Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, México.
Laboratorio de Biología Marina, Departamento de Zoología, Universidad de Sevilla, Avda. Reina Mercedes, 6, 41012, Sevilla, Spain.
Antonie Van Leeuwenhoek. 2021 Dec;114(12):2163-2174. doi: 10.1007/s10482-021-01670-z. Epub 2021 Oct 19.
Members of the proposed phylum 'Candidatus Poribacteria' are among the most abundant microorganisms in the highly diverse microbiome of the sponge mesohyl. Genomic and phylogenetic characteristics of this proposed phylum are barely known. In this study, we analyzed metagenome-assembled genomes (MAGs) obtained from the coral reef excavating sponge Thoosa mismalolli from the Mexican Pacific Ocean. Two MAGs were extracted and analyzed together with 32 MAGs and single-amplified genomes (SAGs) obtained from NCBI. The phylogenetic tree based on the sequences of 139 single-copy genes (SCG) showed two clades. Clade A (23 genomes) represented 67.7% of the total of the genomes, while clade B (11 genomes) comprised 32.3% of the genomes. The Average Nucleotide Identity (ANI) showed values between 66 and 99% for the genomes of the proposed phylum, and the pangenome of genomes revealed a total of 37,234 genes that included 1722 core gene. The number of genes used in the phylogenetic analysis increased from 28 (previous studies) to 139 (this study), which allowed a better resolution of the phylogeny of the proposed phylum. The results supported the two previously described classes, 'Candidatus Entoporibacteria' and 'Candidatus Pelagiporibacteria', and the genomes SB0101 and SB0202 obtained in this study belong to two new species of the class 'Candidatus Entoporibacteria'. This is the first comparative study that includes MAGs from a non-sponge host (Porites lutea) to elucidate the taxonomy of the poorly known Candidatus phylum in a polyphasic approach. Finally, our study also contributes to the sponge microbiome project by reporting the first MAGs of the proposed phylum 'Candidatus Poribacteria' isolated from the excavating sponge T. mismalolli.
拟门“Candidatus Poribacteria”的成员是海绵中层高度多样化微生物组中最丰富的微生物之一。这个拟门的基因组和系统发育特征几乎未知。在这项研究中，我们分析了从墨西哥太平洋的珊瑚礁挖掘海绵 Thoosa mismalolli 获得的宏基因组组装基因组（MAGs）。提取了两个 MAGs，并与从 NCBI 获得的 32 个 MAGs 和单扩增基因组（SAGs）一起进行了分析。基于 139 个单拷贝基因（SCG）序列构建的系统发育树显示了两个分支。A 分支（23 个基因组）代表了总基因组的 67.7%，而 B 分支（11 个基因组）占总基因组的 32.3%。平均核苷酸同一性（ANI）显示，拟门基因组之间的数值在 66%到 99%之间，而基因组的泛基因组则显示共有 37234 个基因，其中包括 1722 个核心基因。系统发育分析中使用的基因数量从 28 个（先前的研究）增加到 139 个（本研究），这使得拟门的系统发育得到了更好的解析。结果支持了先前描述的两个纲，“Candidatus Entoporibacteria”和“Candidatus Pelagiporibacteria”，并且本研究中获得的 SB0101 和 SB0202 基因组属于“Candidatus Entoporibacteria”纲的两个新种。这是第一项包括非海绵宿主（Porites lutea）的 MAGs 的比较研究，通过多相方法阐明了在多相方法中了解甚少的拟门的分类。最后，我们的研究还通过报告从挖掘海绵 T. mismalolli 中分离出的拟门“Candidatus Poribacteria”的第一个 MAGs，为海绵微生物组项目做出了贡献。
