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Grodner B, Wu DT, Hahm S, Takayasu L, Wen N, Kim DM, Chen CY, De Vlaminck I. Microscale Spatial Dysbiosis in Oral biofilms Associated with Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604873. [PMID: 39211202 PMCID: PMC11360903 DOI: 10.1101/2024.07.24.604873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Microbiome dysbiosis has largely been defined using compositional analysis of metagenomic sequencing data; however, differences in the spatial arrangement of bacteria between healthy and diseased microbiomes remain largely unexplored. In this study, we measured the spatial arrangement of bacteria in dental implant biofilms from patients with healthy implants, peri-implant mucositis, or peri-implantitis, an oral microbiome-associated inflammatory disease. We discovered that peri-implant biofilms from patients with mild forms of the disease were characterized by large single-genus patches of bacteria, while biofilms from healthy sites were more complex, mixed structures. Based on these findings, we propose a model of peri-implant dysbiosis where changes in biofilm spatial architecture allow the colonization of new community members. This model indicates that spatial structure could be used as a potential biomarker for community stability and has implications in diagnosis and treatment of peri-implant diseases. These results enhance our understanding of peri-implant disease pathogenesis and may be broadly relevant for spatially structured microbiomes.
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Sanz E, Saa-Requejo A, Díaz-Ambrona CH, Ruiz-Ramos M, Rodríguez A, Iglesias E, Esteve P, Soriano B, Tarquis AM. Generalized Structure Functions and Multifractal Detrended Fluctuation Analysis Applied to Vegetation Index Time Series: An Arid Rangeland Study. ENTROPY (BASEL, SWITZERLAND) 2021; 23:e23050576. [PMID: 34067228 PMCID: PMC8151831 DOI: 10.3390/e23050576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
Estimates suggest that more than 70% of the world’s rangelands are degraded. The Normalized Difference Vegetation Index (NDVI) is commonly used by ecologists and agriculturalists to monitor vegetation and contribute to more sustainable rangeland management. This paper aims to explore the scaling character of NDVI and NDVI anomaly (NDVIa) time series by applying three fractal analyses: generalized structure function (GSF), multifractal detrended fluctuation analysis (MF-DFA), and Hurst index (HI). The study was conducted in four study areas in Southeastern Spain. Results suggest a multifractal character influenced by different land uses and spatial diversity. MF-DFA indicated an antipersistent character in study areas, while GSF and HI results indicated a persistent character. Different behaviors of generalized Hurst and scaling exponents were found between herbaceous and tree dominated areas. MF-DFA and surrogate and shuffle series allow us to study multifractal sources, reflecting the importance of long-range correlations in these areas. Two types of long-range correlation appear to be in place due to short-term memory reflecting seasonality and longer-term memory based on a time scale of a year or longer. The comparison of these series also provides us with a differentiating profile to distinguish among our four study areas that can improve land use and risk management in arid rangelands.
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Affiliation(s)
- Ernesto Sanz
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Grupo de Sistemas Complejos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Correspondence:
| | - Antonio Saa-Requejo
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Evaluación de Recursos Naturales, ETSI Agronómica, Alimentaria y Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Carlos H. Díaz-Ambrona
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- AgSystems, ETSI Agronómica, Alimentaria y Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Margarita Ruiz-Ramos
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- AgSystems, ETSI Agronómica, Alimentaria y Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo Rodríguez
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Departamento de Análisis Económico y Finanzas, Universidad de Castilla-La Mancha, 45071 Toledo, Spain
| | - Eva Iglesias
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Economía Agraria y Gestión de los Recursos Naturales, ETSI Agronómica Alimentaria y Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Paloma Esteve
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Economía Agraria y Gestión de los Recursos Naturales, ETSI Agronómica Alimentaria y Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Bárbara Soriano
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Economía Agraria y Gestión de los Recursos Naturales, ETSI Agronómica Alimentaria y Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Ana M. Tarquis
- CEIGRAM, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (A.S.-R.); (C.H.D.-A.); (M.R.-R.); (A.R.); (E.I.); (P.E.); (B.S.); (A.M.T.)
- Grupo de Sistemas Complejos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Barnes RSK. Local patchiness of macrobenthic faunal abundance displays homogeneity across the disparate seagrass systems of an estuarine bay. MARINE ENVIRONMENTAL RESEARCH 2019; 148:99-107. [PMID: 31170657 DOI: 10.1016/j.marenvres.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/26/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
Spatial variation in the degree of local patchiness of macrobenthic assemblage abundance was assessed across the 16 km2 warm-temperate Knysna estuarine bay (South Africa) where the seagrass Zostera (Zosterella) capensis grows under a broad spectrum of environmental conditions and supports invertebrate assemblages at a wide range of local density (<2000->320000 ind. m-2). Macrobenthic assemblage abundance at all 27 representative sites examined displayed low-level but highly-significant spatial patchiness (mean Lloyd's index, IP = 1.148). Except at high tidal levels, however, the magnitude of this local patchiness did not vary statistically across the system (CV 4.3%) regardless of assemblage abundance, location or species composition. Patchinesses well within ±1 standard deviation of Knysna's value also characterise an equivalent Z. (Zosterella) capricorni assemblage in subtropical Queensland (IP 1.169) and another, Z. (Zosterella) noltei, assemblage in cool-temperate England (IP 1.135), suggesting that at local scales intertidal dwarf-eelgrass macrobenthic abundance displays a characteristic level of patchiness.
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Affiliation(s)
- R S K Barnes
- Department of Zoology and Entomology, Rhodes University, Makhanda (formerly Grahamstown), Eastern Cape, 6140, South Africa; Knysna Basin Project Laboratory, Knysna, Western Cape, 6571, South Africa; Department of Zoology and Conservation Research Institute, University of Cambridge, Cambridge, UK.
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Yakimov BN, Gelashvili DB, Zhang Y, Markelov IN, Zhang S, Ma K. Quantification of non-power-law diversity scaling with local multifractal analysis. ECOL INFORM 2018. [DOI: 10.1016/j.ecoinf.2018.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Barnes RSK, Laurie H. Seagrass macrofaunal abundance shows both multifractality and scale-invariant patchiness. MARINE ENVIRONMENTAL RESEARCH 2018; 138:84-95. [PMID: 29706369 DOI: 10.1016/j.marenvres.2018.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Spatial patterns of abundance of the whole macrobenthic assemblage and of its 10 most numerous species were examined across hierarchically nested scales within a 0.85 ha area of intertidal seagrass in subtropical Moreton Bay, Queensland. Multifractality characterised the assemblage and all ten dominant species across those scales (c. 33, 130, 530 & 2115 m2), with patchiness of assemblage numbers and those of at least some dominants exhibiting scale-invariance. The system displayed several abundance peaks, 12% of stations accounting for 88% of total variance, with many individual dominants showing a series of non-overlapping 'hot-spots'. Scale invariance and multifractality occurred notwithstanding low levels of species interaction consequent on maintenance at very low density. This suggests that critical self-organisation cannot be responsible for such patterning. Contrary to received wisdom, coefficient β of Taylor's power-law cannot form an index of aggregation, although it does indicate direction of change in dispersion pattern with changing numbers.
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Affiliation(s)
- R S K Barnes
- School of Biological Sciences and Centre for Marine Science, University of Queensland, Brisbane 4072, Queensland, Australia; Biodiversity Program, Queensland Museum, Brisbane 4101, Queensland, Australia.
| | - H Laurie
- Department of Mathematics and Applied Mathematics, University of Cape Town, Cape Town, Western Cape 7701, South Africa
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Calabretti C, Citterio S, Delaria M, Gentili R, Montagnani C, Navone A, Caronni S. First record of two potentially toxic dinoflagellates in tide pools along the Sardinian coast. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/14888386.2017.1310058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yakimov BN, Gelashvili DB, Solntsev LA, Iudin DI, Rozenberg GS. Nonconcavity of mass exponents’ spectrum in multifractal analysis of community spatial structure: The problem and possible solutions. ECOLOGICAL COMPLEXITY 2014. [DOI: 10.1016/j.ecocom.2014.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
Multifractals have been applied to characterize complex communities in a spatial context. They were developed for nonlinear systems and are particularly suited to capture multiplicative processes observed in ecological systems. Multifractals characterize variability in a scale-independent way within an experimental range. I have developed an open-source software package to estimate multifractals using a box-counting algorithm (available from https://github.com/lsaravia/mfsba and permanently available at doi: 10.5281/zenodo.8481). The software is specially designed for two dimensional (2D) images such as the ones obtained from remote sensing, but other 2D data types can also be analyzed. Additionally I developed a new metric to analyze MULTISPECIES SPATIAL PATTERNS WITH MULTIFRACTALS: spatial rank surface, which is included in the software.
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Affiliation(s)
- Leonardo A Saravia
- Instituto de Ciencias Básicas, Universidad Nacional de General Sarmiento, Buenos Aires, Argentina
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