Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function.
Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function.
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DOI：
10.3389/fmicb.2018.01073
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发表时间：
2018
影响因子：
5.2
通讯作者：
Small BC
中科院分区：
文献类型：
--
作者：
Bledsoe JW;Waldbieser GC;Swanson KS;Peterson BC;Small BC
在过去的十年里，硬骨鱼的微生物区系得到了极大的研究关注，实验表明，宿主遗传和环境都是塑造鱼类微生物区系细菌组合的强大生态力量。尽管具有重要的商业和科学价值，但斑点叉尾鱼，特别是蓝点叉尾叉尾和斑点叉尾鱼，特别是蓝点叉尾和斑点叉尾在这项研究中，我们利用通过微卫星基因分型验证的多个遗传上不同的蓝点叉尾鱼品系，进一步量化宿主遗传学在塑造鱼类肠道细菌群落中的作用，同时保持环境和饲养参数不变。根据Mantel检验，两个物种之间肠道微生物区系的比较显示，细菌物种丰富度(观察值和Chao1)或总组成(加权和未加权UniFrac)没有差异，UniFrac距离与宿主遗传距离(RST)没有相关性。环境样品(食物和水)的微生物区系明显比与鲶鱼肠道相关的样品多样化，这表明宿主内部的因素正在进一步调节细菌群落，尽管微生物区系组成和宿主基因型之间缺乏明确的联系。梭杆菌门、变形杆菌门和梭状芽胞杆菌门是叉尾鱼肠道群落的优势种；然而，通过微生物群落组成的分析对这两种叉尾鱼进行差异丰度分析，发现了两个不同的属，即蜡样杆菌属和梭状芽胞杆菌属。从我们的数据集推断的元基因组途径特征表明，鲶鱼肠道细菌群落具有有利于宿主的途径，如那些参与营养代谢和抗微生物生物合成的途径，同时也包含与病原体毒力因子有关的途径。DESeq2对推测的KEGG(京都基因和基因组百科全书)途径的测试表明，微生物区系功能略有不同，只有两种不同物种之间检测到差异丰富的元基因组途径。作为第一个研究蓝点叉尾鱼肠道微生物区系特征的研究，我们的研究结果对未来蓝点叉尾鱼的研究具有直接的意义。此外，我们对驱动微生物区系结构的内在因素的洞察对于未来鱼类肠道微生物区系的研究具有基本的意义。
The microbiota of teleost fish has gained a great deal of research attention within the past decade, with experiments suggesting that both host-genetics and environment are strong ecological forces shaping the bacterial assemblages of fish microbiomes. Despite representing great commercial and scientific importance, the catfish within the family Ictaluridae, specifically the blue and channel catfish, have received very little research attention directed toward their gut-associated microbiota using 16S rRNA gene sequencing. Within this study we utilize multiple genetically distinct strains of blue and channel catfish, verified via microsatellite genotyping, to further quantify the role of host-genetics in shaping the bacterial communities in the fish gut, while maintaining environmental and husbandry parameters constant. Comparisons of the gut microbiota among the two catfish species showed no differences in bacterial species richness (observed and Chao1) or overall composition (weighted and unweighted UniFrac) and UniFrac distances showed no correlation with host genetic distances (Rst) according to Mantel tests. The microbiota of environmental samples (diet and water) were found to be significantly more diverse than that of the catfish gut associated samples, suggesting that factors within the host were further regulating the bacterial communities, despite the lack of a clear connection between microbiota composition and host genotype. The catfish gut communities were dominated by the phyla Fusobacteria, Proteobacteria, and Firmicutes; however, differential abundance analysis between the two catfish species using analysis of composition of microbiomes detected two differential genera, Cetobacterium and Clostridium XI. The metagenomic pathway features inferred from our dataset suggests the catfish gut bacterial communities possess pathways beneficial to their host such as those involved in nutrient metabolism and antimicrobial biosynthesis, while also containing pathways involved in virulence factors of pathogens. Testing of the inferred KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways by DESeq2 revealed minor difference in microbiota function, with only two metagenomic pathways detected as differentially abundant between the two catfish species. As the first study to characterize the gut microbiota of blue catfish, our study results have direct implications on future ictalurid catfish research. Additionally, our insight into the intrinsic factors driving microbiota structure has basic implications for the future study of fish gut microbiota.
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影响因子：
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作者：
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DOI：
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发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
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de Hoon MJ
影响因子：
3.7
作者：
Iwai S;Weinmaier T;Schmidt BL;Albertson DG;Poloso NJ;Dabbagh K;DeSantis TZ
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DeSantis TZ
影响因子：
12.3
作者：
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通讯作者：
Zhang J