1
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Yue Y, Hovey KM, Wactawski-Wende J, LaMonte MJ, Andrews CA, Diaz PI, McSkimming DI, Buck M, Sun Y, Millen AE. Association between Healthy Eating Index-2020 and Oral Microbiome among Postmenopausal Women. J Nutr 2024:S0022-3166(24)00474-7. [PMID: 39218399 DOI: 10.1016/j.tjnut.2024.08.023] [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: 04/01/2024] [Revised: 07/30/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Dietary intake has been suggested to be associated with the oral microbiome, but no study has examined the association between overall diet quality and the oral microbiome. OBJECTIVE This study aims to investigate the cross-sectional association between the Healthy Eating Index-2020 (HEI-2020) and the diversity and composition of the oral microbiome among participants in the Buffalo Osteoporosis and Periodontal Disease (OsteoPerio) Study. METHODS In 1,175 postmenopausal women (mean age 67±7.0 yrs), we estimated the HEI-2020 scores for each woman from a food frequency questionnaire administered from 1997-2000. Bacterial DNA was extracted from subgingival plaque samples and analyzed using 16S ribosomal RNA sequencing. The alpha-diversity (within-sample diversity) and beta-diversity (between-sample diversity) across HEI-2020 quartiles were examined using ANCOVA and PERMANOVA, respectively. The associations between the HEI-2020 score and the relative abundance of microbial taxa were examined by linear regression models. The analyses were further conducted for individual components of the HEI-2020. RESULTS No statistically significant associations were observed between the HEI-2020 scores and the alpha- or beta-diversity. However, greater consumption of seafood and plant proteins, as well as total protein, and lower consumption of added sugars, were positively associated with alpha-diversity. After we applied a false detection rate (FDR) correction, higher HEI-2020 scores were significantly associated with decreased abundance of Lautropia, Streptococcus gordonii, Cardiobacterium valvarum, and Cardiobacterium hominis, and increased abundance of Selenomonas sp. oral taxon 133 and Selenomonas dianae (FDR adjusted p-values<0.10). Additionally, 28 other taxa were identified as being associated with HEI-2020 components. CONCLUSION While the HEI-2020 was associated with the composition, but not the diversity, of the oral microbiome, individual HEI-2020 components were associated with both its diversity and composition. Specific dietary components may have more impact on the diversity and composition of oral microbiome than overall diet quality assessed by the HEI-2020.
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Affiliation(s)
- Yihua Yue
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Kathleen M Hovey
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Michael J LaMonte
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Chris A Andrews
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Patricia I Diaz
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, NY, USA
| | - Daniel I McSkimming
- Veterans Affairs (VA) National Oncology Program, Specialty Care Services, VA, Washington, District of Columbia, USA
| | - Michael Buck
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Amy E Millen
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, Buffalo, NY, USA.
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2
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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; 30:1982-1993. [PMID: 38783139 PMCID: PMC11271406 DOI: 10.1038/s41591-024-02999-4] [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: 11/29/2023] [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.
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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
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3
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Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
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Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
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4
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Oda H, Tanaka S, Chen-Yoshikawa TF, Morimura Y, Yamada Y, Yutaka Y, Nakajima D, Hamaji M, Ohsumi A, Menju T, Nagao M, Date H. Impact of perioperative airway pathogens on living-donor lobar lung transplantation outcomes. Surg Today 2024; 54:266-274. [PMID: 37540232 DOI: 10.1007/s00595-023-02730-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/27/2023] [Indexed: 08/05/2023]
Abstract
PURPOSE To elucidate the clinical impact of pathogenic organism (PO) positivity early after transplantation, we evaluated the impact of perioperative airway POs on outcomes after living-donor lobar lung transplantation (LDLLT), where the graft airway is supposed to be sterile from a healthy donor. METHOD A retrospective review of 67 adult LDLLT procedures involving 132 living donors was performed. Presence of POs in the recipients' airways was evaluated preoperatively and postoperatively in intensive-care units. RESULTS POs were detected preoperatively in 13 (19.4%) recipients. No POs were isolated from the donor airways at transplantation. POs were detected in 39 (58.2%) recipients postoperatively; most were different from the POs isolated preoperatively. Postoperative PO isolation was not associated with short-term outcomes other than prolonged postoperative ventilation. The 5-year overall survival was significantly better in the PO-negative group than in the PO-positive group (89.1% vs. 63.7%, P = 0.014). In the multivariate analysis, advanced age (hazard ratio [HR]: 1.041 per 1-year increase, P = 0.033) and posttransplant PO positivity in the airway (HR: 3.684, P = 0.019) significantly affected the survival. CONCLUSIONS The airways of the living-donor grafts were microbiologically sterile. PO positivity in the airway early after transplantation negatively impacted long-term outcomes.
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Affiliation(s)
- Hiromi Oda
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
- Department of Thoracic Surgery, Tazuke Kofukai, Medical Research Institute, Kitano Hospital, 2-4-20 Ohgimachi, Kita-Ku, Osaka City, Osaka, 530-8480, Japan
| | - Satona Tanaka
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan.
| | - Toyofumi F Chen-Yoshikawa
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya City, Aichi, 466-8560, Japan
| | - Yuki Morimura
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Yoshito Yamada
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Yojiro Yutaka
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Daisuke Nakajima
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Masatsugu Hamaji
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Akihiro Ohsumi
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Toshi Menju
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Miki Nagao
- Department of Infection Control and Prevention, Kyoto University Hospital, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Hiroshi Date
- Department of Thoracic Surgery, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-Cho, Sakyo-Ku, Kyoto City, Kyoto, 606-8507, Japan
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5
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Yu X, Yu K, Liao Z, Chen B, Qin Z, Liang J, Gao X. Adaptation strategies of relatively high-latitude marginal reef corals in response to severe temperature fluctuations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166439. [PMID: 37604380 DOI: 10.1016/j.scitotenv.2023.166439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
The large seasonal temperature fluctuations caused by global warming and frequent marine heatwaves pose new challenges to survival of relatively high-latitude marginal reef corals. However, the adaptation strategies of high-latitude marginal corals are not fully understood. We employed integrated approach to investigate the response mechanism of hosts, Symbiodiniaceae, and symbiotic bacteria of marginal reef corals Acropora pruinosa and Pavona decussate in response to large seasonal temperature fluctuations. The coral holobiont maintained a high level of immunity to adapt to seasonal pressure by increasing Symbiodiniaceae energy supply. The symbiotic Symbiodiniaceae of two coral was dominated by C1 subgroup, and was stable across seasons. The α-diversity of symbiotic bacteria P. decussata and A. pruinosa in summer was higher than that in winter. The symbiotic bacterial community of two coral reorganized during different seasons. Scleractinian corals improve adaptability to seasonal stress by increasing energy supply to maintain high levels of immunity, increasing symbiotic bacterial α-diversity, and changing dominant bacteria. This study demonstrates the adaptation strategies of marginal reef corals to seasonal temperature fluctuations and provides novel insights into the study of the adaptation of corals and relatively high-latitude coral refuges in the context of global warming and intensified marine heatwaves.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xu Gao
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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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. Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299130. [PMID: 38077035 PMCID: PMC10705623 DOI: 10.1101/2023.11.29.23299130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes. In this multicenter study, we collected 278 bronchoalveolar lavage (BAL) samples from 229 patients treated at 32 children's hospitals between 2014-2022. Using paired metatranscriptomes and human gene expression data, we identified 4 patient clusters with varying BAL composition. Among those requiring respiratory support prior to sampling, in-hospital mortality varied from 22-60% depending on the cluster (p=0.007). The most common patient subtype, Cluster 1, showed a moderate quantity and high diversity of commensal microbes with robust metabolic activity, low rates of infection, gene expression indicating alveolar macrophage predominance, and low mortality. The second most common cluster showed a very high burden of airway microbes, gene expression enriched for neutrophil signaling, frequent bacterial infections, and moderate mortality. Cluster 3 showed significant depletion of commensal microbes, a loss of biodiversity, gene expression indicative of fibroproliferative pathways, increased viral and fungal pathogens, and high mortality. Finally, Cluster 4 showed profound microbiome depletion with enrichment of Staphylococci and viruses, gene expression driven by lymphocyte activation and cellular injury, and the highest mortality. BAL clusters were modeled with a random forest classifier and reproduced in a geographically distinct validation cohort of 57 patients from The Netherlands, recapitulating similar cluster-based mortality differences (p=0.022). Degree of antibiotic exposure was strongly associated with depletion of BAL microbes and enrichment of fungi. Potential pathogens were parsed from all detected microbes by analyzing each BAL microbe relative to the overall microbiome composition, which yielded increased sensitivity for numerous previously occult pathogens. These findings support personalized interpretation of the pulmonary microenvironment in pediatric HCT, which may facilitate biology-targeted interventions to improve outcomes.
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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, Australia
| | - Courtney M Rowan
- Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- CIBMTR (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
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, UCSF 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
- University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, 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
- Division of Critical Care, Department of Pediatric Medicine, 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
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Division of Pediatric Critical Care, Department of Pediatrics, 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
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, 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
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Paul Castillo
- University of Florida, Gainesville, UF Health Shands Children's Hospital, 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, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Children's National Hospital, Washington, District of Columbia, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Division of Pediatric Hematology/Oncology/BMT, Department of Pediatrics, 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
- Departments 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 (NYU) 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 (NYU) Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, 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 (NYU) Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, 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
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7
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Belizário J, Garay-Malpartida M, Faintuch J. Lung microbiome and origins of the respiratory diseases. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100065. [PMID: 37456520 PMCID: PMC10339129 DOI: 10.1016/j.crimmu.2023.100065] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The studies on the composition of the human microbiomes in healthy individuals, its variability in the course of inflammation, infection, antibiotic therapy, diets and different pathological conditions have revealed their intra and inter-kingdom relationships. The lung microbiome comprises of major species members of the phylum Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Proteobacteria, which are distributed in ecological niches along nasal cavity, nasopharynx, oropharynx, trachea and in the lungs. Commensal and pathogenic species are maintained in equilibrium as they have strong relationships. Bacterial overgrowth after dysbiosis and/or imbalanced of CD4+ helper T cells, CD8+ cytotoxic T cells and regulatory T cells (Treg) populations can promote lung inflammatory reactions and distress, and consequently acute and chronic respiratory diseases. This review is aimed to summarize the latest advances in resident lung microbiome and its participation in most common pulmonary infections and pneumonia, community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), immunodeficiency associated pneumonia, SARS-CoV-2-associated pneumonia, acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). We briefly describe physiological and immunological mechanisms that selectively create advantages or disadvantages for relative growth of pathogenic bacterial species in the respiratory tract. At the end, we propose some directions and analytical methods that may facilitate the identification of key genera and species of resident and transient microbes involved in the respiratory diseases' initiation and progression.
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Affiliation(s)
- José Belizário
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Miguel Garay-Malpartida
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Joel Faintuch
- Department of Gastroenterology of the Clinics Hospital of the University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, São Paulo, CEP 05403-000, Brazil
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8
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Bustos IG, Martín-Loeches I, Acosta-González A, Chotirmall SH, Dickson RP, Reyes LF. Exploring the complex relationship between the lung microbiome and ventilator-associated pneumonia. Expert Rev Respir Med 2023; 17:889-901. [PMID: 37872770 DOI: 10.1080/17476348.2023.2273424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
INTRODUCTION Understanding the presence and function of a diverse lung microbiome in acute lung infections, particularly ventilator-associated pneumonia (VAP), is still limited, evidencing significant gaps in our knowledge. AREAS COVERED In this comprehensive narrative review, we aim to elucidate the contribution of the respiratory microbiome in the development of VAP by examining the current knowledge on the interactions among microorganisms. By exploring these intricate connections, we endeavor to enhance our understanding of the disease's pathophysiology and pave the way for novel ideas and interventions in studying the respiratory tract microbiome. EXPERT OPINION The conventional perception of lungs as sterile is deprecated since it is currently recognized the existence of a diverse microbial community within them. However, despite extensive research on the role of the respiratory microbiome in healthy lungs, respiratory chronic diseases and acute lung infections such as pneumonia are not fully understood. It is crucial to investigate further the relationship between the pathophysiology of VAP and the pulmonary microbiome, elucidating the mechanisms underlying the interactions between the microbiome, host immune response and mechanical ventilation for the development of VAP.
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Affiliation(s)
- Ingrid G Bustos
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Doctorado de Biociencias, Department of Engineering, Universidad de la Sabana, Chia, Colombia
| | - Ignacio Martín-Loeches
- Multidisciplinary Intensive Care Research Organization (MICRO), St James's Hospital, Dublin, Ireland
| | - Alejandro Acosta-González
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Bioprospection Research Group (GIBP), Department of Engineering, Universidad de La Sabana, Chia, Colombia
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Critical Care Department, Clinica Universidad de La Sabana, Chia, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
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9
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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10
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Bach L, Ram A, Ijaz UZ, Evans TJ, Haydon DT, Lindström J. The Effects of Smoking on Human Pharynx Microbiota Composition and Stability. Microbiol Spectr 2023; 11:e0216621. [PMID: 36786634 PMCID: PMC10101099 DOI: 10.1128/spectrum.02166-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
The oral microbiota is essential to the health of the host, yet little is known about how it responds to disturbances. We examined the oropharyngeal microbiota of 30 individuals over 40 weeks. As the oropharynx is an important gateway to pathogens, and as smoking is associated with increased incidence and severity of respiratory infections, we compared the microbiota of smokers and nonsmokers to shed light on its potential for facilitating infections. We hypothesized that decreased species diversity, decreased community stability, or increased differences in community structure could facilitate invading pathogens. We found that smoking is associated with reduced alpha diversity, greater differences in community structure, and increased environmental filtering. The effects of short-term perturbations (antibiotic use and participants exhibiting cold symptoms) were also investigated. Antibiotic use had a negative effect on alpha diversity, irrespective of smoking status, and both antibiotic use and cold symptoms were associated with highly unique bacterial communities. A stability analysis of models built from the data indicated that there were no differences in local or global stability in the microbial communities of smokers, compared to nonsmokers, and that their microbiota are equally resistant to species invasions. Results from these models suggest that smoker microbiota are perturbed but characterized by alternative stable states that are as stable and invasion-resistant as are the microbiota of nonsmokers. Smoking is unlikely to increase the risk of infectious disease through the altered composition and ecological function of the microbiota; this is more likely due to the effects of smoking on the local and systemic immune system. IMPORTANCE Smoking is associated with an increased risk of respiratory infections. Hypothetically, the altered community diversity of smokers' pharyngeal microbiota, together with changes in their ecological stability properties, could facilitate their invasion by pathogens. To address this question, we analyzed longitudinal microbiota data of baseline healthy individuals who were either smokers or nonsmokers. While the results indicate reduced biodiversity and increased species turnover in the smokers' pharyngeal microbiota, their ecological stability properties were not different from those of the microbiota of nonsmokers, implying, in ecological terms, that the smokers' microbial communities are not less resistant to invasions. Therefore, the study suggests that the increased propensity of respiratory infections that is seen in smokers is more likely associated with changes in the local and systemic immune system than with ecological changes in the microbial communities.
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Affiliation(s)
- Lydia Bach
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Asha Ram
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Umer Z. Ijaz
- School of Science and Engineering, University of Glasgow, United Kingdom
| | - Thomas J. Evans
- School of Infection and Immunity, Glasgow Biomedical Research Centre, University of Glasgow, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Jan Lindström
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
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Zhu W, Lu X, Hong C, Hong L, Zhu F, Zhang S, Yao Y. Contributions of carbon source, crop cultivation, and chemical property on microbial community assemblage in soil subjected to reductive disinfestation. Front Microbiol 2023; 14:1146207. [PMID: 37032903 PMCID: PMC10081160 DOI: 10.3389/fmicb.2023.1146207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
In agricultural practice, reductive soil disinfestation (RSD) is an effective method for eliminating soil-borne pathogens that depends heavily on carbon source. However, knowledge regarding the assembly of soil microbial communities in RDS-treated soils amended with different carbon sources after continuous crop cultivation is still not well-characterized. RSD treatments were performed on greenhouse soil with six different carbon sources (ethanol, glucose, alfalfa, wheat bran, rice bran, and sugarcane residue), which have different C:N ratios (Org C/N) and easily oxidized carbon contents (Org EOC). After RSD, two consecutive seasons of pepper pot experiments were conducted. Then, the effects of carbon source property, crop cultivation, and soil chemical property on soil microbial community reestablishment, pathogen reproduction, and crop performance were investigated in the RSD-cropping system. Variation partition analysis indicated that carbon source property, crop cultivation, and soil chemical property explained 66.2 and 39.0% of bacterial and fungal community variation, respectively. Specifically, Mantel tests showed that Org C/N, crop cultivation, soil available phosphorus and potassium were the most important factors shaping bacterial community composition, while Org C/N, Org EOC, and crop cultivation were the most important factors shaping fungal community composition. After two planting seasons, the number of cultivable Fusarium was positively correlated with Org EOC, and negatively correlated with soil total organic carbon, Fungal Chao1, and Fungal PC1. Crop yield of complex-carbon soils (Al, Wh, Ri and Su) was negatively affected by Org C/N after the first season, and it was highest in Al, and lower in Et and Su after the second season. Overall, Org EOC and Org C/N of carbon source were vitally important for soil microbe reestablishment, Fusarium reproduction and crop performance. Our findings further broaden the important role of carbon source in the RSD-cropping system, and provide a theoretical basis for organic carbon selection in RSD practice.
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Affiliation(s)
- Weijing Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaolin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chunlai Hong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Leidong Hong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fengxiang Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shuo Zhang
- Ningbo Agricultural and Rural Green Development Center, Ningbo, China
| | - Yanlai Yao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Yanlai Yao,
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12
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Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River. WATER 2022. [DOI: 10.3390/w14071018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.
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Fromentin M, Ricard JD, Roux D. Lung Microbiome in Critically Ill Patients. Life (Basel) 2021; 12:life12010007. [PMID: 35054400 PMCID: PMC8778861 DOI: 10.3390/life12010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014 Paris, France;
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
| | - Jean-Damien Ricard
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
| | - Damien Roux
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
- Institut Necker-Enfants Malades, Université de Paris, INSERM U1151, CNRS UMR 8253, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-47-60-63-29
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14
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Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Detweiler A, Jones NG, Wu B, Darmanis S, Lynch SV, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.23.21253487. [PMID: 33791731 PMCID: PMC8010763 DOI: 10.1101/2021.03.23.21253487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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15
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Rello J, Schrenzel J, Tejo AM. New insights into pneumonia in patients on prolonged mechanical ventilation: need for a new paradigm addressing dysbiosis. ACTA ACUST UNITED AC 2021; 47:e20210198. [PMID: 34190866 PMCID: PMC8332723 DOI: 10.36416/1806-3756/e20210198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jordi Rello
- . Clinical Research/Epidemiology in Pneumonia & Sepsis-CRIPS-Vall d'Hebron Institut de Recerca-VHIR-Barcelona, España.,. Centro de Investigación Biomedica En Red de Enfermedades Respiratorias - CIBERES - Instituto de Salud Carlos III, Madrid, España.,. Centre Hospitalier Universitaire, Nîmes, France
| | - Jacques Schrenzel
- . Laboratoire de Bactériologie et Laboratoire de Recherche en Génomique, Service des Maladies Infectieuses et Service de Médecine de Laboratoire, Hôpitaux Universitaires Genève, Genève, Suisse
| | - Alexandre M Tejo
- . Divisão de Doenças Infecciosas, Departamento de Medicina Interna, Universidade Estadual de Londrina, Londrina (PR) Brasil
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Zeng Y, Liu H, Zhu T, Han S, Li S. Preparation of Nanomaterial Wettable Powder Formulations of Antagonistic Bacteria from Phellodendron chinense and the Biological Control of Brown Leaf Spot Disease. THE PLANT PATHOLOGY JOURNAL 2021; 37:215-231. [PMID: 34111912 PMCID: PMC8200580 DOI: 10.5423/ppj.oa.02.2021.0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 06/02/2023]
Abstract
Brown leaf spot disease caused by Nigrospora guilinensis on Phellodendron chinense occurs in a large area in Dayi County, Chengdu City, Sichuan Province, China each year. This outbreak has severely reduced the production of Chinese medicinal plants P. chinense and caused substantial economic losses. The bacterial isolate JKB05 was isolated from the healthy leaves of P. chinense, exhibited antagonistic effects against N. guilinensis and was identified as Bacillus megaterium. The following fermentation medium and conditions improved the inhibitory effect of B. megaterium JKB05 on N. guilinensis: 2% glucose, 0.1% soybean powder, 0.1% KCl, and 0.05% MgSO4; initial concentration 6 × 106 cfu/ml, and a 42-h optimal fermentation time. A composite of 0.1% nano-SiO2 JKB05 improved the thermal stability, acid-base stability and ultraviolet resistance by 16%, 12%, and 38.9%, respectively, and nano-SiO2 was added to the fermentation process. The best formula for the wettable powder was 35% kaolin, 4% polyethylene glycol, 8% Tween, and 2% humic acid. The following quality test results for the wettable powder were obtained: wetting time 87.0 s, suspension rate 80.33%, frequency of microbial contamination 0.08%, pH 7.2, fineness 95.8%, drying loss 1.47%, and storage stability ≥83.5%. A pot experiment revealed that the ability of JKB05 to prevent fungal infections on P. chinense increased considerably and achieved levels of control as high as 94%. The use of nanomaterials significantly improved the ability of biocontrol bacteria to control this disease.
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Affiliation(s)
- Yanling Zeng
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Han Liu
- Ganzi Institute of Forestry Research, Kangding 626001, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
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Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. RESEARCH SQUARE 2021:rs.3.rs-380803. [PMID: 34013247 PMCID: PMC8132240 DOI: 10.21203/rs.3.rs-380803/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing (scRNA-seq) we assessed lower respiratory tract immune responses and microbiome dynamics in 28 COVID-19 patients, 15 of whom developed VAP, and eight critically ill uninfected controls. Two days before VAP onset we observed a transcriptional signature of bacterial infection. Two weeks prior to VAP onset, following intubation, we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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Affiliation(s)
- Alexandra Tsitsiklis
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Catherine Devoe
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Sophia Levan
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Rajani Ghale
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alejandra Jauregui
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aartik Sarma
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Thomas J. Deiss
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sidney Carrillo
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - K. Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Aleksandra Leligdowicz
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Norman Jones
- Department of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Bing Wu
- Genentech, Inc. San Francisco, CA, USA
| | | | - Michael A. Matthay
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Susan V. Lynch
- Department of Gastroenterology, University of California, San Francisco, CA, USA
- Benioff Center for Microbiome Medicine, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Carolyn M. Hendrickson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten N. Kangelaris
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - David J. Erle
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Lung Biology Center, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Oren Rosenberg
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles R. Langelier
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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18
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Hartmann JE, Albrich WC, Dmitrijeva M, Kahlert CR. The Effects of Corticosteroids on the Respiratory Microbiome: A Systematic Review. Front Med (Lausanne) 2021; 8:588584. [PMID: 33777968 PMCID: PMC7988087 DOI: 10.3389/fmed.2021.588584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Since its discovery, the respiratory microbiome has been implicated in the pathogenesis of multiple pulmonary diseases. Even though corticosteroid treatments are widely prescribed for pulmonary diseases, their effects on the respiratory microbiome are still poorly understood. This systematic review summarizes the current understanding of the effects of corticosteroids on the microbiome of the airways. Research Question: How does treatment with corticosteroids impact the respiratory microbiome? Study Design and Methods: According to the PRISMA guidelines, Embase, Medline, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases were systematically searched for all observational or randomized-controlled studies comparing the microbiome parameters of patients receiving corticosteroids to those of controls. The primary outcomes of interest were changes in the diversity, composition and total burden of the respiratory microbiome as assessed by culture-independent molecular methods. Results: Out of 1,943 identified reports, five studies could be included: two on patients with asthma, two on patients with chronic obstructive pulmonary disease and one on patients with chronic rhinosinusitis. The studies were highly heterogeneous with regards to the methods used and the populations investigated. Microbiome diversity increased with corticosteroids at least transiently in three studies and decreased in one study. The effects of corticosteroids on the composition of the respiratory microbiome were significant but without a clear shared direction. A significant increase in microbial burden after corticosteroids was seen in one study. Interpretation: Data on the effect of corticosteroids on the respiratory microbiome are still limited, with considerable heterogeneity between studies. However, available data suggest that corticosteroid treatment may have significant effects on the composition and possibly the diversity of the respiratory microbiome. Further research is needed to better understand the influence of corticosteroids on the respiratory microbiome and thus better target its widespread therapeutic use.
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Affiliation(s)
- Julia E. Hartmann
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Werner C. Albrich
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christian R. Kahlert
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
- Division of Infectious Diseases/Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
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Chen J, Xi Z, Shi Y, Liu L, Wang L, Qian L, Lu A. Highly homogeneous microbial communities dominated by Mycoplasma pneumoniae instead of increased resistance to macrolide antibiotics is the characteristic of lower respiratory tract microbiome of children with refractory Mycoplasma pneumoniae pneumonia. Transl Pediatr 2021; 10:604-615. [PMID: 33850819 PMCID: PMC8039789 DOI: 10.21037/tp-20-404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Although researchers have found that the microbiota changed during the lower respiratory tract (LRT) infection, little was known about the association between LRT microbiome and refractory M. pneumoniae pneumonia (RMPP). METHODS From June 28th, 2019 to March 23rd, 2020, we enrolled fifty-two children diagnosed with RMPP or non-refractory M. pneumoniae pneumonia (NRMPP), and characterized the structure and function of microbiota in the bronchoalveolar lavage fluid (BALF) by metagenomic next generation sequencing (mNGS). RESULTS Based on Bray-Curtis distance between samples, samples in RMPP group were highly homogeneous, and Shannon index in the RMPP group was much lower than NRMPP group while Simpson index, which presents the degree of dominance, was higher in RMPP group. The dominant taxon with relative abundance greater than 50% was merely Mycoplasma among RMPP and NRMPP patients, but the proportions of other taxonomic distribution were different. M. pneumoniae was the dominant species and occupied almost all niches in the vast majority of RMPP patients, whereas the other genera were dramatically lower. The NRMPP group was more enriched in antibiotic resistance genes (ARGs) than the RMPP group, and also exhibited a greater relative abundance of macrolide antibiotics resistance gene (macB) and fluoroquinolone antibiotic resistance genes (patA-B) in M. pneumoniae genome. In RMPP patients, higher relative abundance of Streptococcus pneumoniae had a strong correlation with increased hospitalization days while higher relative abundance of Streptococcus pneumoniae had a negative correlation with hospitalization days among NRMPP patients. CONCLUSIONS The microbiota of LRT in children with RMPP was much more homogeneous and simpler than that of the NRMPP group and with lower relative abundance of macrolide antibiotics resistance gene in M. pneumoniae genome. M. pneumoniae was absolutely dominant in the vast majority of RMPP patients. Prolonged hospitalization days was associated with relative abundance of M. pneumoniae in NRMPP patients while it was related with other pathogens' relative abundance (e.g., Streptococcus pneumoniae) in RMPP patients.
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Affiliation(s)
- Jinglong Chen
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Zhimin Xi
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yanyan Shi
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Lijuan Liu
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Libo Wang
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Liling Qian
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Aizhen Lu
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
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20
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Fromentin M, Ricard JD, Roux D. Respiratory microbiome in mechanically ventilated patients: a narrative review. Intensive Care Med 2021; 47:292-306. [PMID: 33559707 PMCID: PMC7871139 DOI: 10.1007/s00134-020-06338-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014, Paris, France.,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France
| | - Jean-Damien Ricard
- Médecine Intensive Réanimation, DMU ESPRIT, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France.,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France
| | - Damien Roux
- Médecine Intensive Réanimation, DMU ESPRIT, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France. .,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France.
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21
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Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific. Sci Rep 2020; 10:19990. [PMID: 33203914 PMCID: PMC7672225 DOI: 10.1038/s41598-020-76792-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022] Open
Abstract
Corals are dependent upon lipids as energy reserves to mount a metabolic response to biotic and abiotic challenges. This study profiled lipids, fatty acids, and microbial communities of healthy and white syndrome (WS) diseased colonies of Acropora hyacinthus sampled from reefs in Western Australia, the Great Barrier Reef, and Palmyra Atoll. Total lipid levels varied significantly among locations, though a consistent stepwise decrease from healthy tissues from healthy colonies (HH) to healthy tissue on WS-diseased colonies (HD; i.e. preceding the lesion boundary) to diseased tissue on diseased colonies (DD; i.e. lesion front) was observed, demonstrating a reduction in energy reserves. Lipids in HH tissues were comprised of high energy lipid classes, while HD and DD tissues contained greater proportions of structural lipids. Bacterial profiling through 16S rRNA gene sequencing and histology showed no bacterial taxa linked to WS causation. However, the relative abundance of Rhodobacteraceae-affiliated sequences increased in DD tissues, suggesting opportunistic proliferation of these taxa. While the cause of WS remains inconclusive, this study demonstrates that the lipid profiles of HD tissues was more similar to DD tissues than to HH tissues, reflecting a colony-wide systemic effect and provides insight into the metabolic immune response of WS-infected Indo-Pacific corals.
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22
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Wang Q, Hamilton PB, Kang F, Zhu X, Zhang Y, Zhao H. Regional-scale investigation for microbial competition-through-environment interactions modulating antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139341. [PMID: 32473450 DOI: 10.1016/j.scitotenv.2020.139341] [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: 03/06/2020] [Revised: 04/30/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Originating from a long history of competition between microbes, antibiotic resistance is a serious global health concern. To avoid the risk of antibiotic resistance, tremendous efforts have been directed towards restricting antibiotic consumption worldwide, but to date with limited success. Resistance is governed by multiple pressures from natural and anthropogenic origins which further create problems with control. This study identifies a chain of links from antibiotic resistant genes (ARGs) to microbial communities to environmental pressures in the surface sediments of forty-two lake clusters across the 1000-km Yangtze Basin of China, and attempts to expound on a control pathway for this resistance risk. Results show that eleven of the 670 bacterial families can be classified as antibiotic-resistant or nonresistant communities which antagonize each other. In natural systems, antagonistic competition controls the increase and decrease in ARGs. Superiority of antibiotic-resistant strains initiates a loss in microbial diversity associated with the prevalence of resistance risk. This study shows that, antibiotics shape the evolution of ARGs in resistant communities through a nonlinear role of orientor; other selected pressures serve as a facilitator to enhance the antibiotic resistance through an investigated chain of links. Furthermore, according to tolerances of the classified communities, abiogenetic development through temperature, salinity and Mg were identified and selected for study from seventy lake parameters. Linear feedbacks to selected pressures make the nonresistant communities outcompete the resistant communities, theoretically modulating the risk of antibiotic resistance.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiangsu 210008, China
| | - Paul B Hamilton
- Canadian Museum of Nature, P. O. Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - Fuxing Kang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China.
| | - Xuezhu Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Yiting Zhang
- College of Public Administration, Nanjing Agricultural University, Jiangsu 210095, China
| | - Haiyan Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiangsu 210008, China
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Yu X, Yu K, Huang W, Liang J, Qin Z, Chen B, Yao Q, Liao Z. Thermal acclimation increases heat tolerance of the scleractinian coral Acropora pruinosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139319. [PMID: 32446076 DOI: 10.1016/j.scitotenv.2020.139319] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/28/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Field ecological observations indicate that scleractinian coral exposed to early thermal stress are likely to develop higher tolerance to subsequent heat stress. The causes of this phenomenon, however, remain enigmatic. To unravel the mechanisms underlying the increased heat tolerance, we applied different thermal treatments to the scleractinian coral Acropora pruinosa and studied the resulting differences in appearance, physiological index, Symbiodiniaceae and bacterial communities, and transcriptome response. We found that early heat stress improved the thermal tolerance of the coral holobiont. After thermal acclimation, the community structure and symbiotic bacterial diversity in the microbiota were reorganized, whereas those of Symbiodiniaceae remained stable. RNA-seq analysis revealed that the downregulated coral host genes were mainly involved in pathways relating to metabolism, particularly the nitrogen metabolism pathway. This indicates that thermal acclimation led to decrease in the metabolism level in the coral host, which might be a self-protection mechanism. We suggest that thermal acclimation may increase scleractinian coral thermal tolerance by slowing host metabolism, altering the dominant bacterial population, and increasing bacterial diversity. This study offers new insights into the adaptive potential of scleractinian coral to heat stress from global warming.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), China.
| | - Wen Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Qiucui Yao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
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Yu X, Yu K, Liao Z, Liang J, Deng C, Huang W, Huang Y. Potential molecular traits underlying environmental tolerance of Pavona decussata and Acropora pruinosa in Weizhou Island, northern South China Sea. MARINE POLLUTION BULLETIN 2020; 156:111199. [PMID: 32510361 DOI: 10.1016/j.marpolbul.2020.111199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Coral species display varying susceptibilities to biotic or abiotic stress. To address the causes underlying this phenomenon, we profiled the Symbiodiniaceae clade type, bacterial communities and coral transcriptome responses in Pavona decussata and Acropora pruinosa, two species displaying different environmental tolerances in the Weizhou Island. We found that C1 was the most dominant Symbiodiniaceae subclade, with no difference detected between A. pruinosa and P. decussata. Nevertheless, P. decussata exhibited higher microbial diversity and significantly different community structure compared with that of A. pruinosa. Transcriptome analysis revealed that coral genes with significantly high expression in P. decussata were mostly related to immune and stress-resistance responses, whereas, those with significantly low expression were metabolism-related. We postulate that the higher tolerance of P. decussata as compared with that of A. pruinosa is the result of several traits, such as higher microbial diversity, different dominant bacteria, higher immune and stress-resistant response, and lower metabolic rate.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China.
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China.
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Wen Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Yanhua Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China
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25
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F. Escapa I, Huang Y, Chen T, Lin M, Kokaras A, Dewhirst FE, Lemon KP. Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets. MICROBIOME 2020; 8:65. [PMID: 32414415 PMCID: PMC7291764 DOI: 10.1186/s40168-020-00841-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/15/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequence variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies. RESULTS To achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interest. When used with the naïve Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are (1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; (2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; (3) trimming the training set to match the sequenced regions, if necessary; and (4) placing species sharing closely related sequences into a training-set-specific supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio single molecule, real-time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets. CONCLUSION Here, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies. Video Abstract.
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Affiliation(s)
- Isabel F. Escapa
- Forsyth Institute (Microbiology), Cambridge, MA USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA USA
- Department of Molecular Virology & Microbiology, Alkek Center for Metagenomics & Microbiome Research, Baylor College of Medicine, Houston, TX USA
| | - Yanmei Huang
- Forsyth Institute (Microbiology), Cambridge, MA USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA USA
| | - Tsute Chen
- Forsyth Institute (Microbiology), Cambridge, MA USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA USA
| | - Maoxuan Lin
- Forsyth Institute (Microbiology), Cambridge, MA USA
| | | | - Floyd E. Dewhirst
- Forsyth Institute (Microbiology), Cambridge, MA USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA USA
| | - Katherine P. Lemon
- Forsyth Institute (Microbiology), Cambridge, MA USA
- Department of Molecular Virology & Microbiology, Alkek Center for Metagenomics & Microbiome Research, Baylor College of Medicine, Houston, TX USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
- Section of Infectious Diseases, Department of Pediatrics, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX USA
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26
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Pollock FJ, Lamb JB, van de Water JAJM, Smith HA, Schaffelke B, Willis BL, Bourne DG. Reduced diversity and stability of coral-associated bacterial communities and suppressed immune function precedes disease onset in corals. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190355. [PMID: 31312497 PMCID: PMC6599770 DOI: 10.1098/rsos.190355] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/08/2019] [Indexed: 05/28/2023]
Abstract
Disease is an emerging threat to coral reef ecosystems worldwide, highlighting the need to understand how environmental conditions interact with coral immune function and associated microbial communities to affect holobiont health. Increased coral disease incidence on reefs adjacent to permanently moored platforms on Australia's Great Barrier Reef provided a unique case study to investigate environment-host-microbe interactions in situ. Here, we evaluate coral-associated bacterial community (16S rRNA amplicon sequencing), immune function (protein-based prophenoloxidase-activating system), and water quality parameters before, during and after a disease event. Over the course of the study, 31% of tagged colonies adjacent to platforms developed signs of white syndrome (WS), while all control colonies on a platform-free reef remained visually healthy. Corals adjacent to platforms experienced significant reductions in coral immune function. Additionally, the corals at platform sites that remained visually healthy throughout the study had reduced bacterial diversity compared to healthy colonies at the platform-free site. Interestingly, prior to the observation of macroscopic disease, corals that would develop WS had reduced bacterial diversity and significantly greater community heterogeneity between colonies compared to healthy corals at the same location. These results suggest that activities associated with offshore marine infrastructure impacts coral immunocompetence and associated bacterial community, which affects the susceptibility of corals to disease.
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Affiliation(s)
- F. Joseph Pollock
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
- Department of Ecology and Evolutionary Biology, Pennsylvania State University, University Park, PA, USA
| | - Joleah B. Lamb
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Jeroen A. J. M. van de Water
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, Monaco
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Britta Schaffelke
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Bette L. Willis
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
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Control of Fusarium wilt of lisianthus by reassembling the microbial community in infested soil through reductive soil disinfestation. Microbiol Res 2019; 220:1-11. [DOI: 10.1016/j.micres.2018.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 11/18/2022]
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28
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Johani K, Malone M, Jensen SO, Dickson HG, Gosbell IB, Hu H, Yang Q, Schultz G, Vickery K. Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo. J Antimicrob Chemother 2019; 73:494-502. [PMID: 29165561 PMCID: PMC5890786 DOI: 10.1093/jac/dkx391] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/26/2017] [Indexed: 11/17/2022] Open
Abstract
Objectives Test the performance of topical antimicrobial wound solutions against microbial biofilms using in vitro, ex vivo and in vivo model systems at clinically relevant exposure times. Methods Topical antimicrobial wound solutions were tested under three different conditions: (in vitro) 4% w/v Melaleuca oil, polyhexamethylene biguanide, chlorhexidine, povidone iodine and hypochlorous acid were tested at short duration exposure times for 15 min against 3 day mature biofilms of Staphylococcus aureus and Pseudomonas aeruginosa; (ex vivo) hypochlorous acid was tested in a porcine skin explant model with 12 cycles of 10 min exposure, over 24 h, against 3 day mature P. aeruginosa biofilms; and (in vivo) 4% w/v Melaleuca oil was applied for 15 min exposure, daily, for 7 days, in 10 patients with chronic non-healing diabetic foot ulcers complicated by biofilm. Results In vitro assessment demonstrated variable efficacy in reducing biofilms ranging from 0.5 log10 reductions to full eradication. Repeated instillation of hypochlorous acid in a porcine model achieved <1 log10 reduction (0.77 log10, P = 0.1). Application of 4% w/v Melaleuca oil in vivo resulted in no change to the total microbial load of diabetic foot ulcers complicated by biofilm (median log10 microbial load pre-treatment = 4.9 log10 versus 4.8 log10, P = 0.43). Conclusions Short durations of exposure to topical antimicrobial wound solutions commonly utilized by clinicians are ineffective against microbial biofilms, particularly when used in vivo. Wound solutions should not be used as a sole therapy and clinicians should consider multifaceted strategies that include sharp debridement as the gold standard.
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Affiliation(s)
- K Johani
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia.,Central Military Laboratories and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - M Malone
- High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, Australia.,Liverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, Australia.,Medical Sciences Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia
| | - S O Jensen
- Medical Sciences Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - H G Dickson
- Ambulatory Care Department (PIXI), Liverpool Hospital, South West Sydney LHD, Sydney, Australia
| | - I B Gosbell
- Medical Sciences Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia.,Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, New South Wales Health Pathology, Liverpool, Sydney, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Q Yang
- Department of Obstetrics and Gynecology, Institute for Wound Research, University of Florida, Gainesville, FL, USA
| | - G Schultz
- Department of Obstetrics and Gynecology, Institute for Wound Research, University of Florida, Gainesville, FL, USA
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
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Common J, Westra ER. CRISPR evolution and bacteriophage persistence in the context of population bottlenecks. RNA Biol 2019; 16:588-594. [PMID: 30722720 DOI: 10.1080/15476286.2019.1578608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Population bottlenecks often cause strong reductions in genetic diversity and alter population structure. In the context of host-parasite interactions, bottlenecks could in theory benefit either the host or the pathogen. We predicted that bottlenecking of bacterial populations that evolve CRISPR immunity against bacteriophages (phage) would benefit the pathogen, because CRISPR spacer diversity can rapidly drive phages extinct. To test this, we bottlenecked populations of bacteria and phage, tracking phage persistence and the evolution of bacterial resistance mechanisms. Contrary to our prediction, bottlenecking worked in the advantage of the host. With some possible exceptions, this effect was not caused by CRISPR immunity. This host benefit is consistent with a dilution effect disproportionately affecting phage. This study provides further insight into how bottlenecking influences bacteria-phage dynamics, the role of dilution in bacteria-phage interactions, and the evolution of host immune systems.
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Affiliation(s)
- Jack Common
- a ESI, Biosciences , University of Exeter , Penryn , UK
| | - Edze R Westra
- a ESI, Biosciences , University of Exeter , Penryn , UK
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30
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Cheng Y, Yam JKH, Cai Z, Ding Y, Zhang LH, Deng Y, Yang L. Population dynamics and transcriptomic responses of Pseudomonas aeruginosa in a complex laboratory microbial community. NPJ Biofilms Microbiomes 2019; 5:1. [PMID: 30675369 PMCID: PMC6334633 DOI: 10.1038/s41522-018-0076-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/13/2018] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas aeruginosa tends to be among the dominant species in multi-species bacterial consortia in diverse environments. To understand P. aeruginosa's physiology and interactions with co-existing bacterial species in different conditions, we established physiologically reproducible 18 species communities, and found that P. aeruginosa dominated in mixed-species biofilm communities but not in planktonic communities. P. aeruginosa's H1 type VI secretion system was highly induced in mixed-species biofilm consortia, compared with its monospecies biofilm, which was further demonstrated to play a key role in P. aeruginosa's enhanced fitness over other bacterial species. In addition, the type IV pili and Psl exopolysaccharide were required for P. aeruginosa to compete with other bacterial species in the biofilm community. Our study showed that the physiology of P. aeruginosa is strongly affected by interspecies interactions, and both biofilm determinants and type VI secretion system contribute to higher P. aeruginosa's fitness over other species in complex biofilm communities.
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Affiliation(s)
- Yingying Cheng
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore 637551
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore 637551
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore 637551
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore 637551
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China 510642
| | - Yinyue Deng
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, South China Agricultural University, Guangzhou, China 510642
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore 637551
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore 637551
- School of Medicine, Southern University of Science and Technology, Shenzhen, China 518055
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Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A 2018; 115:E12353-E12362. [PMID: 30482864 PMCID: PMC6310811 DOI: 10.1073/pnas.1809700115] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lower respiratory tract infections (LRTIs) are the leading cause of infectious disease-related deaths worldwide yet remain challenging to diagnose because of limitations in existing microbiologic tests. In critically ill patients, noninfectious respiratory syndromes that resemble LRTIs further complicate diagnosis and confound targeted treatment. To address this, we developed a metagenomic sequencing-based approach that simultaneously interrogates three core elements of acute airway infections: the pathogen, airway microbiome, and host response. We studied this approach in a prospective cohort of critically ill patients with acute respiratory failure and found that combining pathogen, microbiome, and host gene expression metrics achieved accurate LRTI diagnosis and identified etiologic pathogens in patients with clinically identified infections but otherwise negative testing. Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due to limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved LRTI diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. To differentiate pathogens from respiratory commensals, we developed a rules-based model (RBM) and logistic regression model (LRM) in a derivation cohort of 20 patients with LRTIs or noninfectious acute respiratory illnesses. When tested in an independent validation cohort of 24 patients, both models achieved accuracies of 95.5%. We next developed pathogen, microbiome diversity, and host gene expression metrics to identify LRTI-positive patients and differentiate them from critically ill controls with noninfectious acute respiratory illnesses. When tested in the validation cohort, the pathogen metric performed with an area under the receiver-operating curve (AUC) of 0.96 (95% CI, 0.86–1.00), the diversity metric with an AUC of 0.80 (95% CI, 0.63–0.98), and the host transcriptional classifier with an AUC of 0.88 (95% CI, 0.75–1.00). Combining these achieved a negative predictive value of 100%. This study suggests that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.
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32
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Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract. mSystems 2018; 3:e00187-18. [PMID: 30534599 PMCID: PMC6280432 DOI: 10.1128/msystems.00187-18] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/02/2018] [Indexed: 12/22/2022] Open
Abstract
The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.
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Affiliation(s)
- Isabel F. Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tsute Chen
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Yanmei Huang
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Prasad Gajare
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Li J, Cao J, Zhu YG, Chen QL, Shen F, Wu Y, Xu S, Fan H, Da G, Huang RJ, Wang J, de Jesus AL, Morawska L, Chan CK, Peccia J, Yao M. Global Survey of Antibiotic Resistance Genes in Air. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10975-10984. [PMID: 30043612 DOI: 10.1021/acs.est.8b02204] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Despite its emerging significant public health concern, the presence of antibiotic resistance genes (ARGs) in urban air has not received significant attention. Here, we profiled relative abundances (as a fraction, normalized by 16S rRNA gene) of 30 ARG subtypes resistant to seven common classes of antibiotics, which are quinolones, β-lactams, macrolides, tetracyclines, sulfonamides, aminoglycosides, and vancomycins, in ambient total particulate matter (PM) using a novel protocol across 19 world cities. In addition, their longitudinal changes in PM2.5 samples in Xi'an, China as an example were also studied. Geographically, the ARGs were detected to vary by nearly 100-fold in their abundances, for example, from 0.07 (Bandung, Indonesia) to 5.6 (San Francisco, USA). The β-lactam resistance gene blaTEM was found to be most abundant, seconded by quinolone resistance gene qepA; and their corresponding relative abundances have increased by 178% and 26%, respectively, from 2004 to 2014 in Xi'an. Independent of cities, gene network analysis indicates that airborne ARGs were differentially contributed by bacterial taxa. Results here reveal that urban air is being polluted by ARGs, and different cities are challenged with varying health risks associated with airborne ARG exposure. This work highlights the threat of urban airborne transmission of ARGs and the need of redefining our current air quality standards in terms with public health.
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Affiliation(s)
- Jing Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Junji Cao
- Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment , Chinese Academy of Sciences , Xi'an 710049 , China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Fangxia Shen
- School of Space and Environment , Beihang University , Beijing 100191 , China
| | - Yan Wu
- School of Environmental Science and Engineering , Shandong University , Jinan 250100 , China
| | - Siyu Xu
- Department of Environmental Health Sciences, Graduate School of Public Health , Seoul National University , Seoul 08826 , South Korea
| | - Hanqing Fan
- Department of Earth and Environmental Engineering , Columbia University , New York , New York 10027 , United States
| | - Guillaume Da
- CERTES, Université Paris-Est Créteil , Centre d'études et de Recherche en Thermique, Environnement et Systèmes (CERTES) , Créteil 94000 , France
| | - Ru-Jin Huang
- Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment , Chinese Academy of Sciences , Xi'an 710049 , China
| | - Jing Wang
- Institute of Environmental Engineering , ETH Zurich , Zurich 8093 , Switzerland
- Advanced Analytical Technologies , Empa , Dübendorf 8600 , Switzerland
| | - Alma Lorelei de Jesus
- International Laboratory for Air Quality and Health , Queensland University of Technology , GPO Box 2434, Brisbane , Queensland 4001 , Australia
| | - Lidia Morawska
- International Laboratory for Air Quality and Health , Queensland University of Technology , GPO Box 2434, Brisbane , Queensland 4001 , Australia
| | - Chak K Chan
- School of Energy and Environment , City University of Hong Kong , Tat Chee Avenue , Kowloon , Hong Kong China
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering , Yale University , New Haven , Connecticut 06520 , United States
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
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Wang K, Chen YQ, Salido MM, Kohli GS, Kong JL, Liang HJ, Yao ZT, Xie YT, Wu HY, Cai SQ, Drautz-Moses DI, Darling AE, Schuster SC, Yang L, Ding Y. The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence. Open Biol 2018; 7:rsob.170029. [PMID: 28878043 PMCID: PMC5627047 DOI: 10.1098/rsob.170029] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/26/2017] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe airway infections in humans. These infections are usually difficult to treat and associated with high mortality rates. While colonizing the human airways, P. aeruginosa could accumulate genetic mutations that often lead to its better adaptability to the host environment. Understanding these evolutionary traits may provide important clues for the development of effective therapies to treat P. aeruginosa infections. In this study, 25 P. aeruginosa isolates were longitudinally sampled from the airways of four ventilator-associated pneumonia (VAP) patients. Pacbio and Illumina sequencing were used to analyse the in vivo evolutionary trajectories of these isolates. Our analysis showed that positive selection dominantly shaped P. aeruginosa genomes during VAP infections and led to three convergent evolution events, including loss-of-function mutations of lasR and mpl, and a pyoverdine-deficient phenotype. Specifically, lasR encodes one of the major transcriptional regulators in quorum sensing, whereas mpl encodes an enzyme responsible for recycling cell wall peptidoglycan. We also found that P. aeruginosa isolated at late stages of VAP infections produce less elastase and are less virulent in vivo than their earlier isolated counterparts, suggesting the short-term in vivo evolution of P. aeruginosa leads to attenuated virulence.
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Affiliation(s)
- Ke Wang
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China.,Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Yi-Qiang Chen
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - May M Salido
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Gurjeet S Kohli
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Jin-Liang Kong
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Hong-Jie Liang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Zi-Ting Yao
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Yan-Tong Xie
- The First Clinical School of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Hua-Yu Wu
- Department of Cell Biology and Genetics, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Shuang-Qi Cai
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Aaron E Darling
- The ithree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore .,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.,Interdisciplinary Graduate School, SCELSE, Nanyang Technological University, Singapore 639798, Singapore
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Lanaspa M, Bassat Q, Medeiros MM, Muñoz-Almagro C. Respiratory microbiota and lower respiratory tract disease. Expert Rev Anti Infect Ther 2018; 15:703-711. [PMID: 28661199 DOI: 10.1080/14787210.2017.1349609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION The respiratory airways harbor a complex succession of ecological niches with distinct but related bacterial communities. Particular challenges of respiratory microbiome research have led to limited scientific output compared to other human microbiomes. Areas covered: In this review, we summarize the current state of knowledge of the bacterial respiratory microbiome, with a particular focus on associations between the respiratory microbiome and lower respiratory tract conditions. Expert commentary: There is growing evidence that the respiratory microbiome is associated with lower respiratory infectious diseases and related conditions. Most respiratory microbiome reports are metataxonomic cross-sectional or case-control studies with relatively small sample sizes. Large, prospective projects with metatranscriptomics or metabolomics approach are needed to unravel the effect of the respiratory microbiome on health-related conditions. Moreover, standardization in sampling, library preparation, sequencing techniques and data analysis should be encouraged.
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Affiliation(s)
- Miguel Lanaspa
- a Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical , Universidade Nova de Lisboa , Lisbon , Portugal.,b ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB) , Hospital Clínic - Universitat de Barcelona , Barcelona , Spain
| | - Quique Bassat
- b ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB) , Hospital Clínic - Universitat de Barcelona , Barcelona , Spain.,c Centro de Investigação em Saúde de Manhiça (CISM) , Maputo , Mozambique.,d ICREA , Barcelona , Spain.,e University Hospital Sant Joan de Deu , Barcelona , Spain
| | - Marcia Melo Medeiros
- a Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical , Universidade Nova de Lisboa , Lisbon , Portugal
| | - Camen Muñoz-Almagro
- f Institut de Recerca Pediatrica , Hospital de Sant Joan de Dèu , Barcelona , Spain.,g Ciber de Epidemiología y Salud Pública, CIBERESP , Madrid , Spain.,h Department of Medicine , Universitat Internacional de Catalunya , Barcelona , Spain
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Zeineldin MM, Lowe JF, Grimmer ED, de Godoy MRC, Ghanem MM, Abd El-Raof YM, Aldridge BM. Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattle. BMC Microbiol 2017; 17:138. [PMID: 28645257 PMCID: PMC5481913 DOI: 10.1186/s12866-017-1042-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/02/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next generation sequencing, there is a growing appreciation of the importance of commensal microbial populations in maintaining mucosal health, and a realization that bacteria colonize anatomical locations that were previously considered to be sterile. While upper respiratory tract microbial populations have been described, there are currently no published studies describing the normal microbial populations of the bovine lower respiratory tract. Consequently, we have little understanding of the relationship between upper and lower respiratory tract microbiota in healthy cattle. The primary objective of our study was to characterize the composition, structure and relationship of the lower and upper respiratory microbial communities in clinically healthy feedlot cattle. Nasopharyngeal swabs (NPS), and bronchoalveolar lavage (BAL) fluid, were collected from clinically healthy feedlot calves (n = 8). Genomic DNA from each sample was extracted, and the V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced using Illumina Miseq platform. RESULTS Across all samples, the most predominant phyla were Proteobacteria, Actinobacteria and Firmicutes. The most common genera were Rathayibacter, Mycoplasma, Bibersteinia and Corynebacterium. The microbial community structure was distinct between these two biogeographical sites. Most of the bacterial genera identified in the BAL samples were also present in the NPS, but biogeographical-specific genera were enriched in both the NPS (Rathayibacter) and BAL (Bibersteinia) samples. There were strong associations between the presence of certain taxa at each specific location, and strong correlations between the presence of specific taxa in both the NPS and BAL samples. CONCLUSIONS The correlation between the presence of specific taxa in both the NPS and BAL samples, supports the notion of a mutualistic interrelationship between these microbial communities. Future studies, in large cohorts of animals, are needed to determine the role and clinical importance of the relationships of respiratory tract microbial communities with health, productivity, and susceptibility to the development of respiratory disease, in growing cattle.
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Affiliation(s)
- Mohamed M Zeineldin
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA
| | - James F Lowe
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA
| | - Elsbeth D Grimmer
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA
| | - Maria R C de Godoy
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Mohamed M Ghanem
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Benha, Egypt
| | - Yassein M Abd El-Raof
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Benha, Egypt
| | - Brian M Aldridge
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA.
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Shenoy MK, Iwai S, Lin DL, Worodria W, Ayakaka I, Byanyima P, Kaswabuli S, Fong S, Stone S, Chang E, Davis JL, Faruqi AA, Segal MR, Huang L, Lynch SV. Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia. Am J Respir Crit Care Med 2017; 195:104-114. [PMID: 27447987 PMCID: PMC5214918 DOI: 10.1164/rccm.201603-0523oc] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/22/2016] [Indexed: 02/01/2023] Open
Abstract
RATIONALE The potential role of the airway microbiota in dictating immune responses and infection outcomes in HIV-associated pneumonia is largely unknown. OBJECTIVES To investigate whether microbiologically and immunologically distinct subsets of patients with HIV and pneumonia exist and are related to mortality. METHODS Bronchoalveolar lavage samples from Ugandan patients with HIV and pneumonia (n = 182) were obtained at study enrollment (following antibiotic treatment); patient demographics including 8- and 70-day mortality were collected. Lower airway bacterial community composition was assessed via amplification and sequencing of the V4 region of the 16S ribosomal RNA gene. Host immune response gene expression profiles were generated by quantitative polymerase chain reaction using RNA extracted from bronchoalveolar lavage fluid. Liquid and gas chromatography mass spectrometry was used to profile serum metabolites. MEASUREMENTS AND MAIN RESULTS Based on airway microbiome composition, most patients segregated into three distinct groups, each of which were predicted to encode metagenomes capable of producing metabolites characteristically enriched in paired serum samples from these patients. These three groups also exhibited differences in mortality; those with the highest rate had increased ceftriaxone administration and culturable Aspergillus, and demonstrated significantly increased induction of airway T-helper cell type 2 responses. The group with the lowest mortality was characterized by increased expression of T-cell immunoglobulin and mucin domain 3, which down-regulates T-helper cell type 1 proinflammatory responses and is associated with chronic viral infection. CONCLUSIONS These data provide evidence that compositionally and structurally distinct lower airway microbiomes are associated with discrete local host immune responses, peripheral metabolic reprogramming, and different rates of mortality.
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Affiliation(s)
- Meera K. Shenoy
- Division of Gastroenterology, Department of Medicine
- Biomedical Sciences Graduate Program
| | - Shoko Iwai
- Division of Gastroenterology, Department of Medicine
| | - Din L. Lin
- Division of Gastroenterology, Department of Medicine
| | - William Worodria
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Irene Ayakaka
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Patrick Byanyima
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Sylvia Kaswabuli
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Serena Fong
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
| | - Stephen Stone
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
| | - Emily Chang
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, and
| | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut; and
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut
| | | | - Mark R. Segal
- Division of Biostatistics, University of California San Francisco, San Francisco, California
| | - Laurence Huang
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, and
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Abstract
OBJECTIVE Suspected ventilator-associated infection is the most common reason for antibiotics in the PICU. We sought to characterize the clinical variables associated with continuing antibiotics after initial evaluation for suspected ventilator-associated infection and to determine whether clinical variables or antibiotic treatment influenced outcomes. DESIGN Prospective, observational cohort study conducted in 47 PICUs in the United States, Canada, and Australia. Two hundred twenty-nine pediatric patients ventilated more than 48 hours undergoing respiratory secretion cultures were enrolled as "suspected ventilator-associated infection" in a prospective cohort study, those receiving antibiotics of less than or equal to 3 days were categorized as "evaluation only," and greater than 3 days as "treated." Demographics, diagnoses, comorbidities, culture results, and clinical data were compared between evaluation only and treated subjects and between subjects with positive versus negative cultures. SETTING PICUs in 47 hospitals in the United States, Canada, and Australia. SUBJECTS All patients undergoing respiratory secretion cultures during the 6 study periods. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Treated subjects differed from evaluation-only subjects only in frequency of positive cultures (79% vs 36%; p < 0.0001). Subjects with positive cultures were more likely to have chronic lung disease, tracheostomy, and shorter PICU stay, but there were no differences in ventilator days or mortality. Outcomes were similar in subjects with positive or negative cultures irrespective of antibiotic treatment. Immunocompromise and higher Pediatric Logistic Organ Dysfunction scores were the only variables associated with mortality in the overall population, but treated subjects with endotracheal tubes had significantly lower mortality. CONCLUSIONS Positive respiratory cultures were the primary determinant of continued antibiotic treatment in children with suspected ventilator-associated infection. Positive cultures were not associated with worse outcomes irrespective of antibiotic treatment although the lower mortality in treated subjects with endotracheal tubes is notable. The necessity of continuing antibiotics for a positive respiratory culture in suspected ventilator-associated infection requires further study.
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Freeland JR. The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA. Genome 2016; 60:358-374. [PMID: 28177833 DOI: 10.1139/gen-2016-0100] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity.
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Affiliation(s)
- Joanna R Freeland
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada.,Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada
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Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174. [PMID: 27919253 PMCID: PMC5139081 DOI: 10.1186/s12890-016-0339-5] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background The airways of patients with cystic fibrosis (CF) are highly complex, subject to various environmental conditions as well as a distinct microbiota. Pseudomonas aeruginosa is recognized as one of the most important pulmonary pathogens and the predominant cause of morbidity and mortality in CF. A multifarious interplay between the host, pathogens, microbiota, and the environment shapes the course of the disease. There have been several excellent reviews detailing CF pathology, Pseudomonas and the role of environment in CF but only a few reviews connect these entities with regards to influence on the overall course of the disease. A holistic understanding of contributing factors is pertinent to inform new research and therapeutics. Discussion In this article, we discuss the deterministic alterations in lung physiology as a result of CF. We also revisit the impact of those changes on the microbiota, with special emphasis on P. aeruginosa and the influence of other non-genetic factors on CF. Substantial past and current research on various genetic and non-genetic aspects of cystic fibrosis has been reviewed to assess the effect of different factors on CF pulmonary infection. A thorough review of contributing factors in CF and the alterations in lung physiology indicate that CF lung infection is multi-factorial with no isolated cause that should be solely targeted to control disease progression. A combinatorial approach may be required to ensure better disease outcomes. Conclusion CF lung infection is a complex disease and requires a broad multidisciplinary approach to improve CF disease outcomes. A holistic understanding of the underlying mechanisms and non-genetic contributing factors in CF is central to development of new and targeted therapeutic strategies.
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Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol. Ann Am Thorac Soc 2016; 12:1561-71. [PMID: 26193069 DOI: 10.1513/annalsats.201503-172ot] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sarcoidosis is a systemic disease characterized by noncaseating granulomatous inflammation with tremendous clinical heterogeneity and uncertain pathobiology and lacking in clinically useful biomarkers. The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study is an observational cohort study designed to explore the role of the lung microbiome and genome in these two diseases. This article describes the design and rationale for the GRADS study sarcoidosis protocol. The study addresses the hypothesis that distinct patterns in the lung microbiome are characteristic of sarcoidosis phenotypes and are reflected in changes in systemic inflammatory responses as measured by peripheral blood changes in gene transcription. The goal is to enroll 400 participants, with a minimum of 35 in each of 9 clinical phenotype subgroups prioritized by their clinical relevance to understanding of the pathobiology and clinical heterogeneity of sarcoidosis. Participants with a confirmed diagnosis of sarcoidosis undergo a baseline visit with self-administered questionnaires, chest computed tomography, pulmonary function tests, and blood and urine testing. A research or clinical bronchoscopy with a research bronchoalveolar lavage will be performed to obtain samples for genomic and microbiome analyses. Comparisons will be made by blood genomic analysis and with clinical phenotypic variables. A 6-month follow-up visit is planned to assess each participant's clinical course. By the use of an integrative approach to the analysis of the microbiome and genome in selected clinical phenotypes, the GRADS study is powerfully positioned to inform and direct studies on the pathobiology of sarcoidosis, identify diagnostic or prognostic biomarkers, and provide novel molecular phenotypes that could lead to improved personalized approaches to therapy for sarcoidosis.
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42
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Defining the normal core microbiome of conjunctival microbial communities. Clin Microbiol Infect 2016; 22:643.e7-643.e12. [DOI: 10.1016/j.cmi.2016.04.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 04/06/2016] [Accepted: 04/09/2016] [Indexed: 11/21/2022]
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Krause R, Halwachs B, Thallinger GG, Klymiuk I, Gorkiewicz G, Hoenigl M, Prattes J, Valentin T, Heidrich K, Buzina W, Salzer HJF, Rabensteiner J, Prüller F, Raggam RB, Meinitzer A, Moissl-Eichinger C, Högenauer C, Quehenberger F, Kashofer K, Zollner-Schwetz I. Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients. PLoS One 2016; 11:e0155033. [PMID: 27206014 PMCID: PMC4874575 DOI: 10.1371/journal.pone.0155033] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
Whether the presence of Candida spp. in lower respiratory tract (LRT) secretions is a marker of underlying disease, intensive care unit (ICU) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. We investigated healthy controls, patients with proposed risk factors for Candida growth in LRT (antibiotic therapy, ICU treatment with and without antibiotic therapy), ICU patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly invasive and colonizing Candida spp.). Fungal patterns were determined by conventional culture based microbiology combined with molecular approaches (next generation sequencing, multilocus sequence typing) for description of fungal and concommitant bacterial microbiota in LRT, and host and fungal biomarkes were investigated. Admission to and treatment on ICUs shifted LRT fungal microbiota to Candida spp. dominated fungal profiles but antibiotic therapy did not. Compared to controls, Candida was part of fungal microbiota in LRT of ICU patients without pneumonia with and without antibiotic therapy (63% and 50% of total fungal genera) and of ICU patients with pneumonia with antibiotic therapy (73%) (p<0.05). No case of invasive candidiasis originating from Candida in the LRT was detected. There was no common bacterial microbiota profile associated or dissociated with Candida spp. in LRT. Colonizing and invasive Candida strains (from candidemic patients) did not match to certain clades withdrawing the presence of a particular pathogenic and invasive clade. The presence of Candida spp. in the LRT rather reflected rapidly occurring LRT dysbiosis driven by ICU related factors than was associated with invasive candidiasis.
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Affiliation(s)
- Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- * E-mail:
| | - Bettina Halwachs
- Bioinformatics, Institute for Knowledge Discovery, University of Technology, Graz, Austria and OMICS Center Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | | | - Martin Hoenigl
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Jürgen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Valentin
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Heidrich
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Walter Buzina
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Helmut J. F. Salzer
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibnitz Center for Medicine and Biosciences, Borstel, Germany
| | - Jasmin Rabensteiner
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Florian Prüller
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Reinhard B. Raggam
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- Theodor Escherich Laboratory for Microbiome Research, Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Franz Quehenberger
- Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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Dickson RP. The microbiome and critical illness. THE LANCET. RESPIRATORY MEDICINE 2016; 4:59-72. [PMID: 26700442 PMCID: PMC4752077 DOI: 10.1016/s2213-2600(15)00427-0] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
Abstract
The central role of the microbiome in critical illness is supported by a half century of experimental and clinical study. The physiological effects of critical illness and the clinical interventions of intensive care substantially alter the microbiome. In turn, the microbiome predicts patients' susceptibility to disease, and manipulation of the microbiome has prevented or modulated critical illness in animal models and clinical trials. This Review surveys the microbial ecology of critically ill patients, presents the facts and unanswered questions surrounding gut-derived sepsis, and explores the radically altered ecosystem of the injured alveolus. The revolution in culture-independent microbiology has provided the tools needed to target the microbiome rationally for the prevention and treatment of critical illness, holding great promise to improve the acute and chronic outcomes of the critically ill.
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Affiliation(s)
- Robert P Dickson
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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Constructing personalized longitudinal holo'omes of colon cancer-prone humans and their modeling in flies and mice. Oncotarget 2015; 10:4224-4246. [PMID: 31289620 PMCID: PMC6609240 DOI: 10.18632/oncotarget.6463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022] Open
Abstract
Specific host genes and intestinal microbes, dysbiosis, aberrant immune responses and lifestyle may contribute to intestinal inflammation and cancer, but each of these parameters does not suffice to explain why sporadic colon cancer develops at an old age and only in some of the people with the same profile. To improve our understanding, longitudinal multi-omic and personalized studies will help to pinpoint combinations of host genetic, epigenetic, microbiota and lifestyle-shaped factors, such as blood factors and metabolites that change as we age. The intestinal holo’ome – defined as the combination of host and microbiota genomes, transcriptomes, proteomes, and metabolomes – may be imbalanced and shift to disease when the wrong host gene expression profile meets the wrong microbiota composition. These imbalances can be triggered by the dietary- or lifestyle-shaped intestinal environment. Accordingly, personalized human intestinal holo’omes will differ significantly among individuals and between two critical points in time: long before and upon the onset of disease. Detrimental combinations of factors could therefore be pinpointed computationally and validated using animal models, such as mice and flies. Finally, treatment strategies that break these harmful combinations could be tested in clinical trials. Herein we provide an overview of the literature and a roadmap to this end.
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Koppen IJN, Bosch AATM, Sanders EAM, van Houten MA, Bogaert D. The respiratory microbiota during health and disease: a paediatric perspective. Pneumonia (Nathan) 2015; 6:90-100. [PMID: 31641583 PMCID: PMC5922343 DOI: 10.15172/pneu.2015.6/656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/23/2015] [Indexed: 12/17/2022] Open
Abstract
Recent studies investigating the relationship between the microbiota and disease are demonstrating novel concepts that could significantly alter the way we treat disease and promote health in the future. It is suggested that the microbiota acquired during childhood may shape the microbial community and affect immunological responses for later life, and could therefore be important in the susceptibility towards disease. Several diseases, including asthma, pneumonia, and otitis media, are associated with changes in composition and diversity of the respiratory microbiota. This review summarises current literature, focusing on the composition and development of the respiratory microbiota in children and its relationship with respiratory diseases.
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Affiliation(s)
- Ilan J N Koppen
- 112Department of Paediatric Immunology and Infectious Diseases Wilhelmina Children Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.,212Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
| | - Astrid A T M Bosch
- 112Department of Paediatric Immunology and Infectious Diseases Wilhelmina Children Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.,212Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
| | - Elisabeth A M Sanders
- 112Department of Paediatric Immunology and Infectious Diseases Wilhelmina Children Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | | | - Debby Bogaert
- 112Department of Paediatric Immunology and Infectious Diseases Wilhelmina Children Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
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Huffnagle GB, Dickson RP. The bacterial microbiota in inflammatory lung diseases. Clin Immunol 2015; 159:177-82. [PMID: 26122174 DOI: 10.1016/j.clim.2015.05.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Numerous lines of evidence, ranging from recent studies back to those in the 1920s, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined.
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Affiliation(s)
- Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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Abstract
PURPOSE OF REVIEW Hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) continue to present very significant diagnostic and management challenges. The development, introduction and use of a wider range of immunosuppressive therapies are leading to a broader spectrum of microorganisms causing HAP and VAP. The persistent clinical dilemma regarding their cause is that detection of a microorganism from a respiratory tract sample does not necessarily signify it is the causative agent of the pneumonia. The ever-increasing antibiotic resistance problem means that HAP and VAP are becoming progressively more difficult to treat. In this article, we review the cause, antimicrobial resistance, diagnosis and treatment of HAP and VAP and encapsulate recent developments and concepts in this rapidly moving field. RECENT FINDINGS Although the microbial causes of HAP and VAP remain at present similar to those identified in previous studies, there are marked geographical differences. Resistance rates among Gram-negative bacteria are continually increasing, and for any species, multiresistance is the norm rather than the exception. The development and introduction of rapid point-of-care diagnostics may improve understanding of the cause of HAP and VAP and has immense potential to influence the treatment and clinical outcomes in HAP/VAP, with patients likely to receive much faster, microorganism-specific treatment with obvious downstream improvements to clinical outcome and antimicrobial stewardship. SUMMARY We describe recent trends in aetiology of HAP and VAP and recent trends in antimicrobial resistance, including resistance mechanisms causing particular concern. The potential for novel molecular diagnostics to revolutionize the diagnosis and treatment of HAP/VAP is discussed.
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Cardenas PA, Cookson WO. The Microbiome at Other Mucosal Sites. Mucosal Immunol 2015. [DOI: 10.1016/b978-0-12-415847-4.00006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Vandecandelaere I, Coenye T. Microbial composition and antibiotic resistance of biofilms recovered from endotracheal tubes of mechanically ventilated patients. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 830:137-55. [PMID: 25366226 DOI: 10.1007/978-3-319-11038-7_9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In critically ill patients, breathing is impaired and mechanical ventilation, using an endotracheal tube (ET) connected to a ventilator, is necessary. Although mechanical ventilation is a life-saving procedure, it is not without risk. Because of several reasons, a biofilm often forms at the distal end of the ET and this biofilm is a persistent source of bacteria which can infect the lungs, causing ventilator-associated pneumonia (VAP). There is a link between the microbial flora of ET biofilms and the microorganisms involved in the onset of VAP. Culture dependent and independent techniques were already used to identify the microbial flora of ET biofilms and also, the antibiotic resistance of microorganisms obtained from ET biofilms was determined. The ESKAPE pathogens play a dominant role in the onset of VAP and these organisms were frequently identified in ET biofilms. Also, antibiotic resistant microorganisms were frequently present in ET biofilms. Members of the normal oral flora were also identified in ET biofilms but it is thought that these organisms initiate ET biofilm formation and are not directly involved in the development of VAP.
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Affiliation(s)
- Ilse Vandecandelaere
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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