentration changes clearly above the mentioned variations can be regarded as indicative of infection or colonization.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pritam Sukul
- Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy, University Medicine Rostock, 18057 Rostock, Germany
| |
Collapse
|
8
|
Man MA, Ungur RA, Motoc NS, Pop LA, Berindan-Neagoe I, Ruta VM. Lung Microbiota in Idiopathic Pulmonary Fibrosis, Hypersensitivity Pneumonitis, and Unclassified Interstitial Lung Diseases: A Preliminary Pilot Study. Diagnostics (Basel) 2023; 13:3157. [PMID: 37835899 PMCID: PMC10572521 DOI: 10.3390/diagnostics13193157] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
(1) Introduction: Although historically, the lung has been considered a sterile organ, recent studies through 16S rRNA gene sequencing have identified a substantial number of microorganisms. The human microbiome has been considered an "essential organ," carrying about 150 times more information (genes) than are found in the entire human genome. The purpose of the present study is to characterize and compare the microbiome in three different interstitial lung diseases: idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis, and nondifferential interstitial lung disease. (2) Material and methods: This was a prospective cohort study where the DNA of 28 patients with ILD was extracted from the lavage and then processed using the standard technique of 16S RNA gene sequencing. In a tertiary teaching hospital in the northern, western part of Romania, samples were collected through bronchoscopy and then processed. (3) Results: The same four species were found in all the patients but in different quantities and compositions: Firmicutes, Actinobacteria, Proteobacteria and Bacteroides. Streptococcus was the most prevalent genus, followed by Staphylococcus and Prevotella. Statistically significant differences in the OUT count for the ten most abundant taxa were found for the genus: Gemella, Actinobacteria, Prevotella, Neisseria, Haemophilus, and Bifidobacterium. The comparative analysis showed a richer microbiota in patients with IPF, as shown by the alpha diversity index. (4) Conclusions: In interstitial lung diseases, the microorganisms normally found in the lung are reduced to a restricted flora dominated by the Firmicutes family. These changes significantly disrupt the continuity of the observed bacterial pattern from the oropharynx to the bronchial tree and lung, possibly impacting the evolution and severity of interstitial lung diseases.
Collapse
Affiliation(s)
- Milena Adina Man
- Department of Medical Sciences-Pulmonology, Faculty of Medicine, University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
- “Leon Daniello” Clinical Hospital of Pneumophtysiology, 400371 Cluj-Napoca, Romania;
| | - Rodica Ana Ungur
- Department of Medical Specialties-Rehabilitation Medicine, Faculty of Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Nicoleta Stefania Motoc
- Department of Medical Sciences-Pulmonology, Faculty of Medicine, University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
- “Leon Daniello” Clinical Hospital of Pneumophtysiology, 400371 Cluj-Napoca, Romania;
| | - Laura Ancuta Pop
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (L.A.P.); (I.B.-N.)
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (L.A.P.); (I.B.-N.)
| | - Victoria Maria Ruta
- “Leon Daniello” Clinical Hospital of Pneumophtysiology, 400371 Cluj-Napoca, Romania;
| |
Collapse
|
9
|
Zhang Y, Shen J, Cheng W, Roy B, Zhao R, Chai T, Sheng Y, Zhang Z, Chen X, Liang W, Hu W, Liao Q, Pan S, Zhuang W, Zhang Y, Chen R, Mei J, Wei H, Fang X. Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. J Genet Genomics 2023; 50:688-701. [PMID: 37156441 DOI: 10.1016/j.jgg.2023.04.012] [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: 01/12/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Gut microbes exhibit complex interactions with their hosts and shape an organism's immune system throughout its lifespan. As the largest secondary lymphoid organ, the spleen has a wide range of immunological functions. To explore the role of microbiota in regulating and shaping the spleen, we employ scRNA-seq and Stereo-seq technologies based on germ-free (GF) mice to detect differences in tissue size, anatomical structure, cell types, functions, and spatial molecular characteristics. We identify 18 cell types, 9 subtypes of T cells, and 7 subtypes of B cells. Gene differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp region. Stereo-seq results demonstrate a clear hierarchy of immune cells in the spleen, including marginal zone (MZ) macrophages, MZ B cells, follicular B cells and T cells, distributed in a well-defined pattern from outside to inside. However, this hierarchical structure is disturbed in GF mice. Ccr7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells, respectively. We speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.
Collapse
Affiliation(s)
- Yin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Juan Shen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wei Cheng
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bhaskar Roy
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Ruizhen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Tailiang Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yifei Sheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Zhao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xueting Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Weining Hu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qijun Liao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Wen Zhuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yangrui Zhang
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Rouxi Chen
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Xiaodong Fang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China.
| |
Collapse
|
10
|
Hashimoto K. Emerging role of the host microbiome in neuropsychiatric disorders: overview and future directions. Mol Psychiatry 2023; 28:3625-3637. [PMID: 37845499 PMCID: PMC10730413 DOI: 10.1038/s41380-023-02287-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/23/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023]
Abstract
The human body harbors a diverse ecosystem of microorganisms, including bacteria, viruses, and fungi, collectively known as the microbiota. Current research is increasingly focusing on the potential association between the microbiota and various neuropsychiatric disorders. The microbiota resides in various parts of the body, such as the oral cavity, nasal passages, lungs, gut, skin, bladder, and vagina. The gut microbiota in the gastrointestinal tract has received particular attention due to its high abundance and its potential role in psychiatric and neurodegenerative disorders. However, the microbiota presents in other body tissues, though less abundant, also plays crucial role in immune system and human homeostasis, thus influencing the development and progression of neuropsychiatric disorders. For example, oral microbiota imbalance and associated periodontitis might increase the risk for neuropsychiatric disorders. Additionally, studies using the postmortem brain samples have detected the widespread presence of oral bacteria in the brains of patients with Alzheimer's disease. This article provides an overview of the emerging role of the host microbiota in neuropsychiatric disorders and discusses future directions, such as underlying biological mechanisms, reliable biomarkers associated with the host microbiota, and microbiota-targeted interventions, for research in this field.
Collapse
Affiliation(s)
- Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba, 260-8670, Japan.
| |
Collapse
|
11
|
Aronson MR, Mehta A, Friedman RM, Ghaderi DD, Borek RC, Nguyen HCB, McDaid KS, Jacobs IN, Mirza N, Gottardi R. Amelioration of Subglottic Stenosis by Antimicrobial Peptide Eluting Endotracheal Tubes. Cell Mol Bioeng 2023; 16:369-381. [PMID: 37811005 PMCID: PMC10550884 DOI: 10.1007/s12195-023-00769-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/08/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Pediatric subglottic stenosis (SGS) results from prolonged intubation where scar tissue leads to airway narrowing that requires invasive surgery. We have recently discovered that modulating the laryngotracheal microbiome can prevent SGS. Herein, we show how our patent-pending antimicrobial peptide-eluting endotracheal tube (AMP-ET) effectively modulates the local airway microbiota resulting in reduced inflammation and stenosis resolution. Materials and Methods We fabricated mouse-sized ETs coated with a polymeric AMP-eluting layer, quantified AMP release over 10 days, and validated bactericidal activity for both planktonic and biofilm-resident bacteria against Staphylococcus aureus and Pseudomonas aeruginosa. Ex vivo testing: we inserted AMP-ETs and ET controls into excised laryngotracheal complexes (LTCs) of C57BL/6 mice and assessed biofilm formation after 24 h. In vivo testing: AMP-ETs and ET controls were inserted in sham or SGS-induced LTCs, which were then implanted subcutaneously in receptor mice, and assessed for immune response and SGS severity after 7 days. Results We achieved reproducible, linear AMP release at 1.16 µg/day resulting in strong bacterial inhibition in vitro and ex vivo. In vivo, SGS-induced LTCs exhibited a thickened scar tissue typical of stenosis, while the use of AMP-ETs abrogated stenosis. Notably, SGS airways exhibited high infiltration of T cells and macrophages, which was reversed with AMP-ET treatment. This suggests that by modulating the microbiome, AMP-ETs reduce macrophage activation and antigen specific T cell responses resolving stenosis progression. Conclusion We developed an AMP-ET platform that reduces T cell and macrophage responses and reduces SGS in vivo via airway microbiome modulation. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00769-9.
Collapse
Affiliation(s)
- Matthew R. Aronson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Division of Otolaryngology, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA USA
| | - Amrita Mehta
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Ryan M. Friedman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Daniel D. Ghaderi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Ryan C. Borek
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA USA
| | - Hoang C. B. Nguyen
- Division of Otolaryngology, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA USA
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA USA
| | - Kendra S. McDaid
- Department of Laboratory Animal Services, The Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Ian N. Jacobs
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA USA
| | - Natasha Mirza
- Division of Otolaryngology, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA USA
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA USA
| | - Riccardo Gottardi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA
- Division of Otolaryngology, Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA USA
- Division of Pulmonary Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA USA
- Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, PA USA
- Ri.MED Foundation, Palermo, Italy
- Children’s Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Room 1006, Philadelphia, PA 19107 USA
| |
Collapse
|
12
|
Hyblova M, Hadzega D, Babisova K, Krumpolec P, Gnip A, Sabaka P, Lassan S, Minarik G. Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity. Microorganisms 2023; 11:1804. [PMID: 37512976 PMCID: PMC10384460 DOI: 10.3390/microorganisms11071804] [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: 04/24/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The recent global emergence of the SARS-CoV-2 pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health challenges in the event of emerging infectious agents. We conducted a comprehensive shotgun analysis targeting multiple aspects to compare differences in bacterial spectrum and viral presence through culture-independent RNA sequencing. We conducted a comparative analysis of the microbiome between healthy individuals and those with varying degrees of COVID-19 severity, including a total of 151 participants. Our findings revealed a noteworthy increase in microbial species diversity among patients with COVID-19, irrespective of disease severity. Specifically, our analysis revealed a significant difference in the abundance of bacterial phyla between healthy individuals and those infected with COVID-19. We found that Actinobacteria, among other bacterial phyla, showed a notably higher abundance in healthy individuals compared to infected individuals. Conversely, Bacteroides showed a lower abundance in the latter group. Infected people, regardless of severity and symptoms, have the same proportional representation of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteriales. In addition to SARS-CoV-2 and numerous phage groups, we identified sequences of clinically significant viruses such as Human Herpes Virus 1, Human Mastadenovirus D, and Rhinovirus A in several samples. Analyses were performed retrospectively, therefore, in the case of SARS-CoV-2 various WHO variants such as Alpha (B.1.1.7), Delta (B.1.617.2), Omicron (B.1.1.529), and 20C strains are represented. Additionally, the presence of specific virus strains has a certain effect on the distribution of individual microbial taxa.
Collapse
Affiliation(s)
| | | | | | | | - Andrej Gnip
- Medirex Group Academy, 949 05 Nitra, Slovakia
| | - Peter Sabaka
- Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, 814 99 Bratislava, Slovakia
| | - Stefan Lassan
- Department of Pneumology and Ftizeology I, University Hospital in Bratislava, 831 01 Bratislava, Slovakia
| | | |
Collapse
|
13
|
Xie L, Zhang X, Gao X, Wang L, Cheng Y, Zhang S, Yue J, Tang Y, Deng Y, Zhang B, He X, Tang M, Yang H, Zheng T, You J, Song X, Xiong J, Zuo H, Pei X. Microbiota and mycobiota in bronchoalveolar lavage fluid of silicosis patients. J Occup Med Toxicol 2023; 18:10. [PMID: 37430310 DOI: 10.1186/s12995-023-00377-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The contribution of bronchoalveolar lavage fluid (BALF) microbiota and mycobiota to silicosis has recently been noticed. However, many confounding factors can influence the accuracy of BALF microbiota and mycobiota studies, resulting in inconsistencies in the published results. In this cross-sectional study, we systematically investigated the effects of "sampling in different rounds of BALF" on its microbiota and mycobiota. We further explored the relationship between silicosis fatigue and the microbiota and mycobiota. METHODS After obtaining approval from the ethics board, we collected 100 BALF samples from 10 patients with silicosis. Demographic data, clinical information, and blood test results were also collected from each patient. The characteristics of the microbiota and mycobiota were defined using next-generation sequencing. However, no non-silicosis referent group was examined, which was a major limitation of this study. RESULTS Our analysis indicated that subsampling from different rounds of BALF did not affect the alpha- and beta-diversities of microbial and fungal communities when the centrifuged BALF sediment was sufficient for DNA extraction. In contrast, fatigue status significantly influenced the beta-diversity of microbes and fungi (Principal Coordinates Analysis, P = 0.001; P = 0.002). The abundance of Vibrio alone could distinguish silicosis patients with fatigue from those without fatigue (area under the curve = 0.938, 95% confidence interval [CI] 0.870-1.000). Significant correlations were found between Vibrio and haemoglobin levels (P < 0.001, ρ = -0.64). CONCLUSIONS Sampling in different rounds of BALF showed minimal effect on BALF microbial and fungal diversities; the first round of BALF collection was recommended for microbial and fungal analyses for convenience. In addition, Vibrio may be a potential biomarker for silicosis fatigue screening.
Collapse
Affiliation(s)
- Linshen Xie
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaosi Gao
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Linyao Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yiyang Cheng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shirong Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Ji Yue
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yingru Tang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yufeng Deng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Baochao Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xun He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mingyuan Tang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hua Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Tianli Zheng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xuejiao Song
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Jingyuan Xiong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
| | - Haojiang Zuo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Xiaofang Pei
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, 610041, China
| |
Collapse
|
14
|
Britt RD, Ruwanpathirana A, Ford ML, Lewis BW. Macrophages Orchestrate Airway Inflammation, Remodeling, and Resolution in Asthma. Int J Mol Sci 2023; 24:10451. [PMID: 37445635 PMCID: PMC10341920 DOI: 10.3390/ijms241310451] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Asthma is a heterogenous chronic inflammatory lung disease with endotypes that manifest different immune system profiles, severity, and responses to current therapies. Regardless of endotype, asthma features increased immune cell infiltration, inflammatory cytokine release, and airway remodeling. Lung macrophages are also heterogenous in that there are separate subsets and, depending on the environment, different effector functions. Lung macrophages are important in recruitment of immune cells such as eosinophils, neutrophils, and monocytes that enhance allergic inflammation and initiate T helper cell responses. Persistent lung remodeling including mucus hypersecretion, increased airway smooth muscle mass, and airway fibrosis contributes to progressive lung function decline that is insensitive to current asthma treatments. Macrophages secrete inflammatory mediators that induce airway inflammation and remodeling. Additionally, lung macrophages are instrumental in protecting against pathogens and play a critical role in resolution of inflammation and return to homeostasis. This review summarizes current literature detailing the roles and existing knowledge gaps for macrophages as key inflammatory orchestrators in asthma pathogenesis. We also raise the idea that modulating inflammatory responses in lung macrophages is important for alleviating asthma.
Collapse
Affiliation(s)
- Rodney D. Britt
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Anushka Ruwanpathirana
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Maria L. Ford
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Brandon W. Lewis
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
| |
Collapse
|
15
|
Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [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: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
Collapse
Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| |
Collapse
|
16
|
Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and immune system non-genetically affect offspring phenotypes transgenerationally. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535940. [PMID: 37066207 PMCID: PMC10104111 DOI: 10.1101/2023.04.06.535940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The host-microbiota relationship has evolved to shape mammalian processes, including immunity, metabolism, and development 1-3 . Host phenotypes change in direct response to microbial exposures by the individual. Here we show that the microbiota induces phenotypic change not only in the individual but also in their succeeding generations of progeny. We found that germ-free mice exhibit a robust sebum secretion defect and transcriptional changes in various organs, persisting across multiple generations despite microbial colonization and breeding with conventional mice. Host-microbe interactions could be involved in this process, since T cell-deficient mice, which display defective sebum secretion 4 , also transgenerationally transmit their phenotype to progeny. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that epigenetic information in the gametes is required for phenotypic transmission. Accordingly, small non-coding RNAs that can regulate embryonic gene expression 5 were strikingly and similarly altered in gametes of germ-free and T cell-deficient mice. Thus, we have uncovered a novel mechanism whereby the microbiota and immune system induce phenotypic changes in successive generations of offspring. This epigenetic form of inheritance could be advantageous for host adaptation to environmental perturbation, where phenotypic diversity can be introduced more rapidly than by genetic mutation.
Collapse
|
17
|
McCarthy C, Geraghty P. Respiratory Immune Responses during Infection and Pollution Inhalation. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59020242. [PMID: 36837444 PMCID: PMC9959294 DOI: 10.3390/medicina59020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/03/2023]
Abstract
The COVID-19 pandemic highlighted the importance of lung immune responses to pathogens and environmental factors [...].
Collapse
Affiliation(s)
- Cormac McCarthy
- University College Dublin School of Medicine, Education and Research Centre, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland
- Correspondence: (C.M.); (P.G.); Tel.: +353-1-221-3323 (C.M.); +1-718-270-3141 (P.G.)
| | - Patrick Geraghty
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA
- Correspondence: (C.M.); (P.G.); Tel.: +353-1-221-3323 (C.M.); +1-718-270-3141 (P.G.)
| |
Collapse
|