The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.
The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.
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DOI：
10.1371/journal.pone.0200437
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Trindade-Silva AE
中科院分区：
文献类型：
--
作者：
Brito TL;Campos AB;Bastiaan von Meijenfeldt FA;Daniel JP;Ribeiro GB;Silva GGZ;Wilke DV;de Moraes DT;Dutilh BE;Meirelles PM;Trindade-Silva AE
Teredinidae是一种高度适应性的食木和钻木双壳类动物，通常被称为船虫，其进化与获得在鳃内的细菌细胞中窝藏的纤维素水解γ -变形细菌共生体有关。在目前的工作中，我们应用宏基因组学来表征neteredo reynei的鳃和消化道的微生物组，neteredo reynei是一种在巴西海岸广泛发现的适应红树林的船虫物种。比较宏基因组学对不同棘球绦虫标本的鳃共生体群落进行了分组，表明密切相关的细菌类型是共享的。同样，肠道和消化腺群落是相关的，但比鳃群落更多样化，也没有重叠。对组装的宏基因组序列的注释表明，该菌鳃共生群落编码大量的植物细胞壁多糖降解糖苷水解酶编码基因和生物合成基因簇（BGCs）。相比之下，消化道微生物组在木材消化和次生代谢物的生物合成中似乎起不到什么作用。Metagenome binning从鳃中恢复了两个共生Teredinibacter菌株的几乎完整的基因组序列，其中一个是Teredinibacter turnerae“clade I”菌株的代表，另一个是尚未培养的Teredinibacter属类型。这些teredinibacterium基因组，以及未分类的鳃源γ变形菌群，还包括一个内切-β-1,4-木聚糖酶/乙酰木聚糖酯酶多催化糖活性酶，以及一个反式酰基转移酶聚酮合成酶（trans-AT PKS）基因簇，该基因簇具有在复杂聚酮上产生β分支的基因盒。最后，我们使用多变量分析表明，Teredinibacter代表菌基因组的次级代谢组，包括本文中从N. reynei鳃的宏基因组中提取的基因组，在Cellvibrionaceae家族中以大小和富集的聚酮、非核糖体肽和杂交bgc而突出。本文的研究结果进一步证实了船虫共生微生物群的特征，并表明了N. reynei gill γ -变形菌群落是木材消化和生物活性化合物生产的生物技术相关酶的丰富来源。
Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae “clade I” strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills’ metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.
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影响因子：
4.9
作者：
Altamia MA;Wood N;Fung JM;Dedrick S;Linton EW;Concepcion GP;Haygood MG;Distel DL
通讯作者：
Distel DL
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.4
作者：
Distel, DL;Beaudoin, DJ;Morrill, W
通讯作者：
Morrill, W
DOI：
10.1073/pnas.1620470114
发表时间：
2017-05-02
影响因子：
11.1
作者：
Distel, Daniel L.;Altamia, Marvin A.;Haygood, Margo G.
通讯作者：
Haygood, Margo G.
影响因子：
2.7
作者：
Kang DD;Froula J;Egan R;Wang Z
通讯作者：
Wang Z