Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia.
Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia ; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia.
Gut Pathog. 2015 Feb 26;7:4. doi: 10.1186/s13099-015-0051-7. eCollection 2015.
Chicken gut microbiota has paramount roles in host performance, health and immunity. Understanding the topological difference in gut microbial community composition is crucial to provide knowledge on the functions of each members of microbiota to the physiological maintenance of the host. The gut microbiota profiling of the chicken was commonly performed previously using culture-dependent and early culture-independent methods which had limited coverage and accuracy. Advances in technology based on next-generation sequencing (NGS), offers unparalleled coverage and depth in determining microbial gut dynamics. Thus, the aim of this study was to investigate the ileal and caecal microbiota development as chicken aged, which is important for future effective gut modulation.
Ileal and caecal contents of broiler chicken were extracted from 7, 14, 21 and 42-day old chicken. Genomic DNA was then extracted and amplified based on V3 hyper-variable region of 16S rRNA. Bioinformatics, ecological and statistical analyses such as Principal Coordinate Analysis (PCoA) was performed in mothur software and plotted using PRIMER 6. Additional analyses for predicted metagenomes were performed through PICRUSt and STAMP software package based on Greengenes databases.
A distinctive difference in bacterial communities was observed between ilea and caeca as the chicken aged (P < 0.001). The microbial communities in the caeca were more diverse in comparison to the ilea communities. The potentially pathogenic bacteria such as Clostridium were elevated as the chicken aged and the population of beneficial microbe such as Lactobacillus was low at all intervals. On the other hand, based on predicted metagenomes analysed, clear distinction in functions and roles of gut microbiota such as gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism), and bacterial proliferation and colonization (e.g. bacterial motility proteins, two-component system and bacterial secretion system) were observed between ilea and caeca, respectively (P < 0.05).
The caeca microbial communities were more diverse in comparison to ilea. The main functional differences between the two sites were found to be related to nutrient absorption and bacterial colonization. Based on the composition of the microbial community, future gut modulation with beneficial bacteria such as probiotics may benefit the host.
鸡的肠道微生物群在宿主的表现、健康和免疫中起着至关重要的作用。了解肠道微生物群落组成的拓扑差异对于了解每个微生物成员的功能以维持宿主的生理功能至关重要。以前，鸡的肠道微生物组分析通常使用依赖培养和早期非依赖培养的方法进行，这些方法的覆盖范围和准确性有限。基于下一代测序（NGS）的技术进步，在确定肠道微生物动态方面提供了无与伦比的覆盖范围和深度。因此，本研究旨在研究随着鸡龄的增长，回肠和盲肠微生物群的发育情况，这对于未来有效的肠道调节很重要。
从 7、14、21 和 42 日龄的肉鸡中提取回肠和盲肠内容物。然后提取基因组 DNA，并基于 16S rRNA 的 V3 高变区进行扩增。在 mothur 软件中进行生物信息学、生态和统计分析，如主坐标分析（PCoA），并使用 PRIMER 6 进行绘图。基于 Greengenes 数据库，通过 PICRUSt 和 STAMP 软件包对预测的宏基因组进行额外分析。
随着鸡龄的增长（P<0.001），回肠和盲肠中的细菌群落存在明显差异。与回肠群落相比，盲肠中的微生物群落更加多样化。随着鸡龄的增长，潜在的致病性细菌（如梭菌）增加，而有益微生物（如乳杆菌）的数量在所有时间间隔都较低。另一方面，基于预测的宏基因组分析，观察到回肠和盲肠之间的肠道微生物群的功能和作用明显不同，例如与营养吸收相关的基因途径（例如糖和氨基酸代谢）以及细菌增殖和定植（例如细菌运动蛋白、二组分系统和细菌分泌系统）（P<0.05）。
与回肠相比，盲肠的微生物群落更加多样化。两个部位之间的主要功能差异与营养吸收和细菌定植有关。基于微生物群落的组成，未来使用益生菌等有益细菌进行肠道调节可能对宿主有益。
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