Pinpointing the microbiota of tardigrades: What is really there?,Environmental Microbiology

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Pinpointing the microbiota of tardigrades: What is really there?
Environmental Microbiology ( IF 4.3 ) Pub Date : 2024-06-20 , DOI: 10.1111/1462-2920.16659
Bartłomiej Surmacz _{1,

2,

3} , Daniel Stec _{2,

4} , Monika Prus-Frankowska ₅ , Mateusz Buczek ₅ , Łukasz Michalczyk ₂ , Piotr Łukasik ₅

Affiliation

Microbiota are considered significant in the biology of tardigrades, yet their diversity and distribution remain largely unexplored. This is partly due to the methodological challenges associated with studying the microbiota of small organisms that inhabit microbe‐rich environments. In our study, we characterized the microbiota of 31 species of cultured tardigrades using 16S rRNA amplicon sequencing. We employed various sample preparation strategies and multiple types of controls and estimated the number of microbes in samples using synthetic DNA spike‐ins. We also reanalysed data from previous tardigrade microbiome studies. Our findings suggest that the microbial communities of cultured tardigrades are predominantly composed of bacterial genotypes originating from food, medium, or reagents. Despite numerous experiments, we found it challenging to identify strains that were enriched in certain tardigrades, which would have indicated likely symbiotic associations. Putative tardigrade‐associated microbes rarely constituted more than 20% of the datasets, although some matched symbionts identified in other studies. We also uncovered serious contamination issues in previous tardigrade microbiome studies, casting doubt on some of their conclusions. We concluded that tardigrades are not universally dependent on specialized microbes. Our work underscores the need for rigorous safeguards in studies of the microbiota of microscopic organisms and serves as a cautionary tale for studies involving samples with low microbiome abundance.

中文翻译：

精确定位缓步动物的微生物群：到底有什么？

微生物群被认为在缓步动物的生物学中具有重要意义，但它们的多样性和分布在很大程度上仍未得到探索。这部分是由于研究栖息在微生物丰富的环境中的小生物体的微生物群相关的方法学挑战。在我们的研究中，我们使用 16S rRNA 扩增子测序对 31 种培养缓步动物的微生物群进行了表征。我们采用了各种样品制备策略和多种类型的对照，并使用合成 DNA 掺入物估算了样品中的微生物数量。我们还重新分析了之前缓步动物微生物组研究的数据。我们的研究结果表明，培养的缓步动物的微生物群落主要由源自食物、培养基或试剂的细菌基因型组成。尽管进行了大量实验，我们发现识别富含某些缓步动物的菌株具有挑战性，这表明可能存在共生关联。尽管在其他研究中发现了一些匹配的共生体，但假定的缓步动物相关微生物很少占数据集的 20% 以上。我们还在之前的缓步动物微生物组研究中发现了严重的污染问题，对他们的一些结论提出了质疑。我们得出的结论是，缓步动物并不普遍依赖于特殊的微生物。我们的工作强调了微生物微生物群研究中严格保障措施的必要性，并对涉及低微生物丰度样本的研究起到了警示作用。

更新日期：2024-06-20

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