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Braun T, Feng R, Amir A, Levhar N, Shacham H, Mao R, Hadar R, Toren I, Algavi Y, Abu-Saad K, Zhuo S, Efroni G, Malik A, Picard O, Yavzori M, Agranovich B, Liu TC, Stappenbeck TS, Denson L, Kalter-Leibovici O, Gottlieb E, Borenstein E, Elinav E, Chen M, Ben-Horin S, Haberman Y. Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort. Nat Commun 2024; 15:3764. [PMID: 38704361 PMCID: PMC11069498 DOI: 10.1038/s41467-024-48106-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n = 380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.
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Affiliation(s)
- Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Rui Feng
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning, Guangxi, China
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hila Shacham
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ren Mao
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rotem Hadar
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Itamar Toren
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Department of Military Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yadid Algavi
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kathleen Abu-Saad
- Gertner Institute for Epidemiology and Health Policy Research, Tel Hashomer, Israel
| | - Shuoyu Zhuo
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Gilat Efroni
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Alona Malik
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Orit Picard
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Miri Yavzori
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Bella Agranovich
- Laura and Isaac Perlmutter Metabolomics Center, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ofra Kalter-Leibovici
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Gertner Institute for Epidemiology and Health Policy Research, Tel Hashomer, Israel
| | - Eyal Gottlieb
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Elhanan Borenstein
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, NM, USA
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Microbiome & Cancer Division, German National Cancer Center (DKFZ), Heidelberg, Germany
| | - Minhu Chen
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel.
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Shtossel O, Finkelstein S, Louzoun Y. mi-Mic: a novel multi-layer statistical test for microbiota-disease associations. Genome Biol 2024; 25:113. [PMID: 38693546 PMCID: PMC11064322 DOI: 10.1186/s13059-024-03256-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
mi-Mic, a novel approach for microbiome differential abundance analysis, tackles the key challenges of such statistical tests: a large number of tests, sparsity, varying abundance scales, and taxonomic relationships. mi-Mic first converts microbial counts to a cladogram of means. It then applies a priori tests on the upper levels of the cladogram to detect overall relationships. Finally, it performs a Mann-Whitney test on paths that are consistently significant along the cladogram or on the leaves. mi-Mic has much higher true to false positives ratios than existing tests, as measured by a new real-to-shuffle positive score.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Shani Finkelstein
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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3
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Ashkenazi-Preiser H, Reuven O, Uzan-Yulzari A, Komisarov S, Cirkin R, Turjeman S, Even C, Twaik N, Ben-Meir K, Mikula I, Cohen-Daniel L, Meirow Y, Pikarsky E, Louzoun Y, Koren O, Baniyash M. The Cross-talk Between Intestinal Microbiota and MDSCs Fuels Colitis-associated Cancer Development. CANCER RESEARCH COMMUNICATIONS 2024; 4:1063-1081. [PMID: 38506672 PMCID: PMC11017962 DOI: 10.1158/2767-9764.crc-23-0421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/24/2023] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Intestinal chronic inflammation is associated with microbial dysbiosis and accumulation of various immune cells including myeloid-derived suppressor cells (MDSC), which profoundly impact the immune microenvironment, perturb homeostasis and increase the risk to develop colitis-associated colorectal cancer (CAC). However, the specific MDSCs-dysbiotic microbiota interactions and their collective impact on CAC development remain poorly understood. In this study, using a murine model of CAC, we demonstrate that CAC-bearing mice exhibit significantly elevated levels of highly immunosuppressive MDSCs, accompanied by microbiota alterations. Both MDSCs and bacteria that infiltrate the colon tissue and developing tumors can be found in close proximity, suggesting intricate MDSC-microbiota cross-talk within the tumor microenvironment. To investigate this phenomenon, we employed antibiotic treatment to disrupt MDSC-microbiota interactions. This intervention yielded a remarkable reduction in intestinal inflammation, decreased MDSC levels, and alleviated immunosuppression, all of which were associated with a significant reduction in tumor burden. Furthermore, we underscore the causative role of dysbiotic microbiota in the predisposition toward tumor development, highlighting their potential as biomarkers for predicting tumor load. We shed light on the intimate MDSCs-microbiota cross-talk, revealing how bacteria enhance MDSC suppressive features and activities, inhibit their differentiation into mature beneficial myeloid cells, and redirect some toward M2 macrophage phenotype. Collectively, this study uncovers the role of MDSC-bacteria cross-talk in impairing immune responses and promoting tumor growth, providing new insights into potential therapeutic strategies for CAC. SIGNIFICANCE MDSCs-dysbiotic bacteria interactions in the intestine play a crucial role in intensifying immunosuppression within the CAC microenvironment, ultimately facilitating tumor growth, highlighting potential therapeutic targets for improving the treatment outcomes of CAC.
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Affiliation(s)
- Hadas Ashkenazi-Preiser
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Or Reuven
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | | | - Sharon Komisarov
- Department of mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Roy Cirkin
- Department of mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
| | - Carmel Even
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
| | - Nira Twaik
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Kerem Ben-Meir
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Ivan Mikula
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Leonor Cohen-Daniel
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Yaron Meirow
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Eli Pikarsky
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
| | - Yoram Louzoun
- Department of mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
| | - Michal Baniyash
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, POB 12272, Jerusalem 91120, Israel
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4
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Sun Y, Guo J, Alejandro Jose Mur L, Xu X, Chen H, Yang Y, Yuan H. Nitrogen starvation modulates the sensitivity of rhizobacterial community to drought stress in Stevia rebaudiana. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120486. [PMID: 38417363 DOI: 10.1016/j.jenvman.2024.120486] [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: 09/28/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Alterations in water regimes or nitrogen (N) availability lead to shifts in the assemblage of rhizosphere microbial community; however, how the rhizosphere microbiome response to concurrent changes in water and N availability remains largely unclear. Herein, we investigated the taxonomic and functional characteristics of rhizobacteria associated with stevia (Stevia rebaudiana Bertoni) under varying combinations of water and N levels. Community diversity and predicted functions of rhizobacteria were predominantly altered by drought stress, with N-starvation modulating these effects. Moreover, N fertilization simplified the ecological interactions within rhizobacterial communities and heightened the relative role of stochastic processes on community assembly. In terms of rhizobacterial composition, we observed both common and distinctive changes in drought-responsive bacterial taxa under different N conditions. Generally, the relative abundance of Proteobacteria and Bacteroidetes phyla were depleted by drought stress but the Actinobacteria phylum showed increases. The rhizobacterial responses to drought stress were influenced by N availability, where the positive response of δ-proteobacteria and the negative response of α- and γ-proteobacteria, along with Bacteroidetes, were further heightened under N starvation. By contrast, under N fertilization conditions, an amplified negative or positive response to drought were demonstrated in Firmicutes and Actinobacteria phyla, respectively. Further, the drought-responsive rhizobacteria were mostly phylogenetically similar, but this pattern was modulated under N-rich conditions. Overall, our findings indicate an N-dependent specific restructuring of rhizosphere bacteria under drought stress. These changes in the rhizosphere microbiome could contribute to enhancing plant stress tolerance.
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Affiliation(s)
- Yuming Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Junjie Guo
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
| | - Luis Alejandro Jose Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Xiaoyang Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Hao Chen
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yongheng Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Haiyan Yuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China.
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5
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Bonillo-Lopez L, Obregon-Gutierrez P, Huerta E, Correa-Fiz F, Sibila M, Aragon V. Intensive antibiotic treatment of sows with parenteral crystalline ceftiofur and tulathromycin alters the composition of the nasal microbiota of their offspring. Vet Res 2023; 54:112. [PMID: 38001497 PMCID: PMC10675909 DOI: 10.1186/s13567-023-01237-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/11/2023] [Indexed: 11/26/2023] Open
Abstract
The nasal microbiota plays an important role in animal health and the use of antibiotics is a major factor that influences its composition. Here, we studied the consequences of an intensive antibiotic treatment, applied to sows and/or their offspring, on the piglets' nasal microbiota. Four pregnant sows were treated with crystalline ceftiofur and tulathromycin (CTsows) while two other sows received only crystalline ceftiofur (Csows). Sow treatments were performed at D-4 (four days pre-farrowing), D3, D10 and D17 for ceftiofur and D-3, D4 and D11 for tulathromycin. Half of the piglets born to CTsows were treated at D1 with ceftiofur. Nasal swabs were taken from piglets at 22-24 days of age and bacterial load and nasal microbiota composition were defined by 16 s rRNA gene qPCR and amplicon sequencing. Antibiotic treatment of sows reduced their nasal bacterial load, as well as in their offspring, indicating a reduced bacterial transmission from the dams. In addition, nasal microbiota composition of the piglets exhibited signs of dysbiosis, showing unusual taxa. The addition of tulathromycin to the ceftiofur treatment seemed to enhance the deleterious effect on the microbiota diversity by diminishing some bacteria commonly found in the piglets' nasal cavity, such as Glaesserella, Streptococcus, Prevotella, Staphylococcus and several members of the Ruminococcaceae and Lachnospiraceae families. On the other hand, the additional treatment of piglets with ceftiofur resulted in no further effect beyond the treatment of the sows. Altogether, these results suggest that intensive antibiotic treatments of sows, especially the double antibiotic treatment, disrupt the nasal microbiota of their offspring and highlight the importance of sow-to-piglet microbiota transmission.
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Affiliation(s)
- Laura Bonillo-Lopez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA). Campus de La Universitat Autònoma de Barcelona (UAB), 08193, BellaterraBarcelona, Catalonia, Spain
- IRTA, Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Catalonia, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Pau Obregon-Gutierrez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA). Campus de La Universitat Autònoma de Barcelona (UAB), 08193, BellaterraBarcelona, Catalonia, Spain
- IRTA, Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Catalonia, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Eva Huerta
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA). Campus de La Universitat Autònoma de Barcelona (UAB), 08193, BellaterraBarcelona, Catalonia, Spain
- IRTA, Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Catalonia, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Florencia Correa-Fiz
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA). Campus de La Universitat Autònoma de Barcelona (UAB), 08193, BellaterraBarcelona, Catalonia, Spain
- IRTA, Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Catalonia, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Marina Sibila
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA). Campus de La Universitat Autònoma de Barcelona (UAB), 08193, BellaterraBarcelona, Catalonia, Spain.
- IRTA, Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Catalonia, Spain.
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain.
| | - Virginia Aragon
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA). Campus de La Universitat Autònoma de Barcelona (UAB), 08193, BellaterraBarcelona, Catalonia, Spain
- IRTA, Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Catalonia, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
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Amir A, Ozel E, Haberman Y, Shental N. Achieving pan-microbiome biological insights via the dbBact knowledge base. Nucleic Acids Res 2023; 51:6593-6608. [PMID: 37326027 PMCID: PMC10359611 DOI: 10.1093/nar/gkad527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/26/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023] Open
Abstract
16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of experiments when interpreting their own findings in a broader context. To bridge this gap, we introduce dbBact - a novel pan-microbiome resource. dbBact combines manually curated information from studies across diverse habitats, creating a collaborative central repository of 16S rRNA amplicon sequence variants (ASVs), which are assigned multiple ontology-based terms. To date dbBact contains information from more than 1000 studies, which include 1500000 associations between 360000 ASVs and 6500 ontology terms. Importantly, dbBact offers a set of computational tools allowing users to easily query their own datasets against the database. To demonstrate how dbBact augments standard microbiome analysis we selected 16 published papers, and reanalyzed their data via dbBact. We uncovered novel inter-host similarities, potential intra-host sources of bacteria, commonalities across different diseases and lower host-specificity in disease-associated bacteria. We also demonstrate the ability to detect environmental sources, reagent-borne contaminants, and identify potential cross-sample contaminations. These analyses demonstrate how combining information across multiple studies and over diverse habitats leads to better understanding of underlying biological processes.
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Affiliation(s)
- Amnon Amir
- Microbiome center, Sheba Medical Center, Israel
| | - Eitan Ozel
- Dept. of Computer Science, The Open University of Israel, Israel
| | - Yael Haberman
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Sheba Medical Center, Israel
| | - Noam Shental
- Dept. of Computer Science, The Open University of Israel, Israel
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7
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Fu X, Du B, Meng Y, Li Y, Zhu X, Ou Z, Zhang M, Wen H, Ma'pol A, Hashim JH, Hashim Z, Wieslander G, Chen Q, Jiang J, Wang J, Norbäck D, Xia Y, Chen Q, Sun Y. Associations between environmental characteristics, high-resolution indoor microbiome, metabolome and allergic and non-allergic rhinitis symptoms for junior high school students. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:791-804. [PMID: 36883483 DOI: 10.1039/d2em00480a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rhinitis is one of the most prevalent chronic diseases globally. Microbiome exposure affects the occurrence of rhinitis. However, previous studies did not differentiate allergic rhinitis (AR) and non-allergic rhinitis (NAR) in the microbial association analysis. In this study, we investigate 347 students in 8 junior high schools, Terengganu, Malaysia, who were categorized as healthy (70.9%), AR (13.8%) and NAR (15.3%) based on a self-administered questionnaire and skin prick tests of pollen, pet, mould and house dust mite allergens. Classroom microbial and metabolite exposure in vacuumed dust was characterized by PacBio long-read amplicon sequencing, quantitative PCR and LC-MS-based untargeted metabolomics. Our findings indicate a similar microbial association pattern between AR and NAR. The richness in Gammaproteobacteria was negatively associated with AR and NAR symptoms, whereas total fungal richness was positively associated with AR and NAR symptoms (p < 0.05). Brasilonema bromeliae and Aeromonas enteropelogenes were negatively associated with AR and NAR, and Deinococcus was positively associated with AR and NAR (p < 0.01). Pipecolic acid was protectively associated with AR and NAR symptoms (OR = 0.06 and 0.13, p = 0.009 and 0.045). A neural network analysis showed that B. bromeliae was co-occurring with pipecolic acid, suggesting that the protective role of this species may be mediated by releasing pipecolic acid. Indoor relative humidity and the weight of vacuum dust were associated with AR and NAR, respectively (p < 0.05), but the health effects were mediated by two protective bacterial species, Aliinostoc morphoplasticum and Ilumatobacter fluminis. Overall, our study reported a similar microbial association pattern between AR and NAR and also revealed the complex interactions between microbial species, environmental characteristics, and rhinitis symptoms.
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Affiliation(s)
- Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Bingqian Du
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Yi Meng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xunhua Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huarong Wen
- Baling Health Center, Dangyang, Hubei, 444100, PR China
| | - Aminnuddin Ma'pol
- Gombak District Health Office, Ministry of Health, Batu Caves, Selangor Darul Ehsan, Malaysia
| | | | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Gunilla Wieslander
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Qingmei Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Juan Wang
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Dan Norbäck
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Yun Xia
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Qingsong Chen
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
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8
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Gut microbial signature in lung cancer patients highlights specific taxa as predictors for durable clinical benefit. Sci Rep 2023; 13:2007. [PMID: 36737654 PMCID: PMC9898251 DOI: 10.1038/s41598-023-29136-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
We aimed to determine microbial signature linked with lung cancer (LC) diagnosis and to define taxa linked with durable clinical benefit (DCB) of advanced LC patients. Stool samples for microbial 16S amplicon sequencing and clinical data were collected from 75 LC patients (50 of which were treated with checkpoint inhibitors) and 31 matched healthy volunteers. We compared LC to healthy controls and patients with DCB to those without. LC patients had lower α-diversity and higher between-subject diversity. Random Forests model to differentiate LC cases from controls ROC-AUC was 0.74. Clostridiales, Lachnospiraceae, and Faecalibacterium prausnitzii taxa abundance was decreased in LC compared to controls. High Akkermansia muciniphila correlated with DCB (HR 4.26, 95% CI 1.98-9.16), not only for the immunotherapy-treated patients. In addition, high Alistipes onderdonkii (HR 3.08, 95% CI 1.34-7.06) and high Ruminococcus (HR 7.76, 95% CI 3.23-18.65) correlated with DCB.Our results support the importance of gut microbiome in LC. We have validated the apparent predictive value of Akkermansia muciniphila, and highlighted Alistipes onderdonkii and Ruminococcus taxa correlation with DCB. Upon additional validations those can be used as biomarkers or as targets for future therapeutic interventions.
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Zeus M, Janssen S, Laws HJ, Fischer U, Borkhardt A, Oommen PT. Results from a pilot study on the oral microbiome in children and adolescents with chronic nonbacterial osteomyelitis. Z Rheumatol 2023; 82:123-133. [PMID: 34196794 PMCID: PMC9981501 DOI: 10.1007/s00393-021-01035-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2021] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To analyze the composition of the oral microbiome in children and adolescents with chronic nonbacterial osteomyelitis (CNO) with respect to age distribution, gender differences, effects of medication, disease activity and the influence of body site. METHODS The oral microbiome of 20 patients (12 male and 8 female; median age 10.3 years) and 36 controls were examined. Two different sites of the oral cavity were swabbed at two time points. Current medication and disease activity were evaluated and registered at these time points. Samples were subjected to amplicon sequencing of the V4 region of the 16S rRNA gene and Qiime2 was used to calculate alpha and beta diversity for multiple alternative metrics. RESULTS On the basis of relative abundances of 975 different suboperational taxonomic units in high throughput next generation sequencing, a significant shift in the composition of the oral microbiome (p < 0.02) was observed among patients being treated with different medications. There was a significant difference in bacterial communities between the group aged 3-8 years old and the group aged 9-14 years old. Significant differences were also seen in bacterial colonization on different sites in the oral cavity, but not with respect to gender or disease activity. CONCLUSION We present first data of a pilot study of the oral microbiome in children and adolescents with CNO, a rare autoinflammatory bone disease. Differences of the oral microbiome of diseased children to normal adult controls revealed a possible role of the oral microbiome as modulatory target or biomarker in CNO.
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Affiliation(s)
- Mona Zeus
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Divison of Pediatric Rheumatology, University Children’s Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Stefan Janssen
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Hans-Jürgen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Divison of Pediatric Rheumatology, University Children’s Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Divison of Pediatric Rheumatology, University Children’s Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Divison of Pediatric Rheumatology, University Children’s Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Prasad Thomas Oommen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Divison of Pediatric Rheumatology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
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10
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Brill B, Amir A, Heller R. Testing for differential abundance in compositional counts data, with application to microbiome studies. Ann Appl Stat 2022. [DOI: 10.1214/22-aoas1607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Barak Brill
- Department of Statistics and Operations Research, Tel Aviv University
| | - Amnon Amir
- Microbiome center, The Chaim Sheba Medical Center
| | - Ruth Heller
- Department of Statistics and Operations Research, Tel Aviv University
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11
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Infant Mode of Delivery Shapes the Skin Mycobiome of Prepubescent Children. Microbiol Spectr 2022; 10:e0226722. [PMID: 36073919 PMCID: PMC9603757 DOI: 10.1128/spectrum.02267-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Characterizing the skin mycobiome is necessary to define its association with the host immune system, particularly in children. In this study, we describe the skin mycobiome on the face, ventral forearm, and calf of 72 prepubescent children (aged 1 to 10 years) and their mothers, based on internal transcribed spacer (ITS) amplicon sequencing. The age and delivery mode at birth are the most influential factors shaping the skin mycobiome. Compared with that of the vaginally born children, the skin mycobiome of caesarean-born children is assembled by predominantly deterministic niche-based processes and exhibits a more fragile microbial network at all three sampling sites. Moreover, vaginal delivery leads to clearer intra- and interindividual specialization of fungal structures with increasing age; this phenomenon is not observed in caesarean-born children. The maternal correlation with children also differs based on the mode of delivery; specifically, the mycobiomes of vaginally born children at younger ages are more strongly correlated with vagina-associated fungal genera (Candida and Rhodotorula), whereas those of caesarean-delivered children at elder age include more skin-associated and airborne fungal genera (Malassezia and Alternaria). Based on this ecological framework, our results suggest that the delivery mode is significantly associated with maturation of the skin fungal community in children. IMPORTANCE Human skin is permanently colonized by microbes starting at birth. The hygiene hypothesis suggests that a lack of early-life immune imprinting weakens the body's resilience against atopic disorders later in life. To better understand fungal colonization following early-life periods affected by interruption, we studied the skin mycobiomes of 73 children and their mothers. Our results suggest a differentiation of the skin mycobiomes between caesarean-born and vaginally born children. Caesarean-born children exhibit a mycobiome structure with more fitted deterministic niche-based processes, a fragile network, and an unchanged microbial dissimilarity over time. In vaginally born children, this dissimilarity increases with age. The results indicate that initial microbial colonization has a long-term impact on a child's skin mycobiome. We believe that these findings will inspire further investigations of the "hygiene hypothesis" in the human microbiome, especially in providing novel insights into influences on the development of the early-life microbiome.
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12
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Abeyratne CR, Macaya-Sanz D, Zhou R, Barry KW, Daum C, Haiby K, Lipzen A, Stanton B, Yoshinaga Y, Zane M, Tuskan GA, DiFazio SP. High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3 (BETHESDA, MD.) 2022; 13:6762080. [PMID: 36250890 PMCID: PMC9836356 DOI: 10.1093/g3journal/jkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
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Affiliation(s)
| | - David Macaya-Sanz
- Department of Forest Ecology & Genetics, CIFOR-INIA, CSIC, Madrid 28040, Spain
| | - Ran Zhou
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Anna Lipzen
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Gerald A Tuskan
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Stephen P DiFazio
- Corresponding author: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
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13
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Fu X, Ou Z, Sun Y. Indoor microbiome and allergic diseases: From theoretical advances to prevention strategies. ECO-ENVIRONMENT & HEALTH (ONLINE) 2022; 1:133-146. [PMID: 38075599 PMCID: PMC10702906 DOI: 10.1016/j.eehl.2022.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 12/20/2023]
Abstract
The prevalence of allergic diseases, such as asthma, rhinitis, eczema, and sick building syndrome (SBS), has increased drastically in the past few decades. Current medications can only relieve the symptoms but not cure these diseases whose development is suggested to be greatly impacted by the indoor microbiome. However, no study comprehensively summarizes the progress and general rules in the field, impeding subsequent translational application. To close knowledge gaps between theoretical research and practical application, we conducted a comprehensive literature review to summarize the epidemiological, environmental, and molecular evidence of indoor microbiome studies. Epidemiological evidence shows that the potential protective indoor microorganisms for asthma are mainly from the phyla Actinobacteria and Proteobacteria, and the risk microorganisms are mainly from Bacilli, Clostridia, and Bacteroidia. Due to extremely high microbial diversity and geographic variation, different health-associated species/genera are detected in different regions. Compared with indoor microbial composition, indoor metabolites show more consistent associations with health, including microbial volatile organic compounds (MVOCs), lipopolysaccharides (LPS), indole derivatives, and flavonoids. Therefore, indoor metabolites could be a better indicator than indoor microbial taxa for environmental assessments and health outcome prediction. The interaction between the indoor microbiome and environmental characteristics (surrounding greenness, relative humidity, building confinement, and CO2 concentration) and immunology effects of indoor microorganisms (inflammatory cytokines and pattern recognition receptors) are briefly reviewed to provide new insights for disease prevention and treatment. Widely used tools in indoor microbiome studies are introduced to facilitate standard practice and the precise identification of health-related targets.
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Affiliation(s)
- Xi Fu
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Longitudinal Study of Fecal Microbiota in Calves with or without Diarrhea Episodes before Weaning. Vet Sci 2022; 9:vetsci9090463. [PMID: 36136679 PMCID: PMC9503950 DOI: 10.3390/vetsci9090463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Animal production is searching for ways to reduce antimicrobial use, and the best way is to avoid their use by maintaining the health of the animals. The microbiota is involved in the host health, and when the fecal microbiota was analyzed in calves that developed or not diarrhea, differences linked to the health status were detected. While changes in the fecal microbiota were observed with time (during the first 2 months of age) in all the calves, the microbiota from the healthy animals presented an earlier stabilization and some changes in low abundant bacteria, which may play a role in the subsequent health status of the animals. Bacteria classified in the families Coriobacteriaceae and Phyllobacteriaceae, and the bacterium Epulopiscium were found in the core of the microbiota of the healthy calves (calves that did not have diarrhea) possibly with a protective probiotic effect. On the other hand, several bacteria, such as Lachnospira, Neisseria and Solibacillus, were found only in the core of the microbiota obtained from calves that had diarrhea, indicating that they could be linked to a higher predisposition to suffer diarrhea. These results can help in the development of new probiotics to promote gut health in calves. Abstract The microbiota plays an important role in the development of diarrhea in pre-weaned calves. The characterization of the fecal microbiota in health and disease can be critical to unravel the bacterial dynamics associated with diarrhea and help with its prevention and control. In this study, we aimed to detect changes in the fecal microbiota of calves that experienced early-life diarrhea episodes. Fecal samples were taken from calves remaining healthy and calves with an episode of diarrhea during the study. We sampled at arrival (12 days of age) and after one and two months of life; also, at the time of the diarrhea episode for the diarrheic calves (day 17). Samples were processed to extract total DNA, submitted to 16S rRNA gene sequencing, and bioinformatically analyzed to infer the bacterial populations. Microbiota changes through time were reported for both groups. However, we detected an earlier stabilization in the healthy group. Moreover, we detected changes within low abundant taxa that may play a role in the subsequent health status of the animals. The fecal microbiota of healthy and diarrheic calves showed different dynamics in the diversity through time that may be the reflections of the variations within low-abundant taxa.
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15
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Computational approach to modeling microbiome landscapes associated with chronic human disease progression. PLoS Comput Biol 2022; 18:e1010373. [PMID: 35926003 PMCID: PMC9380910 DOI: 10.1371/journal.pcbi.1010373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/16/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
A microbial community is a dynamic system undergoing constant change in response to internal and external stimuli. These changes can have significant implications for human health. However, due to the difficulty in obtaining longitudinal samples, the study of the dynamic relationship between the microbiome and human health remains a challenge. Here, we introduce a novel computational strategy that uses massive cross-sectional sample data to model microbiome landscapes associated with chronic disease development. The strategy is based on the rationale that each static sample provides a snapshot of the disease process, and if the number of samples is sufficiently large, the footprints of individual samples populate progression trajectories, which enables us to recover disease progression paths along a microbiome landscape by using computational approaches. To demonstrate the validity of the proposed strategy, we developed a bioinformatics pipeline and applied it to a gut microbiome dataset available from a Crohn’s disease study. Our analysis resulted in one of the first working models of microbial progression for Crohn’s disease. We performed a series of interrogations to validate the constructed model. Our analysis suggested that the model recapitulated the longitudinal progression of microbial dysbiosis during the known clinical trajectory of Crohn’s disease. By overcoming restrictions associated with complex longitudinal sampling, the proposed strategy can provide valuable insights into the role of the microbiome in the pathogenesis of chronic disease and facilitate the shift of the field from descriptive research to mechanistic studies. The delineation of system dynamics of a microbial community can provide a wealth of insights into the roles of the microbiome in the pathogenesis of chronic disease. However, due to the difficulty in obtaining longitudinal samples, most existing microbiome studies have been cross-sectional and largely descriptive. Here, we present a novel computational strategy that leverages massive static sample data to model microbiome landscapes associated with chronic disease development. To demonstrate the validity of the proposed strategy, we applied it to a gut microbiome dataset available from a Crohn’s disease study and constructed one of the first microbial progression models of the disease. We performed a series of interrogations on the constructed model. Our analysis suggested that the constructed model recapitulated the longitudinal progression of microbial dysbiosis during the known clinical trajectory of Crohn’s disease. By overcoming the sampling restrictions inherent to slowly progressive diseases, our approach is potentially widely applicable in many different studies across body sites, diseases, and other conditions.
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16
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Diet Fermentation Leads to Microbial Adaptation in Black Soldier Fly (Hermetia illucens; Linnaeus, 1758) Larvae Reared on Palm Oil Side Streams. SUSTAINABILITY 2022. [DOI: 10.3390/su14095626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Insects offer a promising alternative source of protein to mitigate the environmental consequences of conventional livestock farming. Larvae of the black soldier fly (Hermetia illucens; Linnaeus, 1758) efficiently convert a variety of organic side streams and residues into valuable proteins, lipids, and chitin. Here, we evaluated the suitability of two palm oil industry side streams—empty fruit bunches (EFB) and palm kernel meal (PKM)—as larval feed, and their impact on the larval gut microbiome. Among 69 fungal species we screened, Marasmius palmivorus, Irpex consors, and Bjerkandera adusta achieved the fastest growth and lignin degradation, so these fungi were used for the pretreatment of 7:3 mixtures of EFB and PKM. Larvae reared on the mixture pretreated with B. adusta (BAD) developed significantly more quickly and reached a higher final weight than those reared on the other pretreatments or the non-fermented reference (NFR). Amplicon sequencing of the BAD and NFR groups revealed major differences in the larval gut microbiome. The NFR group was dominated by facultatively anaerobic Enterobacteriaceae (typical of H. illucens larvae) whereas the BAD group favored obligately anaerobic, cellulolytic bacteria (Ruminococcaceae and Lachnospiraceae). We hypothesize that fungal lignin degradation led to an accumulation of mycelia and subsequent cellulolytic breakdown of fiber residues, thus improving substrate digestibility.
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17
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Aleti G, Kohn JN, Troyer EA, Weldon K, Huang S, Tripathi A, Dorrestein PC, Swafford AD, Knight R, Hong S. Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides. BMC Microbiol 2022; 22:75. [PMID: 35287577 PMCID: PMC8919597 DOI: 10.1186/s12866-022-02483-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/25/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Depression and obesity are highly prevalent, often co-occurring conditions marked by inflammation. Microbiome perturbations are implicated in obesity-inflammation-depression interrelationships, but how the microbiome mechanistically contributes to pathology remains unclear. Metabolomic investigations into microbial neuroactive metabolites may offer mechanistic insights into host-microbe interactions. Using 16S sequencing and untargeted mass spectrometry of saliva, and blood monocyte inflammation regulation assays, we identified key microbes, metabolites and host inflammation in association with depressive symptomatology, obesity, and depressive symptomatology-obesity comorbidity. RESULTS Gram-negative bacteria with inflammation potential were enriched relative to Gram-positive bacteria in comorbid obesity-depression, supporting the inflammation-oral microbiome link in obesity-depression interrelationships. Oral microbiome was more highly predictive of depressive symptomatology-obesity co-occurrences than of obesity or depressive symptomatology independently, suggesting specific microbial signatures associated with obesity-depression co-occurrences. Mass spectrometry analysis revealed significant changes in levels of signaling molecules of microbiota, microbial or dietary derived signaling peptides and aromatic amino acids among depressive symptomatology, obesity and comorbid obesity-depression. Furthermore, integration of the microbiome and metabolomics data revealed that key oral microbes, many previously shown to have neuroactive potential, co-occurred with potential neuropeptides and biosynthetic precursors of the neurotransmitters dopamine, epinephrine and serotonin. CONCLUSIONS Together, our findings offer novel insights into oral microbial-brain connection and potential neuroactive metabolites involved.
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Affiliation(s)
- Gajender Aleti
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jordan N Kohn
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily A Troyer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kelly Weldon
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shi Huang
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pieter C Dorrestein
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Suzi Hong
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA.
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA.
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Abbas-Egbariya H, Haberman Y, Braun T, Hadar R, Denson L, Gal-Mor O, Amir A. Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal. Genome Biol 2022; 23:61. [PMID: 35197084 PMCID: PMC8867743 DOI: 10.1186/s13059-022-02637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gut microbial alteration is implicated in inflammatory bowel disease but is noted in other diseases. Systematic comparison to define similarities and specificities is hampered since most studies focus on a single disease. RESULTS We develop a pipeline to compare between disease cohorts starting from the raw V4 16S amplicon sequence variants. Including 12,838 subjects, from 59 disease cohorts, we demonstrate a predominant shared signature across diseases, indicating a common bacterial response to different diseases. We show that classifiers trained on one disease cohort predict relatively well other diseases due to this shared signal, and hence, caution should be taken when using such classifiers in real-world scenarios, where diseases are intermixed. Based on this common signature across a large array of diseases, we develop a universal dysbiosis index that successfully differentiates between cases and controls across various diseases and can be used for prioritizing fecal donors and samples with lower disease probability. Finally, we identify a set of IBD-specific bacteria, which can direct mechanistic studies and design of IBD-specific microbial interventions. CONCLUSIONS A robust non-specific general response of the gut microbiome is detected in a large array of diseases. Disease classifiers may confuse between different diseases due to this shared microbial response. Our universal dysbiosis index can be used as a tool to prioritize fecal samples and donors. Finally, the IBD-specific taxa may indicate a more direct association to gut inflammation and disease pathogenesis, and those can be further used as biomarkers and as future targets for interventions.
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Affiliation(s)
- Haya Abbas-Egbariya
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel Aviv, Israel
| | - Yael Haberman
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel Aviv, Israel. .,Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Tzipi Braun
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel Aviv, Israel
| | - Rotem Hadar
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel Aviv, Israel
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, and the Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel Aviv, Israel.
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Brusilovsky M, Bao R, Rochman M, Kemter AM, Nagler CR, Rothenberg ME. Host-Microbiota Interactions in the Esophagus During Homeostasis and Allergic Inflammation. Gastroenterology 2022; 162:521-534.e8. [PMID: 34627858 PMCID: PMC9185752 DOI: 10.1053/j.gastro.2021.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/10/2021] [Accepted: 10/04/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND & AIMS Microbiota composition and mechanisms of host-microbiota interactions in the esophagus are unclear. We aimed to uncover fundamental information about the esophageal microbiome and its potential significance to eosinophilic esophagitis (EoE). METHODS Microbiota composition, transplantation potential, and antibiotic responsiveness in the esophagus were established via 16S ribosomal RNA sequencing. Functional outcomes of microbiota colonization were assessed by RNA sequencing analysis of mouse esophageal epithelium and compared with the human EoE transcriptome. The impact of dysbiosis was assessed using a preclinical model of EoE. RESULTS We found that the murine esophagus is colonized with diverse microbial communities within the first month of life. The esophageal microbiota is distinct, dominated by Lactobacillales, and demonstrates spatial heterogeneity as the proximal and distal esophagus are enriched in Bifidobacteriales and Lactobacillales, respectively. Fecal matter transplantation restores the esophageal microbiota, demonstrating that the local environment drives diversity. Microbiota colonization modifies esophageal tissue morphology and gene expression that is enriched in pathways associated with epithelial barrier function and overlapping with genes involved in EoE, including POSTN, KLK5, and HIF1A. Finally, neonatal antibiotic treatment reduces the abundance of Lactobacillales and exaggerates type 2 inflammation in the esophagus. Clinical data substantiated loss of esophageal Lactobacillales in EoE compared with controls. CONCLUSIONS The esophagus has a unique microbiome with notable differences between its proximal and distal regions. Fecal matter transplantation restores the esophageal microbiome. Antibiotic-induced dysbiosis exacerbates disease in a murine model of EoE. Collectively, these data establish the composition, transplantation potential, antibiotic responsiveness, and host-microbiota interaction in the esophagus and have implications for gastrointestinal health and disease.
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Affiliation(s)
- Michael Brusilovsky
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Riyue Bao
- Department of Pediatrics, University of Chicago, Chicago, Illinois; Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Andrea M Kemter
- Department of Pathology, Biological Sciences Division, University of Chicago, Chicago, Illinois
| | - Cathryn R Nagler
- Department of Pathology, Biological Sciences Division, University of Chicago, Chicago, Illinois; Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois.
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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Amir A, Erez-Granat O, Braun T, Sosnovski K, Hadar R, BenShoshan M, Heiman S, Abbas-Egbariya H, Glick Saar E, Efroni G, Haberman Y. Gut microbiome development in early childhood is affected by day care attendance. NPJ Biofilms Microbiomes 2022; 8:2. [PMID: 35017536 PMCID: PMC8752763 DOI: 10.1038/s41522-021-00265-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022] Open
Abstract
The human gut microbiome develops during the first years of life, followed by a relatively stable adult microbiome. Day care attendance is a drastic change that exposes children to a large group of peers in a diverse environment for prolonged periods, at this critical time of microbial development, and therefore has the potential to affect microbial composition. We characterize the effect of day care on the gut microbial development throughout a single school year in 61 children from 4 different day care facilities, and in additional 24 age-matched home care children (n = 268 samples, median age of entering the study was 12 months). We show that day care attendance is a significant and impactful factor in shaping the microbial composition of the growing child, the specific daycare facility and class influence the gut microbiome, and each child becomes more similar to others in their day care. Furthermore, in comparison to home care children, day care children have a different gut microbial composition, with enrichment of taxa more frequently observed in older populations. Our results provide evidence that daycare may be an external factor that contributes to gut microbiome maturation and make-up in early childhood.
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Affiliation(s)
- Amnon Amir
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Ortal Erez-Granat
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Tzipi Braun
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Katya Sosnovski
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Rotem Hadar
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Marina BenShoshan
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Sophia Heiman
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Haya Abbas-Egbariya
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Efrat Glick Saar
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Gilat Efroni
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Yael Haberman
- Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel. .,Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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21
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Klüber P, Meurer SK, Lambertz J, Schwarz R, Zechel-Gran S, Braunschweig T, Hurka S, Domann E, Weiskirchen R. Depletion of Lipocalin 2 (LCN2) in Mice Leads to Dysbiosis and Persistent Colonization with Segmented Filamentous Bacteria. Int J Mol Sci 2021; 22:ijms222313156. [PMID: 34884961 PMCID: PMC8658549 DOI: 10.3390/ijms222313156] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/15/2022] Open
Abstract
Lipocalin 2 (LCN2) mediates key roles in innate immune responses. It has affinity for many lipophilic ligands and binds various siderophores, thereby limiting bacterial growth by iron sequestration. Furthermore, LCN2 protects against obesity and metabolic syndrome by interfering with the composition of gut microbiota. Consequently, complete or hepatocyte-specific ablation of the Lcn2 gene is associated with higher susceptibility to bacterial infections. In the present study, we comparatively profiled microbiota in fecal samples of wild type and Lcn2 null mice and show, in contrast to previous reports, that the quantity of DNA in feces of Lcn2 null mice is significantly lower than that in wild type mice (p < 0.001). By using the hypervariable V4 region of the 16S rDNA gene and Next-Generation Sequencing methods, we found a statistically significant change in 16 taxonomic units in Lcn2-/- mice, including eight gender-specific deviations. In particular, members of Clostridium, Escherichia, Helicobacter, Lactococcus, Prevotellaceae_UCG-001 and Staphylococcus appeared to expand in the intestinal tract of knockout mice. Interestingly, the proportion of Escherichia (200-fold) and Staphylococcus (10-fold) as well as the abundance of intestinal bacteria encoding the LCN2-sensitive siderphore enterobactin (entA) was significantly increased in male Lcn2 null mice (743-fold, p < 0.001). This was accompanied by significant higher immune cell infiltration in the ileum as demonstrated by increased immunoreactivity against the pan-leukocyte protein CD45, the lymphocyte transcription factor MUM-1/IRF4, and the macrophage antigen CD68/Macrosialin. In addition, we found a higher expression of mucosal mast cell proteases indicating a higher number of those innate immune cells. Finally, the ileum of Lcn2 null mice displayed a high abundance of segmented filamentous bacteria, which are intimately associated with the mucosal cell layer, provoking epithelial antimicrobial responses and affecting T-helper cell polarization.
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Affiliation(s)
- Patrick Klüber
- German Centre for Infection Research, Institute of Medical Microbiology, Justus-Liebig-University, D-35392 Giessen, Germany; (P.K.); (S.Z.-G.)
| | - Steffen K. Meurer
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, D-52074 Aachen, Germany; (S.K.M.); (J.L.)
| | - Jessica Lambertz
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, D-52074 Aachen, Germany; (S.K.M.); (J.L.)
| | - Roman Schwarz
- Labor Mönchengladbach, Medical Care Centre, D-41169 Mönchengladbach, Germany;
| | - Silke Zechel-Gran
- German Centre for Infection Research, Institute of Medical Microbiology, Justus-Liebig-University, D-35392 Giessen, Germany; (P.K.); (S.Z.-G.)
| | - Till Braunschweig
- Institute of Pathology, RWTH Aachen University Hospital, D-52074 Aachen, Germany;
| | - Sabine Hurka
- Institute for Insect Biotechnology, Justus-Liebig-University, D-35392 Giessen, Germany;
| | - Eugen Domann
- German Centre for Infection Research, Institute of Hygiene and Environmental Medicine, Justus-Liebig-University, D-35392 Giessen, Germany
- Correspondence: (E.D.); (R.W.); Tel.: +49-(0)641-99-41280 (E.D.); +49-(0)241-80-88683 (R.W.)
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, D-52074 Aachen, Germany; (S.K.M.); (J.L.)
- Correspondence: (E.D.); (R.W.); Tel.: +49-(0)641-99-41280 (E.D.); +49-(0)241-80-88683 (R.W.)
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22
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Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. Clean room microbiome complexity impacts planetary protection bioburden. MICROBIOME 2021; 9:238. [PMID: 34861887 PMCID: PMC8643001 DOI: 10.1186/s40168-021-01159-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/13/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Spacecraft Assembly Facility (SAF) at the NASA's Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. RESULTS Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. CONCLUSION This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays. Video abstract.
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Affiliation(s)
- Ryan Hendrickson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Heidi S Aronson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Cameron Martino
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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23
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Rosa LH, da Costa Coelho L, Pinto OHB, Carvalho-Silva M, Convey P, Rosa CA, Câmara PEAS. Ecological succession of fungal and bacterial communities in Antarctic mosses affected by a fairy ring disease. Extremophiles 2021; 25:471-481. [PMID: 34480232 DOI: 10.1007/s00792-021-01240-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/26/2021] [Indexed: 01/04/2023]
Abstract
We evaluated fungal and bacterial diversity in an established moss carpet on King George Island, Antarctica, affected by 'fairy ring' disease using metabarcoding. A total of 127 fungal and 706 bacterial taxa were assigned. Ascomycota dominated the fungal assemblages, followed by Basidiomycota, Rozellomycota, Chytridiomycota, Mortierellomycota and Monoblepharomycota. The fungal community displayed high indices of diversity, richness and dominance, which increased from healthy through infected to dead moss samples. A range of fungal taxa were more abundant in dead rather than healthy or fairy ring moss samples. Bacterial diversity and richness were greatest in healthy moss and least within the infected fairy ring. The dominant prokaryotic phyla were Actinobacteriota, Proteobacteria, Bacteroidota and Cyanobacteria. Cyanophyceae sp., whilst consistently dominant, were less abundant in fairy ring samples. Our data confirmed the presence and abundance of a range of plant pathogenic fungi, supporting the hypothesis that the disease is linked with multiple fungal taxa. Further studies are required to characterise the interactions between plant pathogenic fungi and their host Antarctic mosses. Monitoring the dynamics of mutualist, phytopathogenic and decomposer microorganisms associated with moss carpets may provide bioindicators of moss health.
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Affiliation(s)
- Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
| | - Lívia da Costa Coelho
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | | | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.,Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Carlos Augusto Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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24
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Fu X, Ou Z, Zhang M, Meng Y, Li Y, Wen J, Hu Q, Zhang X, Norbäck D, Deng Y, Zhao Z, Sun Y. Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China-association with asthma, rhinitis and rhinoconjunctivitis in high school students. MICROBIOME 2021; 9:138. [PMID: 34118964 PMCID: PMC8199840 DOI: 10.1186/s40168-021-01091-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/09/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries. METHODS Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms. RESULTS Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut. CONCLUSIONS We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects. Video abstract.
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Affiliation(s)
- Xi Fu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yi Meng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Qiansheng Hu
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, People's Republic of China
| | - Dan Norbäck
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237, Uppsala, Sweden
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
| | - Zhuohui Zhao
- Department of Environmental Health, School of Public Health, Fudan University, Key Laboratory of Public Health Safety of the Ministry of Education, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai, 200030, China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
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Obregon-Gutierrez P, Aragon V, Correa-Fiz F. Sow Contact Is a Major Driver in the Development of the Nasal Microbiota of Piglets. Pathogens 2021; 10:pathogens10060697. [PMID: 34205187 PMCID: PMC8227386 DOI: 10.3390/pathogens10060697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/28/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
The nasal microbiota composition is associated with the health status of piglets. Sow-contact in early life is one of the factors influencing the microbial composition in piglets; however, its impact has never been assessed in the nasal microbiota of piglets reared in controlled environmental conditions. Nasal microbiota of weaning piglets in high-biosecurity facilities with different time of contact with their sows (no contact after farrowing, contact limited to few hours or normal contact until weaning at three weeks) was unveiled by 16S rRNA gene sequencing. Contact with sows demonstrated to be a major factor affecting the nasal microbial composition of the piglets. The nasal microbiota of piglets that had contact with sows until weaning, but were reared in high biosecurity facilities, was richer and more similar to the previously described healthy nasal microbiota from conventional farm piglets. On the other hand, the nasal communities inhabiting piglets with no or limited contact with sows was different and dominated by bacteria not commonly abundant in this body site. Furthermore, the length of sow–piglet contact was also an important variable. In addition, the piglets raised in BSL3 conditions showed an increased richness of low-abundant species in the nasal microbiota. Artificially rearing in high biosecurity facilities without the contact of sows as a source of nasal colonizers had dramatic impacts on the nasal microbiota of weaning piglets and may introduce significant bias into animal research under these conditions.
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Affiliation(s)
- Pau Obregon-Gutierrez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (P.O.-G.); (V.A.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193 Barcelona, Spain
| | - Virginia Aragon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (P.O.-G.); (V.A.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193 Barcelona, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (P.O.-G.); (V.A.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193 Barcelona, Spain
- Correspondence:
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26
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Moll JM, Myers PN, Zhang C, Eriksen C, Wolf J, Appelberg KS, Lindberg G, Bahl MI, Zhao H, Pan-Hammarström Q, Cai K, Jia H, Borte S, Nielsen HB, Kristiansen K, Brix S, Hammarström L. Gut Microbiota Perturbation in IgA Deficiency Is Influenced by IgA-Autoantibody Status. Gastroenterology 2021; 160:2423-2434.e5. [PMID: 33662387 DOI: 10.1053/j.gastro.2021.02.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS IgA exerts its primary function at mucosal surfaces, where it binds microbial antigens to regulate bacterial growth and epithelial attachment. One third of individuals with IgA deficiency (IgAD) suffers from recurrent mucosal infections, possibly related to an altered microbiota. We aimed to delineate the impact of IgAD and the IgA-autoantibody status on the composition and functional capacity of the gut microbiota. METHODS We performed a paired, lifestyle-balanced analysis of the effect of IgA on the gut microbiota composition and functionality based on fecal samples from individuals with IgAD and IgA-sufficient household members (n = 100), involving quantitative shotgun metagenomics, species-centric functional annotation of gut bacteria, and strain-level analyses. We supplemented the data set with 32 individuals with IgAD and examined the influence of IgA-autoantibody status on the composition and functionality of the gut microbiota. RESULTS The gut microbiota of individuals with IgAD exhibited decreased richness and diversity and was enriched for bacterial species encoding pathogen-related functions including multidrug and antimicrobial peptide resistance, virulence factors, and type III and VI secretion systems. These functional changes were largely attributed to Escherichia coli but were independent of E coli strain variations and most prominent in individuals with IgAD with IgA-specific autoreactive antibodies. CONCLUSIONS The microbiota of individuals with IgAD is enriched for species holding increased proinflammatory potential, thereby potentially decreasing the resistance to gut barrier-perturbing events. This phenotype is especially pronounced in individuals with IgAD with IgA-specific autoreactive antibodies, thus warranting a screening for IgA-specific autoreactive antibodies in IgAD to identify patients with IgAD with increased risk for gastrointestinal implications.
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Affiliation(s)
- Janne Marie Moll
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pernille Neve Myers
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Carsten Eriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Johannes Wolf
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies at the Municipal Hospital St. Georg Leipzig, Leipzig, Germany
| | - K Sofia Appelberg
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Greger Lindberg
- Department of Medicine, Karolinska Institutet and Department of Gastroenterology at Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Kaiye Cai
- BGI-Shenzhen, Shenzhen, China; Shenzhen Engineering Laboratory for Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, China; Shenzhen Key Laboratory for Human Commensals and Health Research, BGI-Shenzhen, Shenzhen, China
| | - Stephan Borte
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies at the Municipal Hospital St. Georg Leipzig, Leipzig, Germany; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | | | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, Shandong, China.
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark; Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, Shandong, China.
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Stockholm, Sweden.
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Lavrinienko A, Hämäläinen A, Hindström R, Tukalenko E, Boratyński Z, Kivisaari K, Mousseau TA, Watts PC, Mappes T. Comparable response of wild rodent gut microbiome to anthropogenic habitat contamination. Mol Ecol 2021; 30:3485-3499. [PMID: 33955637 DOI: 10.1111/mec.15945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Species identity is thought to dominate over environment in shaping wild rodent gut microbiota, but it remains unknown whether the responses of host gut microbiota to shared anthropogenic habitat impacts are species-specific or if the general gut microbiota response is similar across host species. Here, we compare the influence of exposure to radionuclide contamination on the gut microbiota of four wild mouse species: Apodemus flavicollis, A. sylvaticus, A. speciosus and A. argenteus. Building on the evidence that radiation impacts bank vole (Myodes glareolus) gut microbiota, we hypothesized that radiation exposure has a general impact on rodent gut microbiota. Because we sampled (n = 288) two species pairs of Apodemus mice that occur in sympatry in habitats affected by the Chernobyl and Fukushima nuclear accidents, these comparisons provide an opportunity for a general assessment of the effects of exposure to environmental contamination (radionuclides) on gut microbiota across host phylogeny and geographical areas. In general agreement with our hypothesis, analyses of bacterial 16S rRNA gene sequences revealed that radiation exposure alters the gut microbiota composition and structure in three of the four species of Apodemus mice. The notable lack of an association between the gut microbiota and soil radionuclide contamination in one mouse species from Fukushima (A. argenteus) probably reflects host "radiation escape" through its unique tree-dwelling lifestyle. The finding that host ecology can modulate effects of radiation exposure offers an interesting counterpoint for future analyses into effects of radiation or any other toxic exposure on host and its associated microbiota. Our data show that exposure to radionuclide contamination is linked to comparable gut microbiota responses across multiple species of rodents.
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Affiliation(s)
- Anton Lavrinienko
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anni Hämäläinen
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | | | - Eugene Tukalenko
- Ecology and Genetics, University of Oulu, Oulu, Finland.,National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv, Ukraine
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Kati Kivisaari
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,SURA/LASSO/NASA, ISS Utilization and Life Sciences Division, Kennedy Space Center, Cape Canaveral, FL, USA
| | - Phillip C Watts
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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28
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Braun T, Halevi S, Hadar R, Efroni G, Glick Saar E, Keller N, Amir A, Amit S, Haberman Y. SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition. Sci Rep 2021; 11:8922. [PMID: 33903709 PMCID: PMC8076218 DOI: 10.1038/s41598-021-88536-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.
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Affiliation(s)
- Tzipi Braun
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with the Tel-Aviv University, Tel Hashomer, Israel
| | - Shiraz Halevi
- Clinical Microbiology, The Chaim Sheba Medical Centre, Ramat-Gan, Israel
- Sakler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Hadar
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with the Tel-Aviv University, Tel Hashomer, Israel
| | - Gilate Efroni
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with the Tel-Aviv University, Tel Hashomer, Israel
| | - Efrat Glick Saar
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with the Tel-Aviv University, Tel Hashomer, Israel
| | - Natahan Keller
- Clinical Microbiology, The Chaim Sheba Medical Centre, Ramat-Gan, Israel
- Sakler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with the Tel-Aviv University, Tel Hashomer, Israel
| | - Sharon Amit
- Clinical Microbiology, The Chaim Sheba Medical Centre, Ramat-Gan, Israel
- Sakler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Haberman
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with the Tel-Aviv University, Tel Hashomer, Israel.
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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29
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Caverly LJ, Zimbric M, Azar M, Opron K, LiPuma JJ. Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection. ERJ Open Res 2021; 7:00578-2020. [PMID: 33898611 PMCID: PMC8053818 DOI: 10.1183/23120541.00578-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/29/2021] [Indexed: 01/03/2023] Open
Abstract
Rationale Pulmonary infections with nontuberculous mycobacteria (NTM) are increasingly prevalent in people with cystic fibrosis (CF). Clinical outcomes following NTM acquisition are highly variable, ranging from transient self-resolving infection to NTM pulmonary disease associated with significant morbidity. Relationships between airway microbiota and variability of NTM outcomes in CF are unclear. Objective To identify features of CF airway microbiota associated with outcomes of NTM infection. Methods 188 sputum samples, obtained from 24 subjects with CF, each with three or more samples collected from 3.5 years prior to, and up to 6 months following incident NTM infection, were selected from a sample repository. Sputum DNA underwent bacterial 16S rRNA gene sequencing. Airway microbiota were compared based on the primary outcome, a diagnosis of NTM pulmonary disease, using Wilcoxon rank-sum testing, autoregressive integrated moving average modelling and network analyses. Measurements and main results Subjects with and without NTM pulmonary disease were similar in clinical characteristics, including age and lung function at the time of incident NTM infection. Time-series analyses of sputum samples prior to incident NTM infection identified positive correlations between Pseudomonas, Streptococcus, Veillonella, Prevotella and Rothia with diagnosis of NTM pulmonary disease and with persistent NTM infection. Network analyses identified differences in clustering of taxa between subjects with and without NTM pulmonary disease, and between subjects with persistent versus transient NTM infection. Conclusions CF airway microbiota prior to incident NTM infection are associated with subsequent outcomes, including diagnosis of NTM pulmonary disease, and persistence of NTM infection. Associations between airway microbiota and NTM outcomes represent targets for validation as predictive markers and for future therapies.
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Affiliation(s)
- Lindsay J Caverly
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madsen Zimbric
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michelle Azar
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristopher Opron
- Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John J LiPuma
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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30
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Wang Y, Zhang Y, Qian Y, Xie YH, Jiang SS, Kang ZR, Chen YX, Chen ZF, Fang JY. Alterations in the oral and gut microbiome of colorectal cancer patients and association with host clinical factors. Int J Cancer 2021; 149:925-935. [PMID: 33844851 DOI: 10.1002/ijc.33596] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/16/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
Previous studies have suggested that gut microbiota plays a critical role in colorectal cancer (CRC). Although preliminary comparisons of the oral and gut microbiota between CRC and healthy control (HC) patients have been made, the association between microbiome abundance and host clinical factors has not been fully illustrated, especially oral health conditions. Matching samples of unstimulated saliva, cancer tissues or biopsies and stools were collected from 30 CRC and 30 HC patients from Shanghai Jiao Tong University affiliated Renji Hospital for 16S rRNA sequencing analysis. The diversity in salivary and mucosal microbiome, but not stool microbiome of CRC group, was significantly different from that of HC, as demonstrated by the Principal Component Analysis. Logistic regression analysis revealed that older age and higher oral hygiene index (OHI) were independent risk factors for CRC, with odds ratios and 95% confidence intervals of 1.159 (1.045-1.284) and 4.398 (1.328-14.567), respectively. Salivary Firmicutes to Bacteroides ratio in CRC was significantly higher than that in the HC group (P < .001), while the mucosal ratio was slightly decreased in CRC (P < .05). Salivary Rothia and Streptococcus levels were positively correlated with OHI, while Alloprevotella, Fusobacterium, Peptostreptoccus and Prevotella genera levels were negatively associated with OHI. NetShift analysis revealed that salivary Peptococcus, Centipeda and mucosal Subdoligranulum genus might act as key drivers during the process of carcinogenesis. In conclusion, the current study provides insights into the potential influence of host clinical factors on oral and gut microbiome composition and can be a guide for future studies.
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Affiliation(s)
- Yao Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yao Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yun Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yuan-Hong Xie
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Shan-Shan Jiang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zi-Ran Kang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhao-Fei Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
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31
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Xue J, Allaband C, Zhou D, Poulsen O, Martino C, Jiang L, Tripathi A, Elijah E, Dorrestein PC, Knight R, Zarrinpar A, Haddad GG. Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome. Front Physiol 2021; 12:663950. [PMID: 33897472 PMCID: PMC8060652 DOI: 10.3389/fphys.2021.663950] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/17/2021] [Indexed: 01/05/2023] Open
Abstract
Obstructive sleep apnea (OSA), a common sleep disorder characterized by intermittent hypoxia and hypercapnia (IHC), increases atherosclerosis risk. However, the contribution of intermittent hypoxia (IH) or intermittent hypercapnia (IC) in promoting atherosclerosis remains unclear. Since gut microbiota and metabolites have been implicated in atherosclerosis, we examined whether IH or IC alters the microbiome and metabolome to induce a pro-atherosclerotic state. Apolipoprotein E deficient mice (ApoE-/- ), treated with IH or IC on a high-fat diet (HFD) for 10 weeks, were compared to Air controls. Atherosclerotic lesions were examined, gut microbiome was profiled using 16S rRNA gene amplicon sequencing and metabolome was assessed by untargeted mass spectrometry. In the aorta, IC-induced atherosclerosis was significantly greater than IH and Air controls (aorta, IC 11.1 ± 0.7% vs. IH 7.6 ± 0.4%, p < 0.05 vs. Air 8.1 ± 0.8%, p < 0.05). In the pulmonary artery (PA), however, IH, IC, and Air were significantly different from each other in atherosclerotic formation with the largest lesion observed under IH (PA, IH 40.9 ± 2.0% vs. IC 20.1 ± 2.6% vs. Air 12.2 ± 1.5%, p < 0.05). The most differentially abundant microbial families (p < 0.001) were Peptostreptococcaceae, Ruminococcaceae, and Erysipelotrichaceae. The most differentially abundant metabolites (p < 0.001) were tauro-β-muricholic acid, ursodeoxycholic acid, and lysophosphoethanolamine (18:0). We conclude that IH and IC (a) modulate atherosclerosis progression differently in distinct vascular beds with IC, unlike IH, facilitating atherosclerosis in both aorta and PA and (b) promote an atherosclerotic luminal gut environment that is more evident in IH than IC. We speculate that the resulting changes in the gut metabolome and microbiome interact differently with distinct vascular beds.
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Affiliation(s)
- Jin Xue
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | - Celeste Allaband
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Biomedical Sciences Program, University of California, San Diego, San Diego, CA, United States
- Division of Gastroenterology, University of California, San Diego, San Diego, CA, United States
| | - Dan Zhou
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | - Orit Poulsen
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, San Diego, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, United States
| | - Lingjing Jiang
- Division of Biostatistics, University of California, San Diego, San Diego, CA, United States
| | - Anupriya Tripathi
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Emmanuel Elijah
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, San Diego, CA, United States
| | - Pieter C. Dorrestein
- Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, San Diego, CA, United States
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, San Diego, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, United States
- Division of Gastroenterology, VA San Diego, La Jolla, CA, United States
- Institute of Diabetes and Metabolic Health, University of California, San Diego, San Diego, CA, United States
| | - Gabriel G. Haddad
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
- Rady Children’s Hospital, San Diego, CA, United States
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32
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An intact gut microbiome protects genetically predisposed mice against leukemia. Blood 2021; 136:2003-2017. [PMID: 32911536 DOI: 10.1182/blood.2019004381] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
The majority of childhood leukemias are precursor B-cell acute lymphoblastic leukemias (pB-ALLs) caused by a combination of prenatal genetic predispositions and oncogenic events occurring after birth. Although genetic predispositions are frequent in children (>1% to 5%), fewer than 1% of genetically predisposed carriers will develop pB-ALL. Although infectious stimuli are believed to play a major role in leukemogenesis, the critical determinants are not well defined. Here, by using murine models of pB-ALL, we show that microbiome disturbances incurred by antibiotic treatment early in life were sufficient to induce leukemia in genetically predisposed mice, even in the absence of infectious stimuli and independent of T cells. By using V4 and full-length 16S ribosomal RNA sequencing of a series of fecal samples, we found that genetic predisposition to pB-ALL (Pax5 heterozygosity or ETV6-RUNX1 fusion) shaped a distinct gut microbiome. Machine learning accurately (96.8%) predicted genetic predisposition using 40 of 3983 amplicon sequence variants as proxies for bacterial species. Transplantation of either wild-type (WT) or Pax5+/- hematopoietic bone marrow cells into WT recipient mice revealed that the microbiome is shaped and determined in a donor genotype-specific manner. Gas chromatography-mass spectrometry (GC-MS) analyses of sera from WT and Pax5+/- mice demonstrated the presence of a genotype-specific distinct metabolomic profile. Taken together, our data indicate that it is a lack of commensal microbiota rather than the presence of specific bacteria that promotes leukemia in genetically predisposed mice. Future large-scale longitudinal studies are required to determine whether targeted microbiome modification in children predisposed to pB-ALL could become a successful prevention strategy.
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Zhang L, Shi Y, Do KA, Peterson CB, Jenq RR. ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. BMC Bioinformatics 2021; 22:126. [PMID: 33731016 PMCID: PMC7972227 DOI: 10.1186/s12859-021-04061-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals (differential features between groups) from noise (features that are not differential between groups) becomes challenging and troublesome. For instance, when performing differential abundance tests, multiple testing adjustments tend to be overconservative, as the probability of a type I error (false positive) increases dramatically with the large numbers of hypotheses. Moreover, the grouping effect of interest can be obscured by heterogeneity. These factors can incorrectly lead to the conclusion that there are no differences in the microbiome compositions. RESULTS We translate and represent the problem of identifying differential features, which are differential in two-group comparisons (e.g., treatment versus control), as a dynamic layout of separating the signal from its random background. More specifically, we progressively permute the grouping factor labels of the microbiome samples and perform multiple differential abundance tests in each scenario. We then compare the signal strength of the most differential features from the original data with their performance in permutations, and will observe a visually apparent decreasing trend if these features are true positives identified from the data. Simulations and applications on real data show that the proposed method creates a U-curve when plotting the number of significant features versus the proportion of mixing. The shape of the U-Curve can convey the strength of the overall association between the microbiome and the grouping factor. We also define a fragility index to measure the robustness of the discoveries. Finally, we recommend the identified features by comparing p-values in the observed data with p-values in the fully mixed data. CONCLUSIONS We have developed this into a user-friendly and efficient R-shiny tool with visualizations. By default, we use the Wilcoxon rank sum test to compute the p-values, since it is a robust nonparametric test. Our proposed method can also utilize p-values obtained from other testing methods, such as DESeq. This demonstrates the potential of the progressive permutation method to be extended to new settings.
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Affiliation(s)
- Liangliang Zhang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Yushu Shi
- Department of Statistics, University of Missouri, Columbia, MO USA
| | - Kim-Anh Do
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christine B. Peterson
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Robert R. Jenq
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX USA
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Dysbiosis and Intestinal Barrier Dysfunction in Pediatric Congenital Heart Disease Is Exacerbated Following Cardiopulmonary Bypass. JACC Basic Transl Sci 2021; 6:311-327. [PMID: 33997519 PMCID: PMC8093480 DOI: 10.1016/j.jacbts.2020.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022]
Abstract
There are no data evaluating the microbiome in congenital heart disease following cardiopulmonary bypass. The authors evaluated patients with congenital heart disease undergoing cardiopulmonary bypass and noncardiac patients undergoing surgery without bypass. Patients with congenital heart disease had differences in baseline microbiome compared with control subjects, and this was exacerbated following surgery with bypass. Markers of barrier dysfunction were similar for both groups at baseline, and surgery with bypass induced significant intestinal barrier dysfunction compared with control subjects. This study offers novel evidence of alterations of the microbiome in congenital heart disease and exacerbation along with intestinal barrier dysfunction following cardiopulmonary bypass.
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Key Words
- ANOVA, analysis of variance
- CHD, congenital heart disease
- CPB, cardiopulmonary bypass
- DNA, deoxyribonucleic acid
- EBD, epithelial barrier dysfunction
- FABP2, fatty acid binding protein 2
- LCOS, low–cardiac output syndrome
- NPO, nil per os
- OTU, operational taxonomic unit
- PGE2, prostaglandin E2
- RA, relative abundance
- bacterial interactions
- cardiovascular disease
- enteric bacterial microflora
- intestinal barrier function
- intestinal microbiology
- rRNA, ribosomal ribonucleic acid
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35
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Kong XJ, Wan G, Tian R, Liu S, Liu K, Clairmont C, Lin X, Zhang X, Sherman H, Zhu J, Wang Y, Fong M, Li A, Wang BK, Wang J, Liu J, Yu Z, Shen C, Cui X, Cao H, Du T, Cao X. The Effects of Probiotic Supplementation on Anthropometric Growth and Gut Microbiota Composition in Patients With Prader-Willi Syndrome: A Randomized Double-Blinded Placebo-Controlled Trial. Front Nutr 2021; 8:587974. [PMID: 33681271 PMCID: PMC7933553 DOI: 10.3389/fnut.2021.587974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Prader-Willi Syndrome (PWS) is a rare genetic disorder associated with developmental delay, obesity, and neuropsychiatric comorbidities. Bifidobacterium animalis subsp. lactis has demonstrated anti-obesity and anti-inflammatory effects in previous studies. Aim: To evaluate the effects of Bifidobacterium animalis subsp. lactis probiotics supplementation on anthropometric growth, behavioral symptoms, and gut microbiome composition in patients with PWS. Methods: Ethical Approval was issued by the Internal Review Board (IRB) of the Second Affiliated Hospital of Kunming Medical University (Review-YJ-2016-06). We conducted a 12-week, randomized, double-blind, placebo-controlled trial in 68 patients with Prader-Willi syndrome aged 11 months−16 years (mean = 4.2 years old) who were randomly assigned to receive daily B. lactis-11 probiotics (6 × 1010 CFUs) or a placebo sachet. Weight, height, ASQ-3, ABC, SRS-2, and CGI-I were compared between the two groups at baseline and at 6 and 12 weeks into treatment. Gut microbiome data were analyzed with the QIIME 2 software package, and functional gene analysis was conducted with PICRUSt-2. Results: We found a significant increase in height (mean difference = 2.68 cm, P < 0.05) and improvement in CGI-I (P < 0.05) in the probiotics group compared to the placebo group. No significant change in weight or psychological measures were observed. Probiotic treatment altered the microbiome composition to favor weight loss and gut health and increased the abundance of antioxidant production-related genes. Conclusions: The findings suggest a novel therapeutic potential for Bifidobacterium animalis subsp. lactis probiotics in Prader-Willi syndrome patients, although further investigation is warranted.
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Affiliation(s)
- Xue-Jun Kong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States.,Department of Medicine and Psychiatry, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Guobin Wan
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Ruiyi Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Siyu Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Kevin Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Cullen Clairmont
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | | | | | - Hannah Sherman
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Junli Zhu
- Yale University, New Haven, CT, United States
| | - Yelan Wang
- Bentley University, Waltham, MA, United States
| | - Michelle Fong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Alice Li
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | | | - Jinghan Wang
- New York University, New York, NY, United States
| | - Jun Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Zhehao Yu
- Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Shen
- Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xianghua Cui
- Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hanyu Cao
- Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ting Du
- Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xia Cao
- Second Affiliated Hospital of Kunming Medical University, Kunming, China
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36
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Uzan-Yulzari A, Turta O, Belogolovski A, Ziv O, Kunz C, Perschbacher S, Neuman H, Pasolli E, Oz A, Ben-Amram H, Kumar H, Ollila H, Kaljonen A, Isolauri E, Salminen S, Lagström H, Segata N, Sharon I, Louzoun Y, Ensenauer R, Rautava S, Koren O. Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nat Commun 2021; 12:443. [PMID: 33500411 PMCID: PMC7838415 DOI: 10.1038/s41467-020-20495-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
Exposure to antibiotics in the first days of life is thought to affect various physiological aspects of neonatal development. Here, we investigate the long-term impact of antibiotic treatment in the neonatal period and early childhood on child growth in an unselected birth cohort of 12,422 children born at full term. We find significant attenuation of weight and height gain during the first 6 years of life after neonatal antibiotic exposure in boys, but not in girls, after adjusting for potential confounders. In contrast, antibiotic use after the neonatal period but during the first 6 years of life is associated with significantly higher body mass index throughout the study period in both boys and girls. Neonatal antibiotic exposure is associated with significant differences in the gut microbiome, particularly in decreased abundance and diversity of fecal Bifidobacteria until 2 years of age. Finally, we demonstrate that fecal microbiota transplant from antibiotic-exposed children to germ-free male, but not female, mice results in significant growth impairment. Thus, we conclude that neonatal antibiotic exposure is associated with a long-term gut microbiome perturbation and may result in reduced growth in boys during the first six years of life while antibiotic use later in childhood is associated with increased body mass index.
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Affiliation(s)
| | - Olli Turta
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Oren Ziv
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Christina Kunz
- Institute of Child Nutrition, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Sarah Perschbacher
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hadar Neuman
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- Zefat Academic College, Safed, Israel
| | | | - Aia Oz
- Migal - Galilee Research Institute, Qiryat Shemona, Israel
| | - Hila Ben-Amram
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- Ziv Medical center, Safed, Israel
| | - Himanshu Kumar
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Helena Ollila
- Department of Biostatistics, Faculty of Medicine, University of Turku, Turku, Finland
- Department of Public Health, University of Turku and Turku University Hospital, Turku, Finland
| | - Anne Kaljonen
- Department of Biostatistics, Faculty of Medicine, University of Turku, Turku, Finland
| | - Erika Isolauri
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Hanna Lagström
- Department of Public Health, University of Turku and Turku University Hospital, Turku, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Itai Sharon
- Migal - Galilee Research Institute, Qiryat Shemona, Israel
- Tel-Hai Academic College, Qiryat Shemona, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat-Gan, Israel
| | - Regina Ensenauer
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Samuli Rautava
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland.
- University of Helsinki & Helsinki University Hospital, New Children's Hospital, Pediatric Research Center, Helsinki, Finland.
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
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37
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Bao R, Hesser LA, He Z, Zhou X, Nadeau KC, Nagler CR. Fecal microbiome and metabolome differ in healthy and food-allergic twins. J Clin Invest 2021; 131:141935. [PMID: 33463536 DOI: 10.1172/jci141935] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUNDThere has been a striking generational increase in the prevalence of food allergies. We have proposed that this increase can be explained, in part, by alterations in the commensal microbiome.METHODSTo identify bacterial signatures and metabolic pathways that may influence the expression of this disease, we collected fecal samples from a unique, well-controlled cohort of twins concordant or discordant for food allergy. Samples were analyzed by integrating 16S rRNA gene amplicon sequencing and liquid chromatography-tandem mass spectrometry metabolite profiling.RESULTSA bacterial signature of 64 operational taxonomic units (OTUs) distinguished healthy from allergic twins; the OTUs enriched in the healthy twins were largely taxa from the Clostridia class. We detected significant enrichment in distinct metabolite pathways in each group. The enrichment of diacylglycerol in healthy twins is of particular interest for its potential as a readily measurable fecal biomarker of health. In addition, an integrated microbial-metabolomic analysis identified a significant association between healthy twins and Phascolarctobacterium faecium and Ruminococcus bromii, suggesting new possibilities for the development of live microbiome-modulating biotherapeutics.CONCLUSIONTwin pairs exhibited significant differences in their fecal microbiomes and metabolomes through adulthood, suggesting that the gut microbiota may play a protective role in patients with food allergies beyond the infant stage.TRIAL REGISTRATIONParticipants in this study were recruited as part of an observational study (ClinicalTrials.gov NCT01613885) at multiple sites from 2014 to 2018.FUNDINGThis work was supported by the Sunshine Charitable Foundation; the Moss Family Foundation; the National Institute of Allergy and Infectious Diseases (NIAID) (R56AI134923 and R01AI 140134); the Sean N. Parker Center for Allergy and Asthma Research; the National Heart, Lung, and Blood Institute (R01 HL 118612); the Orsak family; the Kepner family; and the Stanford Institute for Immunity, Transplant and Infection.
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Affiliation(s)
- Riyue Bao
- Department of Pediatrics, University of Chicago, Chicago, Illinois, USA.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA.,Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lauren A Hesser
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Ziyuan He
- Sean N. Parker Center for Allergy and Asthma Research
| | - Xiaoying Zhou
- Sean N. Parker Center for Allergy and Asthma Research
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research.,Division of Pulmonary and Critical Care Medicine, and.,Division of Allergy, Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Cathryn R Nagler
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA.,Department of Pathology, University of Chicago, Chicago, Illinois, USA
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38
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Lavrinienko A, Tukalenko E, Kesäniemi J, Kivisaari K, Masiuk S, Boratyński Z, Mousseau TA, Milinevsky G, Mappes T, Watts PC. Applying the Anna Karenina principle for wild animal gut microbiota: Temporal stability of the bank vole gut microbiota in a disturbed environment. J Anim Ecol 2020; 89:2617-2630. [DOI: 10.1111/1365-2656.13342] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/10/2020] [Indexed: 12/19/2022]
Affiliation(s)
| | - Eugene Tukalenko
- Ecology and Genetics University of Oulu Oulu Finland
- National Research Center for Radiation Medicine of the National Academy of Medical Science Kyiv Ukraine
| | | | - Kati Kivisaari
- Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland
| | - Sergii Masiuk
- National Research Center for Radiation Medicine of the National Academy of Medical Science Kyiv Ukraine
- Ukrainian Radiation Protection Institute Kyiv Ukraine
| | - Zbyszek Boratyński
- CIBIO‐InBIO Associate Laboratory Research Center in Biodiversity and Genetic ResourcesUniversity of Porto Vairão Portugal
| | - Timothy A. Mousseau
- Department of Biological Sciences University of South Carolina Columbia SC USA
| | - Gennadi Milinevsky
- Space Physics Laboratory Taras Shevchenko National University of Kyiv Kyiv Ukraine
- College of Physics International Center of Future Science Jilin University Changchun China
| | - Tapio Mappes
- Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland
| | - Phillip C. Watts
- Ecology and Genetics University of Oulu Oulu Finland
- Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland
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39
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Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic. mSystems 2020; 5:5/5/e00340-20. [PMID: 33024048 PMCID: PMC7542558 DOI: 10.1128/msystems.00340-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a variety of organs and that microbiome alterations were not uniform throughout the gut. As technological advances increase the feasibility of whole-organism studies, we argue that using these approaches can provide further insight on both the wide-ranging effects of antibiotics on health and how to restore microbial communities to mitigate these effects. Antibiotics are a mainstay of modern medicine, but as they kill their target pathogen(s), they often affect the commensal microbiota. Antibiotic-induced microbiome dysbiosis is a growing research focus and health concern, often assessed via analysis of fecal samples. However, such analysis does not inform how antibiotics influence the microbiome across the whole host or how such changes subsequently alter host chemistry. In this study, we investigated the acute (1 day postadministration) and delayed (6 days postadministration) effects of a single parenteral dose of two common antibiotics, ampicillin or vancomycin, on the global metabolome and microbiome of mice across 77 different body sites from 25 different organs. The broader-spectrum agent ampicillin had the greatest impact on the microbiota in the lower gastrointestinal tract (cecum and colon), where microbial diversity is highest. In the metabolome, the greatest effects were seen 1 day posttreatment, and changes in metabolite abundances were not confined to the gut. The local abundance of ampicillin and its metabolites correlated with increased metabolome effect size and a loss of alpha diversity versus control mice. Additionally, small peptides were elevated in the lower gastrointestinal tract of mice 1 day after antibiotic treatment. While a single parenteral dose of antibiotic did not drastically alter the microbiome, nevertheless, changes in the metabolome were observed both within and outside the gut. This study provides a framework for how whole-organism -omics approaches can be employed to understand the impact of antibiotics on the entire host. IMPORTANCE We are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a variety of organs and that microbiome alterations were not uniform throughout the gut. As technological advances increase the feasibility of whole-organism studies, we argue that using these approaches can provide further insight on both the wide-ranging effects of antibiotics on health and how to restore microbial communities to mitigate these effects.
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40
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Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM. Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study. Clin Transl Sci 2020; 13:972-984. [PMID: 32216086 PMCID: PMC7485946 DOI: 10.1111/cts.12785] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/22/2020] [Indexed: 12/22/2022] Open
Abstract
Determining factors that contribute to interindividual and intra-individual variability in pharmacokinetics (PKs) and drug metabolism is essential for the optimal use of drugs in humans. Intestinal microbes are important contributors to variability; however, such gut microbe-drug interactions and the clinical significance of these interactions are still being elucidated. Traditional PKs can be complemented by untargeted mass spectrometry coupled with molecular networking to study the intricacies of drug metabolism. To show the utility of molecular networking on metabolism we investigated the impact of a 7-day course of cefprozil on cytochrome P450 (CYP) activity using a modified Cooperstown cocktail and assessed plasma, urine, and fecal data by targeted and untargeted metabolomics and molecular networking in healthy volunteers. This prospective study revealed that cefprozil decreased the activities of CYP1A2, CYP2C19, and CYP3A, decreased alpha diversity and increased interindividual microbiome variability. We further demonstrate a relationship between the loss of microbiome alpha diversity caused by cefprozil and increased drug and metabolite formation in fecal samples. Untargeted metabolomics/molecular networking revealed several omeprazole metabolites that we hypothesize may be metabolized by both CYP2C19 and bacteria from the gut microbiome. Our observations are consistent with the hypothesis that factors that perturb the gut microbiome, such as antibiotics, alter drug metabolism and ultimately drug efficacy and toxicity but that these effects are most strongly revealed on a per individual basis.
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Affiliation(s)
- Alan K. Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation CenterUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Alison Vrbanac
- Department of PediatricsUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Jeremiah D. Momper
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Joseph D. Ma
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Maher Alhaja
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Marlon Liyanage
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Rob Knight
- Department of PediatricsUniversity of California, San DiegoLa JollaCaliforniaUSA
- Center for Microbiome InnovationUniversity of California, San DiegoLa JollaCaliforniaUSA
- Department of Computer Science and EngineeringUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation CenterUniversity of California, San DiegoLa JollaCaliforniaUSA
- Department of PediatricsUniversity of California, San DiegoLa JollaCaliforniaUSA
- Center for Microbiome InnovationUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Shirley M. Tsunoda
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
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Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, Allen EE. The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment. Front Microbiol 2020; 11:2015. [PMID: 32983024 PMCID: PMC7476325 DOI: 10.3389/fmicb.2020.02015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Aquaculture is the fastest growing primary industry worldwide. Marine finfish culture in open ocean net pens, or pontoons, is one of the largest growth areas and is currently the only way to rear high value fish such as bluefin tuna. Ranching involves catching wild juveniles, stocking in floating net pens and fattening for 4 to 8 months. Tuna experience several parasite-induced disease challenges in culture that can be mitigated by application of praziquantel (PZQ) as a therapeutic. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. Southern bluefin tuna gill, skin, and digesta microbiome communities are unique and potentially influenced by husbandry practices, location of pontoon growout pens, and treatment with the antiparasitic PZQ. There was no significant relationship between the fish mucosal microbiome and incidence or abundance of adult blood fluke in the heart or fluke egg density in the gill. An enhanced understanding of microbiome diversity and function in high-value farmed fish species such as bluefin tuna is needed to optimize fish health and improve aquaculture yield. Comparison of the bluefin tuna microbiome to other fish species, including Seriola lalandi (yellowtail kingfish), a common farmed species from Australia, and Scomber japonicus (Pacific mackerel), a wild caught Scombrid relative of tuna, showed the two Scombrids had more similar microbial communities compared to other families. The finding that mucosal microbial communities are more similar in phylogenetically related fish species exposes an opportunity to develop mackerel as a model for tuna microbiome and parasite research.
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Affiliation(s)
- Jeremiah J. Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Cecilia Power
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, Australia
| | - Michaela Melanson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Claire Webber
- Australian Southern Bluefin Tuna Industry Association, Port Lincoln, SA, Australia
| | - Kirsten Rough
- Australian Southern Bluefin Tuna Industry Association, Port Lincoln, SA, Australia
| | - Nathan J. Bott
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, Australia
| | - Barbara Nowak
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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42
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Then CK, Paillas S, Wang X, Hampson A, Kiltie AE. Association of Bacteroides acidifaciens relative abundance with high-fibre diet-associated radiosensitisation. BMC Biol 2020; 18:102. [PMID: 32811478 PMCID: PMC7437060 DOI: 10.1186/s12915-020-00836-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Patients with pelvic malignancies often receive radiosensitising chemotherapy with radiotherapy to improve survival; however, this is at the expense of increased normal tissue toxicity, particularly in elderly patients. Here, we explore if an alternative, low-cost, and non-toxic approach can achieve radiosensitisation in mice transplanted with human bladder cancer cells. Other investigators have shown slower growth of transplanted tumours in mice fed high-fibre diets. We hypothesised that mice fed a high-fibre diet would have improved tumour control following ionising radiation (IR) and that this would be mediated through the gut microbiota. RESULTS We investigated the effects of four different diets (low-fibre, soluble high-fibre, insoluble high-fibre, and mixed soluble/insoluble high-fibre diets) on tumour growth in immunodeficient mice implanted with human bladder cancer flank xenografts and treated with ionising radiation, simultaneously investigating the composition of their gut microbiomes by 16S rRNA sequencing. A significantly higher relative abundance of Bacteroides acidifaciens was seen in the gut (faecal) microbiome of the soluble high-fibre group, and the soluble high-fibre diet resulted in delayed tumour growth after irradiation compared to the other groups. Within the soluble high-fibre group, responders to irradiation had significantly higher abundance of B. acidifaciens than non-responders. When all mice fed with different diets were pooled, an association was found between the survival time of mice and relative abundance of B. acidifaciens. The gut microbiome in responders was predicted to be enriched for carbohydrate metabolism pathways, and in vitro experiments on the transplanted human bladder cancer cell line suggested a role for microbial-generated short-chain fatty acids and/or other metabolites in the enhanced radiosensitivity of the tumour cells. CONCLUSIONS Soluble high-fibre diets sensitised tumour xenografts to irradiation, and this phenotype was associated with modification of the microbiome and positively correlated with B. acidifaciens abundance. Our findings might be exploitable for improving radiotherapy response in human patients.
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Affiliation(s)
- Chee Kin Then
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Salome Paillas
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Xuedan Wang
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alix Hampson
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Anne E Kiltie
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK.
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Rifkin RF, Vikram S, Ramond JB, Rey-Iglesia A, Brand TB, Porraz G, Val A, Hall G, Woodborne S, Le Bailly M, Potgieter M, Underdown SJ, Koopman JE, Cowan DA, Van de Peer Y, Willerslev E, Hansen AJ. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome. MICROBIOME 2020; 8:62. [PMID: 32375874 PMCID: PMC7204047 DOI: 10.1186/s40168-020-00832-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
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Affiliation(s)
- Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Tina B Brand
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Guillaume Porraz
- CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
| | - Aurore Val
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Stephan Woodborne
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
- iThemba LABS, Braamfontein Johannesburg, South Africa
| | - Matthieu Le Bailly
- University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Yves Van de Peer
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- VIB Centre for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Eske Willerslev
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anders J Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark.
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Noirungsee N, Hackbusch S, Viamonte J, Bubenheim P, Liese A, Müller R. Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico. Sci Rep 2020; 10:7079. [PMID: 32341378 PMCID: PMC7184722 DOI: 10.1038/s41598-020-63190-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 03/26/2020] [Indexed: 11/18/2022] Open
Abstract
The Deepwater Horizon incident in the Gulf of Mexico in 2010 released an unprecedented amount of petroleum hydrocarbons 1500 meters below the sea surface. Few studies have considered the influence of hydrostatic pressure on bacterial community development and activity during such spills. The goal of this study was to investigate the response of indigenous sediment microbial communities to the combination of increased pressure, hydrocarbons and dispersant. Deep-sea sediment samples collected from the northern Gulf of Mexico were incubated at atmospheric pressure (0.1 MPa) and at elevated pressure (10 MPa), with and without the addition of crude oil and dispersant. After incubations at 4 °C for 7 days, Colwellia and Psychrobium were highly abundant in all samples. Pressure differentially impacted members of the Alteromonadales. The influences of pressure on the composition of bacterial communities were most pronounced when dispersant was added to the incubations. Moritella and Thalassotalea were greatly stimulated by the addition of dispersant, suggesting their roles in dispersant biodegradation. However, Moritella was negatively impacted by increasing pressure. The presence of dispersant was shown to decrease the relative abundance of a known hydrocarbon degrader, Cycloclasticus, while increasing pressure increased its relative abundance. This study highlights the significant influence of pressure on the development of microbial communities in the presence of oil and dispersant during oil spills and related response strategies in the deep sea.
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Affiliation(s)
- Nuttapol Noirungsee
- Hamburg University of Technology, Institute of Technical Biocatalysis, Hamburg, 21073, Germany
| | - Steffen Hackbusch
- Hamburg University of Technology, Institute of Technical Biocatalysis, Hamburg, 21073, Germany
| | - Juan Viamonte
- Hamburg University of Technology, Institute of Technical Biocatalysis, Hamburg, 21073, Germany
| | - Paul Bubenheim
- Hamburg University of Technology, Institute of Technical Biocatalysis, Hamburg, 21073, Germany
| | - Andreas Liese
- Hamburg University of Technology, Institute of Technical Biocatalysis, Hamburg, 21073, Germany
| | - Rudolf Müller
- Hamburg University of Technology, Institute of Technical Biocatalysis, Hamburg, 21073, Germany.
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Bichat A, Plassais J, Ambroise C, Mariadassou M. Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control. Front Microbiol 2020; 11:649. [PMID: 32351481 PMCID: PMC7174607 DOI: 10.3389/fmicb.2020.00649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 03/20/2020] [Indexed: 12/18/2022] Open
Abstract
We consider the problem of incorporating evolutionary information (e.g., taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierarchical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non-hierarchical, Benjamini–Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierarchical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini–Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Intuition advocates that the use of hierarchical structures should increase the detection rate of differentially abundant taxa in microbiome studies. However, our results suggest that current hierarchical procedures are still inferior to standard methods and more effective procedures remain to be invented.
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Affiliation(s)
- Antoine Bichat
- LaMME, Université Paris-Saclay, CNRS, Université d'Évry val d'Essonne, Évry, France.,Enterome, Paris, France
| | | | - Christophe Ambroise
- LaMME, Université Paris-Saclay, CNRS, Université d'Évry val d'Essonne, Évry, France
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The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics. mSystems 2020; 5:5/2/e00578-19. [PMID: 32234773 PMCID: PMC7112960 DOI: 10.1128/msystems.00578-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex metabolic syndrome characterized by insulin dysfunction and abnormalities in glucose and lipid metabolism. The gut microbiome has been recently identified as an important factor for development of T2D. In this study, a total of 102 subjects were recruited, and we have looked at the gut microbiota of prediabetics (PreDMs) (n = 17), newly diagnosed diabetics (NewDMs) (n = 11), and diabetics on antidiabetic treatment (KnownDMs) (n = 39) and compared them with healthy nondiabetics (ND) (n = 35). Twenty-five different serum biomarkers were measured to assess the status of diabetes and their association with gut microbiota. Our analysis revealed nine different genera as differentially abundant in four study groups. Among them, Akkermansia, Blautia, and Ruminococcus were found to be significantly (P < 0.05) decreased, while Lactobacillus was increased in NewDMs compared to ND and recovered in KnownDMs. Akkermansia was inversely correlated with HbA1c and positively correlated with total antioxidants. Compared to ND, there was increased abundance of Megasphaera, Escherichia, and Acidaminococcus and decreased abundance of Sutterella in KnownDMs. Among many taxa known to act as community drivers during disease progression, we observed genus Sutterella as a common driver taxon among all diabetic groups. On the basis of the results of random forest analysis, we found that the genera Akkermansia and Sutterella and that the serum metabolites fasting glucose, HbA1c, methionine, and total antioxidants were highly discriminative factors among studied groups. Taken together, our data revealed that gut microbial diversity of NewDMs but not of PreDMs is significantly different from that of ND. Interestingly, after antidiabetic treatment, the microbial diversity of KnownDMs tends to recover toward that of ND.IMPORTANCE Gut microbiota is considered to play a role in disease progression, and previous studies have reported an association of microbiome dysbiosis with T2D. In this study, we have attempted to investigate gut microbiota of ND, PreDMs, NewDMs, and KnownDMs. We found that the genera Akkermansia and Blautia decreased significantly (P < 0.05) in treatment-naive diabetics and were restored in KnownDMs on antidiabetic treatment. To the best of our knowledge, comparative studies on shifts in the microbial community in individuals of different diabetic states are lacking. Understanding the transition of microbiota and its association with serum biomarkers in diabetics with different disease states may pave the way for new therapeutic approaches for T2D.
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Lin JD, Devlin JC, Yeung F, McCauley C, Leung JM, Chen YH, Cronkite A, Hansen C, Drake-Dunn C, Ruggles KV, Cadwell K, Graham AL, Loke P. Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition. Cell Host Microbe 2020; 27:830-840.e4. [PMID: 32209431 DOI: 10.1016/j.chom.2020.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/10/2019] [Accepted: 02/28/2020] [Indexed: 02/07/2023]
Abstract
The relative contributions of genetic and environmental factors to variation in immune responses are poorly understood. Here, we performed a phenotypic analysis of immunological parameters in laboratory mice carrying susceptibility genes implicated in inflammatory bowel disease (IBD) (Nod2 and Atg16l1) upon exposure to environmental microbes. Mice were released into an outdoor enclosure (rewilded) and then profiled for immune responses in the blood and lymph nodes. Variations of immune cell populations were largely driven by the environment, whereas cytokine production elicited by microbial antigens was more affected by the genetic mutations. We identified transcriptional signatures in the lymph nodes associated with differences in T cell populations. Subnetworks associated with responses against Clostridium perfringens, Candida albicans, and Bacteroides vulgatus were also coupled with rewilding. Therefore, exposing laboratory mice with genetic mutations to a natural environment uncovers different contributions to variations in microbial responses and immune cell composition.
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Affiliation(s)
- Jian-Da Lin
- Department of Microbiology, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph C Devlin
- Department of Microbiology, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Sackler Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York University, New York, NY 10016, USA; Institute of Systems Genetics, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Frank Yeung
- Sackler Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York University, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Caroline McCauley
- Department of Microbiology, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jacqueline M Leung
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Alex Cronkite
- Department of Microbiology, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Christina Hansen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Charlotte Drake-Dunn
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Division of Translational Medicine, Department of Medicine, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Institute of Systems Genetics, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Ken Cadwell
- Department of Microbiology, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, NY 10016, USA.
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
| | - P'ng Loke
- Department of Microbiology, NYU Grossman School of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL. Emerging Priorities for Microbiome Research. Front Microbiol 2020; 11:136. [PMID: 32140140 PMCID: PMC7042322 DOI: 10.3389/fmicb.2020.00136] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.
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Affiliation(s)
- Chad M. Cullen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | | | - Sinem Beyhan
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Clara E. Cho
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT, United States
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
- College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Matteo Convertino
- Nexus Group, Faculty of Information Science and Technology, Gi-CoRE Station for Big Data & Cybersecurity, Hokkaido University, Sapporo, Japan
| | - Sophie J. McCoy
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | | | - Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ananya Sen Gupta
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, United States
| | - Kevin Cheung
- Department of Dermatology, The University of Iowa, Iowa City, IA, United States
| | | | - Zhengqiao Zhao
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail L. Rosen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
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Gordon JH, LaMonte MJ, Genco RJ, Zhao J, Li L, Hovey KM, Tsompana M, Buck MJ, Andrews CA, Mcskimming DI, Zheng W, Sun Y, Wactawski-Wende J. Is the Oral Microbiome Associated with Blood Pressure in Older Women? High Blood Press Cardiovasc Prev 2019; 26:217-225. [PMID: 31236901 DOI: 10.1007/s40292-019-00322-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/14/2019] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION A possible role of the oral microbiome, specifically oral nitrate reducing flora, in blood pressure (BP) homeostasis, if proven etiologic in nature, could lead to novel mechanism-based therapy to improve hypertension prevention and control. AIM This cross-sectional study characterized and compared the oral microbiome between four study groups based on BP status among 446 postmenopausal women aged 53-82 years. METHODS Three study groups were not taking hypertension medication and were separated based on BP, as follows: normal BP (systolic < 120 and diastolic < 80; N = 179), elevated BP/Stage I hypertension (systolic 120-139 or diastolic 80-90; N = 106), Stage II hypertension (systolic > 140 or diastolic > 90; N = 42). The forth group consisted of anyone taking hypertension medications, regardless of BP (N = 119). Subgingival microbiome composition was determined using 16S rRNA sequencing with the Illumina MiSeq platform. Kruskal-Wallis tests were used to compare species-level relative abundance of bacterial operational taxonomic units across the four groups. RESULTS Sixty-five bacterial species demonstrated significant differences in relative abundance in women with elevated BP or using hypertension medication as compared to those with normal BP. After correction for multiple testing, two species, Prevotella oral (species 317) and Streptococcus oralis, remained significant and were lower in abundance among women taking antihypertension medications compared to those with normal BP (corrected P < 0.05). CONCLUSIONS These data provide novel description of oral subgingival bacteria grouped according to BP status. Additional larger studies including functional analysis and prospective designs will help further assess the potential role of the oral microbiome in BP regulation and hypertension.
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Affiliation(s)
- Joshua H Gordon
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 273 Farber Hall, 3435 Main Street, Buffalo, NY, 14214, USA
| | - Michael J LaMonte
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 273 Farber Hall, 3435 Main Street, Buffalo, NY, 14214, USA.
| | - Robert J Genco
- Department of Oral Biology, School of Dental Medicine, UB Microbiome Center, University at Buffalo, Buffalo, NY, USA
| | - Jiwei Zhao
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, USA
| | - Lu Li
- Department of Computer and Engineering Science, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kathleen M Hovey
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 273 Farber Hall, 3435 Main Street, Buffalo, NY, 14214, USA
| | - Maria Tsompana
- Department of Biochemistry, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Michael J Buck
- Department of Biochemistry, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Christopher A Andrews
- Department of Ophthalmology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel I Mcskimming
- Genome Environment, and Microbiome Center of Excellence, University at Buffalo, Buffalo, NY, USA
| | - Wei Zheng
- Department of Computer and Engineering Science, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Department of Computer and Engineering Science, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 273 Farber Hall, 3435 Main Street, Buffalo, NY, 14214, USA
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50
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Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy. Cell Rep 2019; 27:730-736.e3. [DOI: 10.1016/j.celrep.2019.03.075] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/12/2019] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
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