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Altın H, Delice B, Yıldırım B, Demircan T, Yıldırım S. Temporal microbiome changes in axolotl limb regeneration: Stage-specific restructuring of bacterial and fungal communities with a Flavobacterium bloom during blastema proliferation. Wound Repair Regen 2024. [PMID: 39105277 DOI: 10.1111/wrr.13207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/08/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
The 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.
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Affiliation(s)
- Hanne Altın
- Department of Medical Microbiology, Istanbul Medipol University International School of Medicine, Istanbul, Türkiye
| | - Büşra Delice
- Department of Medical Microbiology, Istanbul Medipol University International School of Medicine, Istanbul, Türkiye
| | - Berna Yıldırım
- Department of Histology and Embryology, Atlas University School of Medicine, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, İstanbul & Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
| | - Turan Demircan
- Medical Biology Department, Muğla Sıtkı Koçman University School of Medicine, Muğla, Turkey
| | - Süleyman Yıldırım
- Department of Medical Microbiology, Istanbul Medipol University International School of Medicine, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, İstanbul & Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
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Demircan T, Gül S, Taşçı EA. Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:291-302. [PMID: 38808529 DOI: 10.1089/omi.2024.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.
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Affiliation(s)
- Turan Demircan
- School of Medicine, Department of Medical Biology, Muğla Sıtkı Koçman University, Muğla, Türkiye
| | - Sultan Gül
- Institute of Health Sciences, İstanbul Medipol University, İstanbul, Türkiye
- Graduate School of Science And Engineering, Yıldız Technical University, İstanbul, Türkiye
| | - Ebru Altuntaş Taşçı
- Institute of Natural Sciences, Muğla Sıtkı Koçman University, Muğla, Türkiye
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Demircan T, Süzek BE. The Dynamic Landscapes of Circular RNAs in Axolotl, a Regenerative Medicine Model, with Implications for Early Phase of Limb Regeneration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:526-535. [PMID: 37943672 DOI: 10.1089/omi.2023.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Circular RNAs (circRNAs) are of relevance to regenerative medicine and play crucial roles in post-transcriptional and translational regulation of biological processes. circRNAs are a class of RNA molecules that are formed through a unique splicing process, resulting in a covalently closed-loop structure. Recent advancements in RNA sequencing technologies and specialized computational tools have facilitated the identification and functional characterization of circRNAs. These molecules are known to exhibit stability, developmental regulation, and specific expression patterns in different tissues and cell types across various organisms. However, our understanding of circRNA expression and putative function in model organisms for regeneration is limited. In this context, this study reports, for the first time, on the repertoire of circRNAs in axolotl, a widely used model organism for regeneration. We generated RNA-seq data from intact limb, wound, and blastema tissues of axolotl during limb regeneration. The analysis revealed the presence of 35,956 putative axolotl circRNAs, among which 5331 unique circRNAs exhibited orthology with human circRNAs. In silico data analysis underlined the potential roles of axolotl circRNAs in cell cycle, cell death, and cell senescence-related pathways during limb regeneration, suggesting the participation of circRNAs in regulation of diverse functions pertinent to regenerative medicine. These new observations help advance our understanding of the dynamic landscape of axolotl circRNAs, and by extension, inform future regenerative medicine research and innovation that harness this model organism.
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Affiliation(s)
- Turan Demircan
- Medical Biology Department, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
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Bay S, Öztürk G, Emekli N, Demircan T. Downregulation of Yap1 during limb regeneration results in defective bone formation in axolotl. Dev Biol 2023:S0012-1606(23)00094-5. [PMID: 37271360 DOI: 10.1016/j.ydbio.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
The Hippo pathway plays an imperative role in cellular processes such as differentiation, regeneration, cell migration, organ growth, apoptosis, and cell cycle. Transcription coregulator component of Hippo pathway, YAP1, promotes transcription of genes involved in cell proliferation, migration, differentiation, and suppressing apoptosis. However, its role in epimorphic regeneration has not been fully explored. The axolotl is a well-established model organism for developmental biology and regeneration studies. By exploiting its remarkable regenerative capacity, we investigated the role of Yap1 in the early blastema stage of limb regeneration. Depleting Yap1 using gene-specific morpholinos attenuated the competence of axolotl limb regeneration evident in bone formation defects. To explore the affected downstream pathways from Yap1 down-regulation, the gene expression profile was examined by employing LC-MS/MS technology. Based on the generated data, we provided a new layer of evidence on the putative roles of increased protease inhibition and immune system activities and altered ECM composition in diminished bone formation capacity during axolotl limb regeneration upon Yap1 deficiency. We believe that new insights into the roles of the Hippo pathway in complex structure regeneration were granted in this study.
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Affiliation(s)
- Sadık Bay
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, 34810, Turkey; Graduate School of Health Sciences, İstanbul Medipol University, İstanbul, Turkey.
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, 34810, Turkey; Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Turan Demircan
- Department of Medical Biology, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey; Department of Bioinformatics, Muğla Sıtkı Koçman University, Muğla, Turkey.
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Vickers E, Kerney R. Screening Salamanders for Symbionts. Methods Mol Biol 2023; 2562:425-442. [PMID: 36272092 DOI: 10.1007/978-1-0716-2659-7_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbial symbionts are broadly categorized by their impacts on host fitness: commensals, pathogens, and mutualists. However, recent investigations into the physiological basis of these impacts have revealed nuanced microbial influences on a wide range of host developmental, immunological, and physiological processes, including regeneration. Exploring these impacts begins with knowing which microbes are present. This methodological pipeline contains both targeted assays using PCR and culturing, as well as culture-independent approaches, to survey host salamander tissues for common and unknown microbial symbionts.
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Affiliation(s)
- Elli Vickers
- Gettysburg College, Department of Biology, Gettysburg, PA, USA
| | - Ryan Kerney
- Gettysburg College, Department of Biology, Gettysburg, PA, USA.
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Díaz-Díaz LM, Rodríguez-Villafañe A, García-Arrarás JE. The Role of the Microbiota in Regeneration-Associated Processes. Front Cell Dev Biol 2022; 9:768783. [PMID: 35155442 PMCID: PMC8826689 DOI: 10.3389/fcell.2021.768783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
The microbiota, the set of microorganisms associated with a particular environment or host, has acquired a prominent role in the study of many physiological and developmental processes. Among these, is the relationship between the microbiota and regenerative processes in various organisms. Here we introduce the concept of the microbiota and its involvement in regeneration-related cellular events. We then review the role of the microbiota in regenerative models that extend from the repair of tissue layers to the regeneration of complete organs or animals. We highlight the role of the microbiota in the digestive tract, since it accounts for a significant percentage of an animal microbiota, and at the same time provides an outstanding system to study microbiota effects on regeneration. Lastly, while this review serves to highlight echinoderms, primarily holothuroids, as models for regeneration studies, it also provides multiple examples of microbiota-related interactions in other processes in different organisms.
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Affiliation(s)
- Lymarie M Díaz-Díaz
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
| | | | - José E García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
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Sibai M, Altuntaş E, Yıldırım B, Öztürk G, Yıldırım S, Demircan T. Microbiome and Longevity: High Abundance of Longevity-Linked Muribaculaceae in the Gut of the Long-Living Rodent Spalax leucodon. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:592-601. [PMID: 32907488 DOI: 10.1089/omi.2020.0116] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With a world population living longer as well as marked disparities in life expectancy, understanding the determinants of longevity is one of the priority research agendas in 21st century life sciences. To this end, the blind mole-rat (Spalax leucodon), a subterranean mammalian, has emerged as an exceptional model organism due to its astonishing features such as remarkable longevity, hypoxia and hypercapnia tolerance, and cancer resistance. The microbiome has been found to be a vital parameter for cellular physiology and it is safe to assume that it has an impact on life expectancy. Although the unique characteristics of Spalax make it an ideal experimental model for longevity research, there is limited knowledge of the bacterial composition of Spalax microbiome, which limits its in-depth utilization. In this study, using 16S rRNA amplicon sequencing, we report the gut and skin bacterial structure of Spalax for the first time. The diversity between fecal and skin samples was manifested in the distant clustering, as revealed by beta diversity analysis. Importantly, the longevity-linked Muribaculaceae bacterial family was found to be the dominating bacterial taxa in Spalax fecal samples. These new findings contribute toward further development of Spalax as a model for longevity research and potential linkages between microbiome composition and longevity.
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Affiliation(s)
- Mustafa Sibai
- Graduate School of Natural and Applied Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Ebru Altuntaş
- Graduate School of Natural and Applied Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Berna Yıldırım
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.,Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Süleyman Yıldırım
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Microbiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Turan Demircan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey
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Demircan T, Sibai M, Altuntaş E. Proteome data to explore the axolotl limb regeneration capacity at neotenic and metamorphic stages. Data Brief 2020; 29:105179. [PMID: 32055664 PMCID: PMC7005509 DOI: 10.1016/j.dib.2020.105179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/02/2020] [Accepted: 01/16/2020] [Indexed: 12/04/2022] Open
Abstract
The presented data article reports protein expression profiles during a time course of limb regeneration in the highly regenerative neotenic and regeneration-deficient metamorphic axolotl (Ambystoma mexicanum). A protein database was first generated from transcriptome data, which was used concomitantly with nanoLC-MS/MS to identify and assess significant changes of protein levels among 0, 1, 4, and 7 days post-amputation (dpa) in both animal stages, yielding a total of 714 significant differentially expressed proteins. Gene ontology categories of these identified proteins were examined in terms of biological processes, molecular function and cellular components. Innate clustering patterns of the samples were investigated using hierarchical clustering and were visualized on a heatmap. The data reported here constitutes an extension of “Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl” article Sibai et al., 2019 [1]. The associated mass spectrometry raw data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) with the dataset identifier PXD014806.
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Affiliation(s)
- Turan Demircan
- Muğla Sıtkı Koçman University, School of Medicine, Department of Medical Biology, Turkey.,Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Mustafa Sibai
- Muğla Sıtkı Koçman University, Graduate School of Natural and Applied Sciences, Turkey
| | - Ebru Altuntaş
- Muğla Sıtkı Koçman University, Graduate School of Natural and Applied Sciences, Turkey
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Sibai M, Altuntaş E, Süzek BE, Şahin B, Parlayan C, Öztürk G, Baykal AT, Demircan T. Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl. Biochem Biophys Res Commun 2019; 522:428-434. [PMID: 31767146 DOI: 10.1016/j.bbrc.2019.11.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022]
Abstract
The axolotl (Ambystoma mexicanum) salamander, a urodele amphibian, has an exceptional regenerative capacity to fully restore an amputated limb throughout the life-long lasting neoteny. By contrast, when axolotls are experimentally induced to metamorphosis, attenuation of the limb's regenerative competence is noticeable. Here, we sought to discern the proteomic profiles of the early stages of blastema formation of neotenic and metamorphic axolotls after limb amputation by employing LC-MS/MS technology. We quantified a total of 714 proteins and qRT-PCR for selected genes was performed to validate the proteomics results and provide evidence for the putative link between immune system activity and regenerative potential. This study provides new insights for examination of common and distinct molecular mechanisms in regeneration-permissive neotenic and regeneration-deficient metamorphic stages at the proteome level.
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Affiliation(s)
- Mustafa Sibai
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Ebru Altuntaş
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Mugla Sitki Kocman University, Mugla, Turkey; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Betül Şahin
- Acibadem Labmed Research and Development Center, Istanbul, Turkey
| | - Cüneyd Parlayan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Biomedical Engineering, Faculty of Engineering, Istanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem Labmed Research and Development Center, Istanbul, Turkey; Department of Biochemistry, School of Medicine, Istanbul Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Turan Demircan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey.
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