Discrete patterns of microbiome variability across timescales in a wild rodent population.
Discrete patterns of microbiome variability across timescales in a wild rodent population.
复制标题
DOI：
10.1186/s12866-023-02824-x
复制
发表时间：
2023-03-30
期刊：
影响因子：
4.2
通讯作者：
Bradley, Jan
中科院分区：
文献类型：
--
作者：
Fenn, Jonathan;Taylor, Christopher;Goertz, Sarah;Wanelik, Klara M. M.;Paterson, Steve;Begon, Mike;Jackson, Joe;Bradley, Jan
哺乳动物的胃肠道微生物组在个体内和群体间都是高度可变的，与时间和衰老有关的变化被广泛报道。因此，识别野生哺乳动物种群的变化模式可能具有挑战性。我们使用高通量的社区测序方法，从12个现场诱捕现场会议收集的粪便样本中检测野生田鼠（田鼠）的微生物组，然后在剔除。在三个时间尺度上模拟α和β多样性的变化。分析捕获和剔除之间的短期差异（1-2天圈养后），以确定环境快速变化后微生物组的变化程度。中期变化之间的连续诱捕会话（间隔12-16天），和长期变化之间的第一次和最终捕获的一个人（从24至129天）。捕获和扑杀之间的短期内的特点是物种丰富度的显着损失，而在中长期的领域，丰富度略有增加。在短时间和长时间尺度上的变化表明从厚壁菌占主导地位的微生物群转变为拟杆菌占主导地位的微生物群。圈养后的巨大变化表明，随着环境（食物来源、温度、光照等）的变化，微生物组多样性的变化可能很快。中期和长期的变化模式表明与衰老相关的肠道细菌的增加，这些新细菌主要由拟杆菌属代表。虽然观察到的变化模式不太可能普遍适用于野生哺乳动物种群，但在研究野生动物微生物组时，应考虑跨时间尺度类似变化的可能性。如果研究涉及动物圈养，尤其如此，因为对动物健康和数据本身作为动物“自然”状态的反映的有效性都有潜在的影响。 在线版本包含补充材料，可通过10.1186/s12866-023-02824-x获得。
Mammalian gastrointestinal microbiomes are highly variable, both within individuals and across populations, with changes linked to time and ageing being widely reported. Discerning patterns of change in wild mammal populations can therefore prove challenging. We used high-throughput community sequencing methods to characterise the microbiome of wild field voles (Microtus agrestis) from faecal samples collected across 12 live-trapping field sessions, and then at cull. Changes in α- and β-diversity were modelled over three timescales. Short-term differences (following 1–2 days captivity) were analysed between capture and cull, to ascertain the degree to which the microbiome can change following a rapid change in environment. Medium-term changes were measured between successive trapping sessions (12–16 days apart), and long-term changes between the first and final capture of an individual (from 24 to 129 days). The short period between capture and cull was characterised by a marked loss of species richness, while over medium and long-term in the field, richness slightly increased. Changes across both short and long timescales indicated shifts from a Firmicutes-dominant to a Bacteroidetes-dominant microbiome. Dramatic changes following captivity indicate that changes in microbiome diversity can be rapid, following a change of environment (food sources, temperature, lighting etc.). Medium- and long-term patterns of change indicate an accrual of gut bacteria associated with ageing, with these new bacteria being predominately represented by Bacteroidetes. While the patterns of change observed are unlikely to be universal to wild mammal populations, the potential for analogous shifts across timescales should be considered whenever studying wild animal microbiomes. This is especially true if studies involve animal captivity, as there are potential ramifications both for animal health, and the validity of the data itself as a reflection of a ‘natural’ state of an animal. The online version contains supplementary material available at 10.1186/s12866-023-02824-x.
登录
查看更多内容
DOI：
10.1073/pnas.1000080107
发表时间：
2011-03-15
影响因子：
11.1
作者：
Caporaso, J. Gregory;Lauber, Christian L.;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
64.8
作者：
Claesson, Marcus J.;Jeffery, Ian B.;O'Toole, Paul W.
通讯作者：
O'Toole, Paul W.
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
12.3
作者：
Caporaso JG;Lauber CL;Costello EK;Berg-Lyons D;Gonzalez A;Stombaugh J;Knights D;Gajer P;Ravel J;Fierer N;Gordon JI;Knight R
通讯作者：
Knight R
影响因子：
3.1
作者：
Bailey, Michael T.;Dowd, Scot E.;Lyte, Mark
通讯作者：
Lyte, Mark