The microbiota of long-living and cancer-free blind mole rat $\textit{(Nannospalax xanthodon)}$ from the edge of its distribution in Northern Anatolia

Year 2023, Volume: 32 Issue: 2, 105 - 118, 30.12.2023

Halil Mert Solak , Efe Sezgin , Dagmar Cizkova , Jakub Kreisinger , Faruk Çolak , Ortaç Çetintaş , Alexey Yanchukov

https://doi.org/10.53447/communc.1281221

Cited By: 1

Abstract

The mammalian gut is colonized by microorganisms that affect development, immune system, energy metabolism, and reproduction. The majority of studies focused on laboratory or domestic animals in artificial setups, leaving the research focused on wild species underrepresented. The Anatolian Blind Molerat (hereafter ABMR), $\textit{Nannospalax xanthodon}$, is a subterranean rodent that receives much attention due to its unique traits, such as tolerance to extreme hypoxic stress, resistance to cancer, and longer lifespan compared to similarly sized rodents. In this study, we characterize the gut microbiota of ABMR from its northernmost geographic distribution using 16S rRNA metabarcoding and compare our results with the microbiome characteristics of a few other ABMR populations studied previously, as well as other rodent species. The 16S rRNA barcode dataset revealed that approximately 90% of the ABMR gut microbiota comprises Firmicutes and Bacteriodota bacterial phyla, typical of most mammals. In addition, the ABMR gut microbiota has a high abundance of performance- and longevity-linked bacterial families. Overall, our results generally align well with the previous studies on blind molerats and emphasize the importance of studying the microbiome of natural populations.

Keywords

16S rRNA, metabarcoding, microbiota, wild, rodent, mole rats

Thanks

This study was supported by TÜBİTAK grant 220Z032, and the collection of samples was funded by TUBITAK 119Z400. DC and JK were supported by Czech Science Foundation (19-19307S). The numerical calculations reported in this paper were partially performed at TÜBİTAK ULAKBİM, High Performance and Grid Computing Center (TRUBA resources).

References

• Lin, L., Zhang, J., Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunology, 18 (1) (2017), 2. https://doi.org/10.1186/s12865-016-0187-3.
• Sender, R., Fuchs, S., Milo, R., Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14 (8) (2016), e1002533. https://doi.org/10.1371/journal.pbio.1002533.
• Knight, R., Callewaert, C., Marotz, C., Hyde, E.R., Debelius, J.W., McDonald, D., Sogin, M.L., The microbiome and human biology. Annual Review of Genomics and Human Genetics, 18 (2017), 65–86. https://doi.org/10.1146/annurev-genom-083115-022438.
• Lindsay, E.C., Metcalfe, N.B., Llewellyn, M.S., The potential role of the gut microbiota in shaping host energetics and metabolic rate. The Journal of Animal Ecology, 89 (11) (2020), 2415–2426. https://doi.org/10.1111/1365-2656.13327.
• McFall-Ngai, M., Hadfield, M.G., Bosch, T.C.G., Carey, H.V., Domazet-Lošo, T., Douglas, A.E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S.F., Hentschel, U., King, N., Kjelleberg, S., Knoll, A.H., Kremer, N., Mazmanian, S.K., Metcalf, J.L., Nealson, K., Pierce, N.E., Rawls, J.F., Reid, A., Ruby, E.G., Rumpho, M., Sanders, J.G., Tautz, D., Wernegreen, J.J., Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences of the United States of America, 110 (9) (2013), 3229–3236. https://doi.org/10.1073/pnas.1218525110.
• Suzuki, T.A., Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals. Integrative and Comparative Biology, 57 (4) (2017), 756–769. https://doi.org/10.1093/icb/icx104.
• Lynch, S.V., Pedersen, O., The human intestinal microbiome in health and disease. The New England Journal of Medicine, 375 (24) (2016), 2369–2379. https://doi.org/10.1056/NEJMra1600266.
• Thursby, E., Juge, N., Introduction to the human gut microbiota. The Biochemical Journal, 474 (11) (2017), 1823–1836. https://doi.org/10.1042/BCJ20160510.
• Wang, J., Lang, T., Shen, J., Dai, J., Tian, L., Wang, X., Core gut bacteria analysis of healthy mice. Frontiers in Microbiology, 10 (2019), 887. https://doi.org/10.3389/fmicb.2019.00887.
• Bäckhed, F., Manchester, J.K., Semenkovich, C.F., Gordon, J.I., Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proceedings of the National Academy of Sciences of the United States of America, 104 (3) (2007), 979–984. https://doi.org/10.1073/pnas.0605374104.
• Rogers, G.B., Kozlowska, J., Keeble, J., Metcalfe, K., Fao, M., Dowd, S.E., Mason, A.J., McGuckin, M.A., Bruce, K.D., Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice. Scientific Reports, 4 (2014), 5437. https://doi.org/10.1038/srep05437.
• Roeselers, G., Mittge, E.K., Stephens, W.Z., Parichy, D.M., Cavanaugh, C.M., Guillemin, K., Rawls, J.F., Evidence for a core gut microbiota in the zebrafish. The ISME Journal, 5 (10) (2011), 1595–1608. https://doi.org/10.1038/ismej.2011.38.
• van Leeuwen, P., Mykytczuk, N., Mastromonaco, G.F., Schulte-Hostedde, A.I., Effects of captivity, diet, and relocation on the gut bacterial communities of white-footed mice. Ecology and Evolution, 10 (11) (2020), 4677–4690. https://doi.org/10.1002/ece3.6221.
• Belheouane, M., Vallier, M., Čepić, A., Chung, C.J., Ibrahim, S., Baines, J.F., Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice. The ISME Journal, 14 (10) (2020), 2367–2380. https://doi.org/10.1038/s41396-020-0690-7.
• Wang, J., Linnenbrink, M., Künzel, S., Fernandes, R., Nadeau, M.-J., Rosenstiel, P., Baines, J.F., Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proceedings of the National Academy of Sciences of the United States of America, 111 (26) (2014), E2703-10. https://doi.org/10.1073/pnas.1402342111.
• Kreisinger, J., Cížková, D., Vohánka, J., Piálek, J., Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing. Molecular Ecology, 23 (20) (2014), 5048–5060. https://doi.org/10.1111/mec.12909.
• Weldon, L., Abolins, S., Lenzi, L., Bourne, C., Riley, E.M., Viney, M., The gut microbiota of wild mice. Plos One, 10 (8) (2015), e0134643. https://doi.org/10.1371/journal.pone.0134643.
• Debebe, T., Biagi, E., Soverini, M., Holtze, S., Hildebrandt, T.B., Birkemeyer, C., Wyohannis, D., Lemma, A., Brigidi, P., Savkovic, V., König, B., Candela, M., Birkenmeier, G., Unraveling the gut microbiome of the long-lived naked mole-rat. Scientific Reports, 7 (1) (2017), 9590. https://doi.org/10.1038/s41598-017-10287-0.
• Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., Gordon, J.I., Evolution of mammals and their gut microbes. Science, 320 (5883) (2008), 1647–1651. https://doi.org/10.1126/science.1155725.
• Zhou, T., Liu, S., Jiang, A., Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia (Leiothrix argentauris) living in mining area. Frontiers in Microbiology, 14 (2023), 1076523. https://doi.org/10.3389/fmicb.2023.1076523.
• Linnenbrink, M., Wang, J., Hardouin, E.A., Künzel, S., Metzler, D., Baines, J.F., The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Molecular Ecology, 22 (7) (2013), 1904–1916. https://doi.org/10.1111/mec.12206.
• Arslan, A., Kryštufek, B., Matur, F., Zima, J., Review of chromosome races in blind molerats (Spalax and Nannospalax). Folia Zoologica, 65 (4) (2016), 249–301. https://doi.org/10.25225/fozo.v65.i4.a1.2016.
• Shams, I., Avivi, A., Nevo, E., Oxygen and carbon dioxide fluctuations in burrows of subterranean blind molerats indicate tolerance to hypoxic-hypercapnic stresses. Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology, 142 (3) (2005), 376–382. https://doi.org/10.1016/j.cbpa.2005.09.003.
• Altwasser, R., Paz, A., Korol, A., Manov, I., Avivi, A., Shams, I., The transcriptome landscape of the carcinogenic treatment response in the blind molerat: insights into cancer resistance mechanisms. BMC Genomics, 20 (1) (2019), 17. https://doi.org/10.1186/s12864-018-5417-z.
• Lagunas-Rangel, F.A., Cancer-free aging: Insights from Spalax ehrenbergi superspecies. Ageing Research Reviews, 47 (2018), 18–23. https://doi.org/10.1016/j.arr.2018.06.004.
• Schmidt, H., Malik, A., Bicker, A., Poetzsch, G., Avivi, A., Shams, I., Hankeln, T., Hypoxia tolerance, longevity and cancer-resistance in the molerat Spalax - a liver transcriptomics approach. Scientific Reports, 7 (1) (2017), 14348. https://doi.org/10.1038/s41598-017-13905-z.
• Sözen, M., Sevindik, M., Matur, F., Karyological and some morphological characteristics of Spalax leucodon Nordmann, 1840 (Mammalia: Rodentia) superspecies around Kastamonu province, Turkey. Turkish Journal of Zoology, 30 (2) (2006), 205–219.
• Wertheim, G., Nevo, E., Helminths of birds and mammals from Israel: III. Helminths from chromosomal forms of the mole-rat, Spalax ehrenbergi. Journal of Helminthology, 45 (2–3) (1971), 161–169. https://doi.org/10.1017/S0022149X00007045.
• Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., Glöckner, F.O., Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Research, 41 (1) (2013), e1. https://doi.org/10.1093/nar/gks808.
• Jiang, H., Lei, R., Ding, S.-W., Zhu, S., Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics, 15 (2014), 182. https://doi.org/10.1186/1471-2105-15-182.
• Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., Holmes, S.P., DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13 (7) (2016), 581–583. https://doi.org/10.1038/nmeth.3869.
• Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., Knight, R., UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27 (16) (2011), 2194–2200. https://doi.org/10.1093/bioinformatics/btr381.
• Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., Glöckner, F.O., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41 (Database issue) (2013), D590-6. https://doi.org/10.1093/nar/gks1219.
• McMurdie, P.J., Holmes, S., phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. Plos One, 8 (4) (2013), e61217. https://doi.org/10.1371/journal.pone.0061217.
• Chung, H., Kasper, D.L., Microbiota-stimulated immune mechanisms to maintain gut homeostasis. Current Opinion in Immunology, 22 (4) (2010), 455–460. https://doi.org/10.1016/j.coi.2010.06.008.
• Stappenbeck, T.S., Hooper, L.V., Gordon, J.I., Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proceedings of the National Academy of Sciences of the United States of America, 99 (24) (2002), 15451–15455. https://doi.org/10.1073/pnas.202604299.
• Semova, I., Carten, J.D., Stombaugh, J., Mackey, L.C., Knight, R., Farber, S.A., Rawls, J.F., Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host & Microbe, 12 (3) (2012), 277–288. https://doi.org/10.1016/j.chom.2012.08.003.
• Vaikunthanathan, T., Safinia, N., Lombardi, G., Lechler, R.I., Microbiota, immunity and the liver. Immunology Letters, 171 (2016), 36–49. https://doi.org/10.1016/j.imlet.2016.01.008.
• Kotzampassi, K., Giamarellos-Bourboulis, E.J., Stavrou, G., Obesity as a consequence of gut bacteria and diet interactions. ISRN Obesity, 2014 (2014), 651895. https://doi.org/10.1155/2014/651895.
• van Leeuwen, P.M.L., Schulte-Hostedde, A.I., Fournier-Chambrillon, C., Fournier, P., Pigneur, L.-M., Aranda, C.M., Urra-Maya, F., Michaux, J.R., A microbial tale of farming, invasion and conservation: on the gut bacteria of European and American mink in Western Europe. Biological Invasions, (2023), https://doi.org/10.1007/s10530-023-03007-5.
• Wang, X.-W., Liu, Y.-Y., Origins of scaling laws in microbial dynamics. Physical Review Research, 5 (1) (2023), 013004. https://doi.org/10.1103/PhysRevResearch.5.013004.
• Nielsen, D.P., Harrison, J.G., Byer, N.W., Faske, T.M., Parchman, T.L., Simison, W.B., Matocq, M.D., The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone. Ecology Letters, 26 (1) (2023), 63–75. https://doi.org/10.1111/ele.14135.
• Wang, Z., Zhang, C., Li, G., Yi, X., The influence of species identity and geographic locations on gut microbiota of small rodents. Frontiers in Microbiology, 13 (2022), 983660. https://doi.org/10.3389/fmicb.2022.983660.
• 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, 24 (10) (2020), 592–601. https://doi.org/10.1089/omi.2020.0116.
• Kuang, Z., Li, F., Duan, Q., Tian, C., Nevo, E., Li, K., Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind molerats in Upper Galilee, Israel. Frontiers in Microbiology, 13 (2022), 1062763. https://doi.org/10.3389/fmicb.2022.1062763.
• Bendová, B., Piálek, J., Ďureje, Ľ., Schmiedová, L., Čížková, D., Martin, J.-F., Kreisinger, J., How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies. BMC Microbiology, 20 (1) (2020), 194. https://doi.org/10.1186/s12866-020-01859-8.
• Kreisinger, J., Bastien, G., Hauffe, H.C., Marchesi, J., Perkins, S.E., Interactions between multiple helminths and the gut microbiota in wild rodents. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 370 (1675) (2015). https://doi.org/10.1098/rstb.2014.0295.
• Cong, W., Xing, J., Feng, Y., Wang, J., Fu, R., Yue, B., He, Z., Lin, L., Yang, W., Cheng, J., Sun, W., Cui, S., The microbiota in the intestinal and respiratory tracts of naked mole-rats revealed by high-throughput sequencing. BMC Microbiology, 18 (1) (2018), 89. https://doi.org/10.1186/s12866-018-1226-4.
• Biddle, A., Stewart, L., Blanchard, J., Leschine, S., Untangling the genetic basis of fibrolytic specialization by lachnospiraceae and ruminococcaceae in diverse gut communities. Diversity, 5 (3) (2013), 627–640. https://doi.org/10.3390/d5030627.
• Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G.A.D., Gasbarrini, A., Mele, M.C., What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms, 7 (1) (2019). https://doi.org/10.3390/microorganisms7010014.
• Smith, B.J., Miller, R.A., Ericsson, A.C., Harrison, D.C., Strong, R., Schmidt, T.M., Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice. BMC Microbiology, 19 (1) (2019), 130. https://doi.org/10.1186/s12866-019-1494-7.
• Ormerod, K.L., Wood, D.L.A., Lachner, N., Gellatly, S.L., Daly, J.N., Parsons, J.D., Dal’Molin, C.G.O., Palfreyman, R.W., Nielsen, L.K., Cooper, M.A., Morrison, M., Hansbro, P.M., Hugenholtz, P., Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) (2016), 36. https://doi.org/10.1186/s40168-016-0181-2.
• Zhao, N., Zhao, M., Jin, H., Microplastic-induced gut microbiota and serum metabolic disruption in Sprague-Dawley rats. Environmental Pollution, 320 (2023), 121071. https://doi.org/10.1016/j.envpol.2023.121071.
• Siddiqui, R., Qaisar, R., Khan, N.A., Alharbi, A.M., Alfahemi, H., Elmoselhi, A., Effect of microgravity on the gut microbiota bacterial composition in a hindlimb unloading model. Life (Basel, Switzerland), 12 (11) (2022). https://doi.org/10.3390/life12111865.
• Zou, Y., Liang, N., Zhang, X., Han, C., Nan, X., Functional differentiation related to decomposing complex carbohydrates of intestinal microbes between two wild zokor species based on 16SrRNA sequences. BMC Veterinary Research, 17 (1) (2021), 216. https://doi.org/10.1186/s12917-021-02911-z.
• Li, C., Li, X., Guo, R., Ni, W., Liu, K., Liu, Z., Dai, J., Xu, Y., Abduriyim, S., Wu, Z., Zeng, Y., Lei, B., Zhang, Y., Wang, Y., Zeng, W., Zhang, Q., Chen, C., Qiao, J., Liu, C., Hu, S., Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse. Microbiome, 11 (1) (2023), 7. https://doi.org/10.1186/s40168-022-01448-z.
• Han, M., Yang, K., Yang, P., Zhong, C., Chen, C., Wang, S., Lu, Q., Ning, K., Stratification of athletes’ gut microbiota: the multifaceted hubs associated with dietary factors, physical characteristics and performance. Gut Microbes, 12 (1) (2020), 1–18. https://doi.org/10.1080/19490976.2020.1842991.