In the late 1800s,Robert Koch and Fredrich Loefflerlaid out guidelines for identifying which microbe was the causative agent of a specific disease. It follows then that diagnostics are targeted towards specific, known pathogens and are often developed to identify a particular species of pathogen or parasite.
But how are infectious agents studied when we don’t know what they are? For many non-human hosts, we lack an understanding of the microbes that cause disease. New sequencing technology that enables genetic characterization WITHOUT prior knowledge of what is there has lead to a dramatic increase in our understanding of the diversity and evolution of microbes.
我们会关注recent study利用这一点metagenomicsto study whole communities of microbes found in waterbird fecal samples. Characterizing the genetics of a whole community of microbes is only possible because sequencing technology allows unbiased characterization (i.e. non-targeted) and prices are falling dramatically.
Study design
Scientists aimed to quantify and characterize eukaryotic and microeukaryotic organisms in fecal samples collected from a diversity of migratory waterbirds (ducks, geese, gulls, shorebirds). They were interested in the organisms that may infect the birds themselves but also what organisms may be dispersed by migratory birds.
他们总共收集了西班牙西南部两个国家公园的27个人的粪便样本。九种不同的鸟类贡献了样品 - 包括邓林，欧亚wigeon和Great Cormorant。这些代表了共享类似的多种鸟类。从每个样品中提取DNA - 直接测序提取的DNA的一部分，并进一步处理另一部分以扩增和靶向特定基因。第二种方法的好处是您可以增加细菌的检测，但会导致微生物多样性的评估偏见。除了确定每个样品中的内容外，宏基因组学允许科学家通过比较遗传序列来确定相关生物的紧密相关。
Findings
- The DNA from lots of diverse microorganisms were found, including: nematodes, digenean, and cestodes.
- Most of the identified organisms reflect the diet (i.e. chromodorean nematode sequences in fish-eating species, algae and plants in ducks)
- Microsporidia were only found in Dunlin and ducks, but quite common
- Primer-amplified sequencing data revelaed more and new diversity with a specific group, but biased the dataset
- There were many similar microbes between the different bird species, but also some that were unique. Shared microbes may likely reflect a shared environment and similar diets.
What next?
New sequencing technology has revolutionized how we study diverse microbe communities in wild populations. This study demonstrates that metagenomics and fecal samples can be used to characterize diversity in wild birds and future studies can build on this to understand how this changes over time and in different environments.
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