Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
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# Something-in-the-Water 1. Title: **Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior** 2. Author Information A. Principal Investigator Contact Information Name: Dr. Sarah Woodley Institution: Duquesne University Address: Pittsburgh, PA USA Email: B. Associate or Co-investigator Contact Information Name: Kyle Emerson Institution: Duquesne University Address: Pittsburgh,PA USA Email: 3. Date of data collection (single date, range, approximate date): 2021-2022 4. Geographic location of data collection: Pittsburgh, PA USA 5. Information about funding sources that supported the collection of the data: NIH grant P51 OD011092 for operation of the Oregon National Primate Research Center. ## SHARING/ACCESS INFORMATION 1. Links to publications that cite or use the data: Emerson, Kyle; Woodley, Sarah (Forthcoming 2024). Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior. Proceedings of the Royal Society B. 1. Recommended citation for this dataset: Emerson, Kyle; Woodley, Sarah (Forthcoming 2024). Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior [Dataset]. Dryad. ## DATA & FILE OVERVIEW 1. File List: A) Emerson_2023_data.xlsx B) Emerson - Sheet Information.csv C) Emerson - metadata.csv D) Emerson - Baseline Behavior.csv E) Emerson - Empty Vial Behavior.csv F) Emerson - Vial With Food Behavior.csv G) Emerson - Food Slurry Behavior.csv 1. Relationship between files, if important: File A is the entire data set. File B contains all of the abbreviations used in the data files. Files D - G are separate files for behavioral assays. 2. Additional related data collected that was not included in the current data package: None 3. Are there multiple versions of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the file updated? NA ii. When was the file updated? NA ## DATA-SPECIFIC INFORMATION FOR: Emerson - metadata.csv 1. Number of variables: 40 2. Number of cases/rows: 72 3. Variable List: * Microbial_Trtmt: Whether tadpoles were raised in Natural pond water (1) or autoclaved pond water (2) * Replicate: What bin they were housed in * Date_Euthanized: Date of euthanasia after dependent variable collection * Date_Died: Date a tadpole naturally died during the experiment * Corticosterone: Plasma Corticosterone levels (ng/mL) * TW: Telencephalon Width (mm) * TL: Telencephalon Length (mm) * OTW: Optic Tectum Width (mm) * OTL: Optic Tectum Length (mm) * DW: Diencephalon Width (mm) * DL: Diencephalon Length (mm) * MW: Medulla Width (mm) * RC1 - RC3: Principal Components 1-3 (PCs) calculated for Relative Brain Shape using Principal Component Analysis * ASV: Amplicon Sequence Variants calculated for the gut microbiota * Shannon: Shannon Diversity Index calculated for the gut microbiota * Faiths: Faith's Phylogenetic Diversity calculated for the gut microbiota * VisEmpty_RC1 - RC3: Principal Components 1-3 (PCs) calculated for tadpole behavioral responses during the Empty Vial test using Principal Component Analysis * VisFood_RC1 - RC3: Principal Components 1-3 (PCs) calculated for tadpole behavioral responses during the Vial filled with Frog Brittle test using Principal Component Analysis. * Olfactory_RC1 - RC3: Principal Components 1-3 (PCs) calculated for tadpole behavioral responses during the Food Slurry test using Principal Component Analysis. 1. Missing data codes: None 2. Specialized formats or other abbreviations used: None ## DATA-SPECIFIC INFORMATION FOR: Emerson - Baseline Behavior.csv, Emerson - Empty Vial Behavior.csv, Emerson - Vial with Food Behavior. csv, and Emerson - Food Slurry Behavior.csv 1. Number of variables: 40 2. Number of cases/rows: 20 3. Variable List: * Microbial_Trtmt: Whether tadpoles were raised in Natural pond water (1) or autoclaved pond water (2) * Av. Speed: Average Speed of tadpoles during behavioral test * Mob. Av. Speed: Average speed of tadpoles when mobile during behavioral test * Average Accel: Average acceleration of tadpoles during behavioral test * Mobility Rate: Percentage of time mobile of tadpoles during behavioral test * Visible Frames: Number of video frames in which the tadpole was visible during the behavioral test. * Invisible Frames: Number of video frames in which the tadpole was invisible during the behavioral test. * Explored areas: Number of different segmented areas tadpoles entered during the behavioral test. * Exploration Rate: Percentage of total areas tadpoles entered during the behavioral test. * Total Distance: Total distance a tadpole traveled during a behavioral test. * Frozen Events: Number of instances that a tadpole was not moving for longer than one cumulative second during a behavioral test. * Total Time Frozen: Total time a tadpole spent stationary during a behavioral test. * Average time frozen: Average amount of cumulative time a tadpole spent stationary during a behavioral test. * Time in Center: Total time a tadpole spent in an area of the arena that was not adjacent to the walls of the arena during a behavioral test. * Time near object/cue: Time a tadpole spent in the same area as an added visual or olfactory cue during a behavioral test. 1. Missing data codes: None 2. Specialized formats or other abbreviations used: None ## Abstract and Further Experimental Information We tested the hypothesis that larval amphibian neurodevelopment is affected by the aquatic microbial community present in their housing water. Newly hatched Northern Leopard Frog (*Lithobates pipiens*) tadpoles were raised in pond water that was unmanipulated (natural) or autoclaved. Tadpoles raised in autoclaved pond water had a gut microbiota with reduced bacterial diversity and altered community composition, had decreased behavioral responses to sensory stimuli, were larger in overall body mass, had relatively heavier brains, and had altered brain shape when compared with tadpoles raised in natural pond water. Further, the diversity and composition of the gut microbiota were associated with tadpole behavioral responses and brain measurements. Our results suggest that aquatic microbial communities shape tadpole behavior and brain development, providing strong support for the occurrence of the MGB axis in amphibians. Lastly, the dramatic role played by aquatic microbial communities on vertebrate neurodevelopment and behavior should be considered in future wildlife conservation efforts.
# 水中微生物 1. 标题：**水生微生物群落影响两栖动物幼体的肠道菌群、神经发育与行为** 2. 作者信息 A. 项目负责人联系方式 姓名：Sarah Woodley博士 机构：杜肯大学（Duquesne University） 地址：美国宾夕法尼亚州匹兹堡市 邮箱： B. 副研究员/合作研究者联系方式 姓名：Kyle Emerson 机构：杜肯大学 地址：美国宾夕法尼亚州匹兹堡市 邮箱： 3. 数据收集日期：2021年-2022年 4. 数据收集地理区域：美国宾夕法尼亚州匹兹堡市 5. 数据收集资助信息：由美国国立卫生研究院（NIH）资助的俄勒冈国家灵长类研究中心运营项目P51 OD011092支持。 ## 共享/获取信息 1. 引用或使用本数据的出版物链接：Emerson, Kyle; Woodley, Sarah (2024年待刊). 《水中微生物：水生微生物群落影响两栖动物幼体的肠道菌群、神经发育与行为》. 《英国皇家学会学报B辑》. 2. 本数据集推荐引用格式：Emerson, Kyle; Woodley, Sarah (2024年待刊). 水中微生物：水生微生物群落影响两栖动物幼体的肠道菌群、神经发育与行为 [数据集]. Dryad. ## 数据与文件概览 1. 文件列表： A) Emerson_2023_data.xlsx B) Emerson - Sheet Information.csv C) Emerson - metadata.csv D) Emerson - Baseline Behavior.csv E) Emerson - Empty Vial Behavior.csv F) Emerson - Vial With Food Behavior.csv G) Emerson - Food Slurry Behavior.csv 1. 文件间关联（若有重要关联）：文件A为完整数据集；文件B包含所有数据文件中使用的缩写；文件D至G为行为学测定的独立文件。 2. 当前数据包未包含的额外相关收集数据：无 3. 本数据集是否存在多个版本：否 A. 若是，请列出更新的文件：不适用 i. 文件更新原因：不适用 ii. 文件更新时间：不适用 ## 针对Emerson - metadata.csv的特定数据信息 1. 变量数量：40个 2. 样本/行数：72条 3. 变量列表： * 微生物处理组（Microbial_Trtmt）：蝌蚪饲养于天然池塘水(1)还是高压灭菌池塘水(2) * 重复组编号（Replicate）：蝌蚪饲养所在的饲养箱编号 * 处死日期（Date_Euthanized）：完成因变量采集后的处死日期 * 自然死亡日期（Date_Died）：实验期间蝌蚪自然死亡的日期 * 皮质酮（Corticosterone）：血浆皮质酮浓度（ng/mL） * 端脑宽度（TW, Telencephalon Width）：端脑宽度（mm） * 端脑长度（TL, Telencephalon Length）：端脑长度（mm） * 视顶盖宽度（OTW, Optic Tectum Width）：视顶盖宽度（mm） * 视顶盖长度（OTL, Optic Tectum Length）：视顶盖长度（mm） * 间脑宽度（DW, Diencephalon Width）：间脑宽度（mm） * 间脑长度（DL, Diencephalon Length）：间脑长度（mm） * 延髓宽度（MW, Medulla Width）：延髓宽度（mm） * RC1-RC3：基于主成分分析（Principal Component Analysis, PCA）计算的相对脑形态主成分1-3 * ASV（扩增子序列变异, Amplicon Sequence Variants）：肠道菌群的扩增子序列变异数据 * Shannon多样性指数（Shannon Diversity Index）：肠道菌群的Shannon多样性指数 * Faith系统发育多样性（Faith's Phylogenetic Diversity）：肠道菌群的Faith系统发育多样性 * VisEmpty_RC1-RC3：基于主成分分析计算的空瓶试验中蝌蚪行为反应的主成分1-3 * VisFood_RC1-RC3：基于主成分分析计算的装有食物的瓶子试验中蝌蚪行为反应的主成分1-3 * Olfactory_RC1-RC3：基于主成分分析计算的食物匀浆试验中蝌蚪行为反应的主成分1-3 1. 缺失数据编码：无 2. 使用的特殊格式或缩写：无 ## 针对Emerson - Baseline Behavior.csv、Emerson - Empty Vial Behavior.csv、Emerson - Vial with Food Behavior.csv及Emerson - Food Slurry Behavior.csv的特定数据信息 1. 变量数量：40个 2. 样本/行数：20条 3. 变量列表： * 微生物处理组（Microbial_Trtmt）：蝌蚪饲养于天然池塘水(1)还是高压灭菌池塘水(2) * 平均移动速度（Av. Speed）：行为学试验期间蝌蚪的平均移动速度 * 移动时段平均速度（Mob. Av. Speed）：行为学试验期间蝌蚪处于移动状态时的平均速度 * 平均加速度（Average Accel）：行为学试验期间蝌蚪的平均加速度 * 移动率（Mobility Rate）：行为学试验期间蝌蚪处于移动状态的时间占比 * 可见帧数（Visible Frames）：行为学试验视频中蝌蚪可见的帧数 * 不可见帧数（Invisible Frames）：行为学试验视频中蝌蚪不可见的帧数 * 探索区域数（Explored areas）：行为学试验期间蝌蚪进入的不同分割区域数量 * 探索率（Exploration Rate）：行为学试验期间蝌蚪进入的区域占总区域的百分比 * 总移动距离（Total Distance）：行为学试验期间蝌蚪的总移动距离 * 静止事件数（Frozen Events）：行为学试验期间蝌蚪单次静止时长超过1秒的事件次数 * 总静止时长（Total Time Frozen）：行为学试验期间蝌蚪的总静止时长 * 平均静止时长（Average time frozen）：行为学试验期间蝌蚪每次静止的平均累计时长 * 中心区域停留时间（Time in Center）：行为学试验期间蝌蚪在试验箱非邻壁中心区域的停留总时长 * 线索区域停留时间（Time near object/cue）：行为学试验期间蝌蚪在添加的视觉或嗅觉线索所在区域的停留总时长 1. 缺失数据编码：无 2. 使用的特殊格式或缩写：无 ## 摘要与补充实验信息 本研究验证假说：两栖动物幼体的神经发育会受到其饲养水体中水生微生物群落的调控。将新孵化的北方豹蛙（*Lithobates pipiens*）蝌蚪分别饲养于未处理（天然）或高压灭菌的池塘水中。与饲养于天然池塘水的蝌蚪相比，高压灭菌池塘水饲养的蝌蚪肠道菌群细菌多样性降低、群落组成改变，对感官刺激的行为反应减弱，整体体型更大，相对脑重更高，且脑形态发生改变。此外，肠道菌群的多样性与组成与蝌蚪的行为反应及脑测量指标显著相关。本研究结果表明，水生微生物群落可塑造蝌蚪的行为与脑发育，为两栖动物存在微生物-肠-脑轴（Microbiota-Gut-Brain axis, MGB轴）提供了强有力的实验证据。最后，水生微生物群落对脊椎动物神经发育与行为的显著调控作用，应在未来野生动物保护工作中予以重视。
