Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.
Central European Institute of Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.
BMC Genomics. 2018 Jul 31;19(1):561. doi: 10.1186/s12864-018-4959-4.
In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.
Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla - Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation.
Major gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.
为了开始了解肠道微生物群个体成员的功能，我们从鸡盲肠中培养、测序和分析了细菌厌氧菌。
使用威尔金斯-查尔格兰厌氧菌琼脂和厌氧生长条件，从鸡盲肠中纯培养获得了总共 204 个分离株。使用 NextSeq 平台测定所有分离株的基因组，并进行生物信息学分析。在 204 个测序分离株中，我们鉴定出属于 7 个不同门的 133 个不同菌株 - 厚壁菌门、拟杆菌门、放线菌门、变形菌门、疣微菌门、互养菌门和互营菌门。基因组大小范围从 Elusimicrobium minutum 的 1.51 Mb 到 Bacteroides ovatus 的 6.70 Mb。基于编码蛋白基因的存在进行聚类表明，来自变形菌门、疣微菌门、互养菌门和互营菌门的分离株与其余分离株没有聚类。厚壁菌门分为乳杆菌科、肠球菌科、韦荣球菌科和梭菌目，其中产气荚膜梭菌分离株形成一个独特的亚群。所有拟杆菌门分离株形成一个单独的聚类，所有分离株的遗传组成相似，但与其他肠道厌氧菌不同。大多数放线菌紧密聚类，除了戈登氏菌属的代表外，该属的基因组与本研究中测序的其他放线菌不同。拟杆菌门的代表通常编码可使其与宿主相互作用的蛋白（胶原酶、血凝素、溶血素、透明质酸酶、肝素酶、软骨素酶、粘蛋白脱硫硫酸酯酶或谷氨酸脱羧酶）。在 Akkermansia 和 Cloacibacillus 中记录到了耐氧性，并且在拟杆菌门的代表中也很常见。另一方面，尽管具有形成孢子的潜力，但 Elusimicrobium 和大多数梭菌目对空气暴露非常敏感。
主要的肠道微生物群成员利用不同的策略进行肠道定植。厚壁菌门的高氧气敏感性可能解释了它们在肠道炎症期间氧化爆发后通常报道的减少。
