Temporal microbiome changes in axolotl limb regeneration: stage-specific restructuring of bacterial and fungal communities with a flavobacterium bloom during blastema proliferation

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dc.contributor.authorAltın, Hanne
dc.contributor.authorDelice, Büşra
dc.contributor.authorYıldırım, Berna
dc.contributor.authorDemircan, Turan
dc.contributor.authorYıldırım, Süleyman
dc.date.accessioned2025-11-24T12:28:47Z
dc.date.available2025-11-24T12:28:47Z
dc.date.issued2024
dc.departmentİstanbul Medipol Üniversitesi, Rektörlük, Rejeneratif ve Restoratif Tıp Araştırmaları Merkezi (REMER)
dc.departmentİstanbul Medipol Üniversitesi, Rektörlük, Sağlık Bilim ve Teknolojileri Araştırma Enstitüsü
dc.departmentİstanbul Medipol Üniversitesi, Uluslararası Tıp Fakültesi, Temel Tıp Bilimleri Bölümü, Tıbbi Mikrobiyoloji Ana Bilim Dalı
dc.description.abstractThe intricate relationship between regeneration and microbiota has recently gained attention, spanning diverse model organisms. Axolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite its significance, a noticeable gap exists in understanding the interplay between axolotl regeneration and its microbiome. Here, we analyse in depth bacterial 16S rRNA amplicon dataset that we reported before as data resource and profile fungal community by sequencing ITS amplicons at the critical stages of limb regeneration (0–1–4–7–30–60 days post amputation, ‘dpa’). Results reveal a decline in richness and evenness in the course of limb regeneration, with bacterial community richness recovering beyond 30 dpa unlike fungi community. Beta diversity analysis reveals precise restructuring of the bacterial community along the three phases of limb regeneration, contrasting with less congruent changes in the fungal community. Temporal dynamics of the bacterial community highlight prevalent anaerobic bacteria in initiation phase and Flavobacterium bloom in the early phase correlating with limb blastema proliferation. Predicted functional analysis mirrors these shifts, emphasising a transition from amino acid metabolism to lipid metabolism control. Fungal communities shift from Blastomycota to Ascomycota dominance in the late regeneration stage. Our findings provide ecologically relevant insights into stage specific role of microbiome contributions to axolotl limb regeneration.
dc.description.sponsorshipMedipol University Research Fund
dc.identifier.citationAltın, H., Delice, B., Yıldırım, B., Demircan, T. ve Yıldırım, S. (2024). Temporal microbiome changes in axolotl limb regeneration: stage-specific restructuring of bacterial and fungal communities with a flavobacterium bloom during blastema proliferation. Wound Repair and Regeneration, 32(6), 826-839. http://dx.doi.org/10.1111/wrr.13207
dc.identifier.doi10.1111/wrr.13207
dc.identifier.endpage839
dc.identifier.issn1067-1927
dc.identifier.issn1524-475X
dc.identifier.issue6
dc.identifier.pmid39105277
dc.identifier.scopus2-s2.0-85200482035
dc.identifier.scopusqualityQ1
dc.identifier.startpage826
dc.identifier.urihttp://dx.doi.org/10.1111/wrr.13207
dc.identifier.urihttps://hdl.handle.net/20.500.12511/13235
dc.identifier.volume32
dc.identifier.wosWOS:001285264100001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorAltın, Hanne
dc.institutionauthorDelice, Büşra
dc.institutionauthorYıldırım, Berna
dc.institutionauthorYıldırım, Süleyman
dc.institutionauthorid0000-0001-6068-3892
dc.institutionauthorid0009-0007-2444-6380
dc.institutionauthorid0000-0002-4479-2586
dc.institutionauthorid0000-0002-2752-1223
dc.language.isoen
dc.relation.ispartofWound Repair and Regeneration
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.rightsAttribution-NonCommercial 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectAxolotl
dc.subjectFlavobacterium
dc.subjectLimb
dc.subjectMicrobiome
dc.subjectRegeneration
dc.titleTemporal microbiome changes in axolotl limb regeneration: stage-specific restructuring of bacterial and fungal communities with a flavobacterium bloom during blastema proliferation
dc.typeArticle

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