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  • Chapter Two - Analytical approaches for microbiome research
  • Edited by Rachael E. Antwis, University of Salford, Xavier A. Harrison, University of Exeter, Michael J. Cox, University of Birmingham
  • Book: Microbiomes of Soils, Plants and Animals
  • Published online: 07 March 2020
  • Print publication: 12 March 2020, pp 8-28
  • View extract

    Summary

    Two major outstanding questions in microbiome research ask what microbes are present in a community and how they interact with each other and their hosts. Recent, rapid improvements in nucleic acid (DNA and RNA) sequencing allow us to study the composition and function of microbiomes in unprecedented detail, leading to a step change in our understanding of host–microbe interactions. This chapter gives a broad overview of the basic toolkit available to modern microbiologists and microbial ecologists, exploring their application to key questions about microbiome structure and function. We cover tools based on nucleic acid sequencing (e.g. amplicon sequencing, metagenomics, metatranscriptomics) as well as approaches targeting larger molecules such as metabolomics and proteomics. We discuss the use of microbial culture as a means of measuring functional capacity of individual microbes, or building artificial communities to understand emergent properties of consortia. We emphasise the advantages of combining multiple techniques alongside robust experimental design to garner powerful quantitative estimates of microbiome structure, and how this relates to host–microbe interactions.

  • Poisoning causing the decline in South-East Asia’s largest vulture population
  • ROBIN LOVERIDGE, GERARD EDWARD RYAN, PHEARUN SUM, OLIVER GRAY-READ, SIMON P. MAHOOD, ALISTAIR MOULD, STEFAN HARRISON, RACHEL CROUTHERS, SOK KO, TOM CLEMENTS, JONATHAN C. EAMES, MATHIEU PRUVOT
  • Journal: Bird Conservation International / Volume 29 / Issue 1 / March 2019
  • Published online by Cambridge University Press: 25 September 2018, pp. 41-54
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    Cambodia supports populations of three Critically Endangered vulture species that are believed to have become isolated from the rest of the species’ global range. Until recently Cambodia’s vulture populations had remained stable. However a recent spike in the number of reports of the use of poisons in hunting practices suggests the need to re-evaluate the conservation situation in Cambodia. Population trend analysis showed that since 2010 populations of the White-rumped Vulture Gyps bengalensis and Red-headed Vulture Sarcogyps calvus have declined, while the Slender-billed Vulture Gyps tenuirostris may also have started to decline since 2013. These trends are supported by evidence of reduced nesting success. A survey of veterinary drug availability revealed that diclofenac, the non-steroid anti-inflammatory drug responsible for vulture declines in South Asia was not available for sale in any of the 74 pharmacies surveyed. However, a poisoned Slender-billed Vulture tested positive for carbofuran in toxicology tests. This provides the first evidence of a vulture mortality resulting from carbofuran in Cambodia. The findings suggest the urgent need to tackle use of carbamate pesticides in hunting. Proposed conservation actions are: a) prevention of poisoning through national bans on harmful carbamate pesticides and diclofenac and education campaigns to reduce demand and use; b) training of personnel in priority protected areas in detection and response to poisoning incidents; c) maintenance of a safe and reliable food source through vulture restaurants to ensure short-term survival, and d) protection and restoration of large areas of deciduous dipterocarp forests to enable long-term species recovery.

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