Ijaz Umer Zeeshan, Sivaloganathan Lojika, McKenna Aaron, Richmond Anne, Kelly Carmel, Linton Mark, Stratakos Alexandros Ch, Lavery Ursula, Elmi Abdi, Wren Brendan W, Dorrell Nick, Corcionivoschi Nicolae, Gundogdu Ozan
School of Engineering, University of Glasgow, Glasgow, United Kingdom.
Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
Front Microbiol. 2018 Oct 15;9:2452. doi: 10.3389/fmicb.2018.02452. eCollection 2018.
Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of , how and when appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and . Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby can appear. was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of within the food chain.
鸡是人类重要的食物来源，但其微生物群中含有对人类致病的细菌，甚至对鸡本身也可能致病。这种细菌存在于鸡的肠道内，是全球人类细菌性食源性肠胃炎的主要病因。感染可导致继发性后遗症，如吉兰 - 巴雷综合征，以及资源匮乏地区儿童生长发育迟缓。尽管这种细菌对全球健康有影响且造成经济负担，但它如何以及何时在鸡体内出现仍不清楚。缺乏具有重复样本的日常微生物群数据、相关元数据以及自然感染研究，阻碍了我们对鸡肠道微生物群和这种细菌的了解。在此，我们对鸡盲肠从第3天到第35天进行了全面的日常微生物群分析（每天12个重复样本；最终n = 379）。我们结合了鸡体重和饲料转化率等元数据，以研究随着时间推移鸡肠道内微生物变化的驱动因素，以及这与在自然栖息地环境中该细菌出现的关系。我们发现，在第12天之前微生物多样性迅速增加，在属和丰度方面都有变化，之后在第20天微生物多样性趋于稳定。特别是，我们发现从第12天到第20天，微生物群落的驱动因素从竞争性转变为环境性，从而创造了该细菌可能出现的机会窗口。在第16天发现了这种细菌，这是在观察到代谢谱最显著变化后的1天。此外，微生物随时间的变化很可能受鸡的饮食影响，样本的OTU丰度和β离散度的显著变化往往与饲料变化相对应。与最近的研究相比，本研究具有独特性，因为采样既不是零星的，也没有人工引入该细菌，因此实验是在自然环境中进行的。我们相信我们的发现对未来的干预策略可能有用，并有助于减轻食物链中该细菌造成的负担。
