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养猪发酵床微生物宏基因组基本分析方法 总被引:5,自引:0,他引:5
养猪微生物发酵床分解猪粪、消除恶臭,将猪粪形成生物菌肥,实现了养猪污染的微生物治理和猪粪的资源化利用,微生物起到关键作用。然而,关于发酵床微生物群落的种类、数量、结构等方面系统研究鲜见报道。课题组采用高通量宏基因组学方法,系统地开展了微生物发酵床的微生物组研究,揭示不同空间、不同深度、不同发酵程度、不同垫料组成、不同季节发酵床中的微生物组成及其区系演替规律。本文就相关的宏基因组测序的样本采集、样本处理、测序原理、分析模型、数据统计、结果表述等分析流程和方法进行了归纳,阐明微生物组操作分类单元(OTU)鉴定,物种累积曲线,核心微生物组,种类丰度主成分分析,种类秩-多度曲线,物种组成丰度柱状图、热图、星图等分析的原理与方法,列举微生物组种类复杂度α-多样性分析、β-多样性分析、种类显著性差异LEfSe分析,冗余分析等实例,为深入研究发酵床微生物群落提供了完整的分析思路和范例。 相似文献
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Javier Rocha-Martin Catriona Harrington Alan D.W. Dobson Fergal O’Gara 《Marine drugs》2014,12(6):3516-3559
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds. 相似文献
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Opportunistic pathogens are abundant in the gut of cultured giant spiny frog (Paa spinosa) 下载免费PDF全文
Jianguo Xiang Tuoyu He Pengpeng Wang Min Xie Jing Xiang Jiajia Ni 《Aquaculture Research》2018,49(5):2033-2041
Pathogen infection poses a serious threat to the survival and commercial quality of cultured Paa spinosa, which provide protection as a substitute for wild P. spinosa. The gut microbiota plays vital roles in host health and immunity. To provide guidance for preventing intestinal diseases of artificial P. spinosa culture, we compared gut microbiota compositions of wild and cultured P. spinosa using high‐throughput sequencing. A total of 11,526 operational taxonomic units (OTUs) were identified from 14,043 sequences from each sample. Cetobacterium, PW3 Bacteroides and some unidentified species from Bacteroidales, Rikenellaceae and Clostridiales were significantly increased in the gut microbiota from cultured P. spinosa, whereas Faecalibacterium and unidentified bacteria from Ruminococcaceae were significantly decreased in the gut microbiota from cultured P. spinosa. According to the gut microbiota composition, we hypothesized that the cultured P. spinosa in Jing'an would exhibit a higher risk of pathogenic infection than those in Cili. These results provided a method to forecast the pathogenic infection risk of cultured P. spinosa, which could guide the artificial culture of and prevent diseases in P. spinosa through gut microbiota. 相似文献
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Heike Schmidt-Posthaus Michel Koch Torsten Seuberlich Christoph Birrer Regula Hirschi Michael Kugler 《Journal of fish diseases》2020,43(10):1317-1324
Since 2016, annually occurring species-specific die-offs of brown trout (Salmo trutta fario) occurred in the Thur River, situated in the Eastern part of Switzerland. These events lead to drastically reduced population densities in the impacted river regions. Clinical signs in brown trout and mortality were restricted to few weeks in August/September. To characterize the syndrome and to find possible causes, from end of March to November 2018, one-year-old brown trout (Salmo trutta fario) and rainbow trout (Oncorhynchus mykiss) were exposed to water from Thur River, fish were sampled regularly and screened for infectious agents, including viral metagenomics, and pathology was described. Starting approximately four months post-exposure, brown trout showed severe lymphohistiocytic pancarditis and necrotizing and haemorrhagic hepatitis. These lesions were recorded until the end of the experiment in November. Rainbow trout were not affected at any point in time. No infectious agents could be identified so far as cause of disease, especially no viral aetiology. Even if pathogenesis and pathology point in the direction of an infectious agent, a causative relationship could not be confirmed and aetiology remains unclear. 相似文献
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Qing Liu Teng Li Lin Chen Sai Zhang Yingxing Zhao Yuanquan Chen Jin Liu Wangsheng Gao Peng Sui 《European Journal of Soil Science》2023,74(5):e13410
Intensive cropping is considered to contribute to negative effects both on soil physiochemical properties and on long-term grain yield, which can be alleviated by appropriate crop rotations. The soil microbial community can vary with different crop rotations, which in turn affect soil quality and grain yield. Therefore, it is of great significance to elucidate the response of the soil microbial community to crop rotation. In this study, the structural and functional changes of microbial community in different crop rotations were analyzed using high-throughput sequencing and metagenomics analysis in a field experiment. The continuous winter wheat-summer maize cropping system was the control, and three crop rotations were established in October 2016 as follows: (1) spring peanut→winter wheat-summer maize, (2) winter wheat-summer peanut→winter wheat-summer maize and (3) spring sweet potato→winter wheat-summer maize. Soil samples were collected in September 2021 for soil microbial assessment. The results showed that the relative abundance of Actinobacteriota in the soil of spring sweet potato→winter wheat-summer maize was significantly higher (15.2%) than that in the control. The relative abundance of Ascomycota was significantly higher (19.8%–23.2%) in the soil following crop rotation compared with the control. Compared with the control, spring peanut→winter wheat-summer maize enriched energy metabolism genes, and spring sweet potato→winter wheat-summer maize reduced the genes related to plant–pathogen interaction. Compared with the control, crop rotation significantly decreased the relative abundance of the inorganic phosphorus solubilization gene (gcd) and the phosphorus transport gene (upgE) and increased the abundance of organic phosphorus mineralization genes (phoA and phyA). Based on these results, we concluded that the composition of the soil microbial community and functional genes can be altered by crop rotation, and spring peanut→winter wheat-summer maize and spring sweet potato→winter wheat-summer maize had more significant effects. This study provided a reference for the selection of crop rotations in the North China Plain based on the soil microbial community and its function. 相似文献