Assist conservation with microbiome? An investigation using native Amphibian species in Hong Kong

  • Pui Yin LAM

Student thesis: MPhil Thesis (Lingnan)


Microorganisms often have a negative connotation of disease, especially during the recent COVID-19 pandemic. However, many microorganisms are essential to health, from assisting nutrient acquisition to providing insights in advanced medicine. The diverse microorganisms (including bacteria, viruses, fungi, archaea, and protozoans) inhabiting a host are collectively known as the “microbiota”. The importance of microbiota is not limited to humans, but also applies to wildlife. Recent research highlighted the tremendous potential of applying microbiota research to wildlife conservation, such as understanding host’s health in relation to anthropogenic effects. Amphibians, being one of the most diverse but threatened groups of vertebrates, are an ideal study system for conservation-based microbiome studies.

In this study, I collect five types of amphibian microbiota samples (skin, small intestine, large intestine, faeces, and undigested content) in two native amphibian species — the Lesser Spiny Frog (Quasipaa exilispinosa) and the Hong Kong Cascade Frog (Amolops hongkongensis); and two types of environmental microbiota samples (water and sediment) across seven sites. I adopt a compositional data analysis approach for robust statistical analysis to address the following research question. In this thesis, I aim to gain a better understanding of wildlife microbiome, using amphibian as a study system. I hope that the results will highlight the importance of microbiome research, serve as a model for future studies, and assist in amphibian conservation.

In Chapter 1, I present a literature review summarising findings of recent microbiome studies — methodologies, analytical approaches, and major findings. In Chapter 2, I first characterise the microbiota of two local frog species (Q. exilispinosa and A. hongkongensis), followed by investigate the impact of common factors on amphibian microbiota — species identity, locality, and the environment. I found species identity is an important factor driving amphibian microbiota, but not for small intestinal microbiota. Locality has a non-significant effect on amphibian microbiota across the seven sampling sites in Hong Kong, presumably due to the relatively narrow geographic range of my study. Lastly, I found the environment (water and sediment) had significant difference with amphibian microbiota, raising the possibility that rare taxa in the environment can colonise and dominate on the host. In Chapter 3, I validate two intestinal sampling strategy in amphibians. Firstly, the use of faecal sample as an intestinal microbiota proxy — a widely used, but recently heavily criticised sampling methodology. I found that faeces only partially represent microbial profile and community structure in both the small and large intestine. The result raises caution on equating faecal and intestinal microbiota, interpretation should be made carefully. Secondly, I evaluate the risk of undigested material contaminating intestinal samples. In the comparison of undigested content with faeces showed a significant difference in community structure, emphasising the necessity of removing undigested content when sampling intestinal microbiota. In Chapter 4, I summarise the major findings of each chapter, then discuss the application of microbiome studies to amphibian conservation. Hong Kong has a limited foundation in the study and application of microbiota research to conservation, and I hope my work highlights the importance and stimulates the adoption of such approaches.

Date of Award30 Aug 2022
Original languageEnglish
Awarding Institution
  • Lingnan University
SupervisorJonathan FONG (Supervisor)

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