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Franklin S, Aitken SL, Shi Y, Sahasrabhojane PV, Robinson S, Peterson CB, Daver N, Ajami NA, Kontoyiannis DP, Shelburne SA, Galloway-Peña J. Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients. Front Cell Infect Microbiol 2022; 12:848580. [PMID: 35433514 PMCID: PMC9010033 DOI: 10.3389/fcimb.2022.848580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 – 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 – 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 – 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 – 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 – 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.
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Affiliation(s)
- Samantha Franklin
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
| | - Samuel L. Aitken
- Department of Pharmacy, Michigan Medicine, Ann Arbor, MI, United States
| | - Yushi Shi
- Department of Statistics and Center for Biomedical Informatics, University of Missouri, Columbia, MO, United States
| | - Pranoti V. Sahasrabhojane
- Department of Infectious Disease, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sarah Robinson
- Department of Statistics, Rice University, Houston, TX, United States
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nadim A. Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dimitrios P. Kontoyiannis
- Department of Infectious Disease, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Samuel A. Shelburne
- Department of Infectious Disease, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jessica Galloway-Peña
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- *Correspondence: Jessica Galloway-Peña,
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Ankori‐Karlinsky R, Kalyuzhny M, Barnes KF, Wilson AM, Flather C, Renfrew R, Walsh J, Guk E, Kadmon R. North American Breeding Bird Survey underestimates regional bird richness compared to Breeding Bird Atlases. Ecosphere 2022. [DOI: 10.1002/ecs2.3925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Roi Ankori‐Karlinsky
- Department of Ecology, Evolution, and Environmental Biology Columbia University New York New York USA
| | - Michael Kalyuzhny
- Department of Ecology, Evolution & Behavior Institute of Life Sciences, The Hebrew University of Jerusalem, Campus Edmond J. Safra, Givat Ram Jerusalem Israel
| | | | - Andrew M. Wilson
- Environmental Studies, Science Center Gettysburg College Gettysburg Pennsylvania USA
| | - Curtis Flather
- USDA Forest Service, Rocky Mountain Research Station Fort Collins Colorado USA
| | - Rosalind Renfrew
- Rubenstein School of Environment and Natural Resources, The University of Vermont Burlington Vermont USA
| | - Joan Walsh
- Massachusetts Audubon Headquarters Lincoln Massachusetts USA
| | - Edna Guk
- Department of Geography, Faculty of Social Sciences The Hebrew University of Jerusalem, Mt. Scopus Jerusalem Israel
| | - Ronen Kadmon
- Department of Ecology, Evolution & Behavior Institute of Life Sciences, The Hebrew University of Jerusalem, Campus Edmond J. Safra, Givat Ram Jerusalem Israel
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Roos AL, Giehl ELH, Hernández MIM. Local species turnover increases regional bird diversity in mangroves. AUSTRAL ECOL 2020. [DOI: 10.1111/aec.12969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrei Langeloh Roos
- Programa de Pós‐Graduação em Ecologia Departamento de Ecologia e Zoologia Centro de Ciências Biológicas Universidade Federal de Santa Catarina Florianópolis SC88040‐900Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade Resex Pirajubaé Florianópolis SC Brazil
| | - Eduardo Luis Hettwer Giehl
- Programa de Pós‐Graduação em Ecologia Departamento de Ecologia e Zoologia Centro de Ciências Biológicas Universidade Federal de Santa Catarina Florianópolis SC88040‐900Brazil
| | - Malva Isabel Medina Hernández
- Programa de Pós‐Graduação em Ecologia Departamento de Ecologia e Zoologia Centro de Ciências Biológicas Universidade Federal de Santa Catarina Florianópolis SC88040‐900Brazil
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Loranger J, Munoz F, Shipley B, Violle C. What makes trait-abundance relationships when both environmental filtering and stochastic neutral dynamics are at play? OIKOS 2018. [DOI: 10.1111/oik.05398] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jessy Loranger
- CNRS, CEFE UMR 5175, Univ. de Montpellier - Univ. Paul Valéry - EPHE; Montpellier Cedex 5 France
- Univ. de Sherbrooke; Sherbrooke Canada
| | - François Munoz
- Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes; FR-38000 Grenoble France
| | | | - Cyrille Violle
- CNRS, CEFE UMR 5175, Univ. de Montpellier - Univ. Paul Valéry - EPHE; Montpellier Cedex 5 France
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Duarte LDS, Debastiani VJ, Freitas AVL, Pillar VD. Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12547] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leandro D. S. Duarte
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul CP 15007 Porto Alegre 91501‐970 Brazil
| | - Vanderlei J. Debastiani
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul CP 15007 Porto Alegre 91501‐970 Brazil
| | - André V. L. Freitas
- Departamento de Biologia Animal Instituto de Biologia Universidade Estadual de Campinas CP 6109 Campinas São Paulo 13083‐970 Brazil
| | - Valério D. Pillar
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul CP 15007 Porto Alegre 91501‐970 Brazil
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Suzán G, García-Peña GE, Castro-Arellano I, Rico O, Rubio AV, Tolsá MJ, Roche B, Hosseini PR, Rizzoli A, Murray KA, Zambrana-Torrelio C, Vittecoq M, Bailly X, Aguirre AA, Daszak P, Prieur-Richard AH, Mills JN, Guégan JF. Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space. Ecol Evol 2015; 5:865-73. [PMID: 25750713 PMCID: PMC4338969 DOI: 10.1002/ece3.1404] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/22/2014] [Accepted: 01/02/2015] [Indexed: 01/07/2023] Open
Abstract
The potential for disease transmission at the interface of wildlife, domestic animals and humans has become a major concern for public health and conservation biology. Research in this subject is commonly conducted at local scales while the regional context is neglected. We argue that prevalence of infection at local and regional levels is influenced by three mechanisms occurring at the landscape level in a metacommunity context. First, (1) dispersal, colonization, and extinction of pathogens, reservoir or vector hosts, and nonreservoir hosts, may be due to stochastic and niche-based processes, thus determining distribution of all species, and then their potential interactions, across local communities (metacommunity structure). Second, (2) anthropogenic processes may drive environmental filtering of hosts, nonhosts, and pathogens. Finally, (3) phylogenetic diversity relative to reservoir or vector host(s), within and between local communities may facilitate pathogen persistence and circulation. Using a metacommunity approach, public heath scientists may better evaluate the factors that predispose certain times and places for the origin and emergence of infectious diseases. The multidisciplinary approach we describe fits within a comprehensive One Health and Ecohealth framework addressing zoonotic infectious disease outbreaks and their relationship to their hosts, other animals, humans, and the environment.
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Affiliation(s)
- Gerardo Suzán
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria Zootecnia, Universidad Nacional Autónoma de MéxicoMéxico, Distrito Federal, México
| | - Gabriel E García-Peña
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria Zootecnia, Universidad Nacional Autónoma de MéxicoMéxico, Distrito Federal, México
- UMR MIVEGEC, Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle UMR 5290 CNRS-IRD-UM1-UM2, Centre de Recherche IRD34394, Montpellier Cedex 5, France
- Centre de Synthèse et d'Analyse sur la Biodiversité – CESAB13857, Aix-en-Provence Cedex 3, France
| | | | - Oscar Rico
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria Zootecnia, Universidad Nacional Autónoma de MéxicoMéxico, Distrito Federal, México
| | - André V Rubio
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria Zootecnia, Universidad Nacional Autónoma de MéxicoMéxico, Distrito Federal, México
| | - María J Tolsá
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria Zootecnia, Universidad Nacional Autónoma de MéxicoMéxico, Distrito Federal, México
| | - Benjamin Roche
- UMR MIVEGEC, Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle UMR 5290 CNRS-IRD-UM1-UM2, Centre de Recherche IRD34394, Montpellier Cedex 5, France
| | | | - Annapaola Rizzoli
- Biodiversity and Molecular Ecology Department Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'AdigeTrento, Italy
| | | | | | - Marion Vittecoq
- UMR MIVEGEC, Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle UMR 5290 CNRS-IRD-UM1-UM2, Centre de Recherche IRD34394, Montpellier Cedex 5, France
| | - Xavier Bailly
- INRA, UR346 Epidémiologie AnimaleSaint Genès Champanelle, France
| | - A Alonso Aguirre
- Department of Environmental Science and Policy, George Mason UniversityFairfax, Virginia
| | | | | | - James N Mills
- Population Biology, Ecology and Evolution Program, Emory UniversityAtlanta, Georgia
| | - Jean-Francois Guégan
- UMR MIVEGEC, Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle UMR 5290 CNRS-IRD-UM1-UM2, Centre de Recherche IRD34394, Montpellier Cedex 5, France
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