in

Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar

[adace-ad id="91168"]
  • Peixoto, R. S., Harkins, D. M. & Nelson, K. E. Advances in microbiome research for animal health. Annu. Rev. Anim. Biosci. 9, 289–311 (2021).

    Article 

    Google Scholar 

  • Amato, K. R. et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 7, 1344 (2013).

    Article 

    Google Scholar 

  • West, A. G. et al. The microbiome in threatened species conservation. Biol. Conserv. 229, 85–98 (2019).

    Article 

    Google Scholar 

  • Robinson, J. M., Mills, J. G. & Breed, M. F. Walking ecosystems in microbiome-inspired green infrastructure: An ecological perspective on enhancing personal and planetary health. Challenges 9, 40 (2018).

    Article 

    Google Scholar 

  • Mills, J. G. et al. Urban habitat restoration provides a human health benefit through microbiome rewilding: The Microbiome Rewilding Hypothesis. Restor. Ecol. 25, 866–872 (2017).

    Article 

    Google Scholar 

  • Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B 286, 20182448 (2019).

    Article 

    Google Scholar 

  • Dallas, J. W. & Warne, R. W. Captivity and animal microbiomes: Potential roles of microbiota for influencing animal conservation. Microb. Ecol. https://doi.org/10.1007/s00248-022-01991-0 (2022).

    Article 

    Google Scholar 

  • Bornbusch, S. L. et al. Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota. Anim. Microbiome 4, 1–19 (2022).

    Article 

    Google Scholar 

  • Greene, L. K. et al. Gut microbiota of frugo-folivorous sifakas across environments. Anim. Microbiome 3, 39 (2021).

    Article 

    Google Scholar 

  • McKenzie, V. J. et al. The effects of captivity on the mammalian gut microbiome. Integr. Comp. Biol. 57, 690–704 (2017).

    Article 

    Google Scholar 

  • Bornbusch, S. L. & Drea, C. M. Antibiotic resistance genes in lemur gut and soil microbiota along a gradient of anthropogenic disturbance. Front. Ecol. Evol. 9, 514 (2021).

    Article 

    Google Scholar 

  • Hyde, E. R. et al. The oral and skin microbiomes of captive komodo dragons are significantly shared with their habitat. mSystems 1, e00046-e116 (2016).

    Article 

    Google Scholar 

  • LaFleur, M., Clarke, T. A., Reuter, K. E. & Schaefer, M. S. Illegal trade of wild-captured Lemur catta within Madagascar. Folia Primatol. 90, 199–214 (2019).

    Article 

    Google Scholar 

  • Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).

    Article 

    Google Scholar 

  • Choo, J. M., Leong, L. E. & Rogers, G. B. Sample storage conditions significantly influence faecal microbiome profiles. Sci. Rep. 5, 16350 (2015).

    Article 
    ADS 

    Google Scholar 

  • Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).

    Article 

    Google Scholar 

  • Hasan, N. A. et al. Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS ONE 9, e97699 (2014).

    Article 
    ADS 

    Google Scholar 

  • Bornbusch, S. L. et al. Stable and transient structural variation in lemur vaginal, labial and axillary microbiomes: Patterns by species, body site, ovarian hormones and forest access. FEMS Microbiol. Ecol. 96, fiaa090 (2020).

    Article 

    Google Scholar 

  • Bolyen, E. et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ 37, 852–857 (2018).

    Google Scholar 

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581 (2016).

    Article 

    Google Scholar 

  • Trosvik, P., Rueness, E. K., de Muinck, E. J., Moges, A. & Mekonnen, A. Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys. Sci. Rep. 8, 1–10 (2018).

    Article 

    Google Scholar 

  • Wills, M. O. et al. Host species and captivity distinguish the microbiome compositions of a diverse zoo-resident non-human primate population. Diversity 14, 715 (2022).

    Article 

    Google Scholar 

  • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    Article 

    Google Scholar 

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 
    ADS 

    Google Scholar 

  • Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).

    Article 

    Google Scholar 

  • Yarza, P. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12, 635 (2014).

    Article 

    Google Scholar 

  • Aitchison, J. The statistical analysis of compositional data. J. R. Stat. Soc. Ser. B 44, 139–160 (1982).

    MathSciNet 
    MATH 

    Google Scholar 

  • Quinn, T. P., Erb, I., Richardson, M. F. & Crowley, T. M. Understanding sequencing data as compositions: An outlook and review. Bioinformatics 34, 2870–2878 (2018).

    Article 

    Google Scholar 

  • Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: And this is not optional. Front. Microbiol. 8, 2224 (2017).

    Article 

    Google Scholar 

  • Ottesen, A. et al. Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak. BMC Microbiol. 16, 1–11 (2016).

    Article 

    Google Scholar 

  • Lax, S. et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345, 1048–1052 (2014).

    Article 
    ADS 

    Google Scholar 

  • Shenhav, L. et al. FEAST: Fast expectation-maximization for microbial source tracking. Nat. Methods 16, 627 (2019).

    Article 

    Google Scholar 

  • Barelli, C. et al. The gut microbiota communities of wild arboreal and ground-feeding tropical primates are affected differently by habitat disturbance. mSystems 5, e00061 (2020).

    Article 

    Google Scholar 

  • Frankel, J. S., Mallott, E. K., Hopper, L. M., Ross, S. R. & Amato, K. R. The effect of captivity on the primate gut microbiome varies with host dietary niche. Am. J. Primatol. 81, e23061 (2019).

    Article 

    Google Scholar 

  • Bornbusch, S. L. et al. Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts. Anim. Microbiome 3, 65 (2021).

    Article 

    Google Scholar 

  • Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576–587 (2019).

    Article 

    Google Scholar 

  • Bornbusch, S. L. et al. A comparative study of gut microbiomes in captive nocturnal strepsirrhines. Am. J. Primatol. 81, e22986 (2019).

    Article 

    Google Scholar 

  • Nishida, A. H. & Ochman, H. A great-ape view of the gut microbiome. Nat. Rev. Genet. 20, 195–206 (2019).

    Article 

    Google Scholar 

  • Nagpal, R. et al. Gut microbiome composition in non-human primates consuming a Western or Mediterranean diet. Front. Nutr. 5, 28 (2018).

    Article 

    Google Scholar 

  • Deng, H. et al. Bacteroides fragilis prevents Clostridium difficile infection in a mouse model by restoring gut barrier and microbiome regulation. Front. Microbiol. 9, 2976 (2018).

    Article 

    Google Scholar 

  • Wang, C. et al. Roles of intestinal bacteroides in human health and diseases. Crit. Rev. Food Sci. Nutr. 61, 3518–3536 (2021).

    Article 

    Google Scholar 

  • Townsend, G. E. et al. Dietary sugar silences a colonization factor in a mammalian gut symbiont. Proc. Natl. Acad. Sci. USA 116, 233–238 (2019).

    Article 
    ADS 

    Google Scholar 

  • LaFleur, M. et al. Drug-resistant tuberculosis in pet ring-tailed lemur, Madagascar. Emerg. Infect. Dis. 27, 977 (2021).

    Article 

    Google Scholar 

  • Gálvez, E. J. C. et al. Distinct polysaccharide utilization determines interspecies competition between intestinal Prevotella spp. Cell Host Microbe 28, 838–852 (2020).

    Article 

    Google Scholar 

  • Costea, P. I. et al. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3, 8–16 (2018).

    Article 

    Google Scholar 

  • Roager, H. M., Licht, T. R., Poulsen, S. K., Larsen, T. M. & Bahl, M. I. Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet. Appl. Environ. Microbiol. 80, 1142–1149 (2014).

    Article 
    ADS 

    Google Scholar 

  • Hjorth, M. F. et al. Pretreatment Prevotella-to-Bacteroides ratio and markers of glucose metabolism as prognostic markers for dietary weight loss maintenance. Eur. J. Clin. Nutr. 74, 338–347 (2020).

    Article 

    Google Scholar 

  • Hjorth, M. F. et al. Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. Int. J. Obes. 42, 580–583 (2018).

    Article 

    Google Scholar 

  • DeMartino, P. & Cockburn, D. W. Resistant starch: Impact on the gut microbiome and health. Curr. Opin. Biotechnol. 61, 66–71 (2020).

    Article 

    Google Scholar 

  • Wang, K. et al. Diet with a high proportion of rice alters profiles and potential function of digesta-associated microbiota in the ileum of goats. Animals 10, 1261 (2020).

    Article 

    Google Scholar 

  • Greene, L. K., McKenney, E. A., O’Connell, T. M. & Drea, C. M. The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas. Sci. Rep. 8, 14482 (2018).

    Article 
    ADS 

    Google Scholar 

  • Allen, H. K. et al. Call of the wild: Antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).

    Article 

    Google Scholar 

  • Daszak, P., Cunningham, A. A. & Hyatt, A. D. Anthropogenic environmental change and the emergence of infectious diseases in wildlife. Acta Trop. 78, 103–116 (2001).

    Article 

    Google Scholar 

  • Shapira, M. Gut microbiotas and host evolution: Scaling up symbiosis. Trends Ecol. Evol. 31, 539–549 (2016).

    Article 

    Google Scholar 

  • Sbihi, H. et al. Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy 74, 2103–2115 (2019).

    Article 

    Google Scholar 

  • Bendiks, M. & Kopp, M. V. The relationship between advances in understanding the microbiome and the maturing hygiene hypothesis. Curr. Allergy Asthma Rep. 13, 487–494 (2013).

    Article 

    Google Scholar 

  • Alexandre-Silva, G. M. et al. The hygiene hypothesis at a glance: Early exposures, immune mechanism and novel therapies. Acta Trop. 188, 16–26 (2018).

    Article 

    Google Scholar 

  • Yao, R. et al. The, “wildness” of the giant panda gut microbiome and its relevance to effective translocation. Glob. Ecol. Conserv. 18, e00644 (2019).

    Article 

    Google Scholar 


  • Source: Ecology - nature.com

    Validation of SNP markers for thermotolerance adaptation in Ovis aries adapted to different climatic regions using KASP-PCR technique

    Investigation of anticoagulant rodenticide resistance induced by Vkorc1 mutations in rodents in Lebanon