Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs

Background:
Sesarmid crabs dominate mangrove habitat as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory is not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove forest ecosystems. Although endogenous cellulases expressions were reported in crab species, it remains unknown if the endogenous enzymes alone can complete the whole lignocellulolytic pathway, or they also depend on the contribution from their intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.
Results:
Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, inc..., , , # Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs.

[Access this dataset on Dryad](https://doi.org/10.5061/dryad.s7h44j1d4)

This dataset contains the assembled metagenomes of 43 gut microbiome biological samples in 23 species of mangrove crabs in Hong Kong collected during 2019-2021. The raw metagenomic reads are available at NCBI SRA under accession PRJNA1017629. The assembly was conducted using MEGAHIT 1.2.9. The unnormalized bacterial read counts tables on bacterial phyla and functional features in CAZy (release V10, 07292021) and KEGG databases (release v58) were generated using an integrated pipeline SqueezeMeta v1.4.0, which includes ORF prediction with Prodigal v2.6.3, taxonomic/functional read annotation with DIAMOND v2.0.8.146, and read mapping to annotations with Bowtie2 v2.3.4.1.

The raw count table were further processed using SQMtools to filter only bacterial read counts. To repeat...

研究背景：
相手蟹科（Sesarmid）蟹类为红树林生境中的优势类群，作为主要初级消费者推动了生态系统内的营养联结与养分循环。因此，相手蟹科蟹类适应植食性的策略与内在机制，不仅对其陆生演化进程与进化成功至关重要，也直接影响红树林森林生态系统的健康运转。尽管已有研究报道蟹类物种可表达内源性纤维素酶，但目前仍不清楚仅靠内源性酶是否足以完成完整的木质纤维素降解通路，亦或它们还需依赖肠道微生物组的协同贡献。本研究采用比较宏基因组学方法，旨在探究以红树林植物为食的相手蟹科蟹类的肠道共生微生物在植物消化过程中的作用。

研究结果：
对23种红树林蟹类的43份肠道样本开展宏基因组分析后发现，在所分析的全部物种中，均可覆盖到127个碳水化合物活性酶（CAZy）家族以及9个靶向木质纤维素及其衍生物的KEGG直系同源基因簇（KOs），……
# 肠道微生物组宏基因组分析揭示红树林植食性蟹类的木质纤维素降解机制与进化

[可在Dryad数据库访问本数据集](https://doi.org/10.5061/dryad.s7h44j1d4)

本数据集包含2019-2021年间于香港采集的23种红树林蟹类的43份肠道微生物组生物样本的组装宏基因组序列。原始宏基因组测序读段可在美国国家生物技术信息中心序列读取归档（NCBI SRA）数据库中通过登录号PRJNA1017629获取。基因组组装采用MEGAHIT 1.2.9完成。基于碳水化合物活性酶数据库（CAZy，版本V10，发布日期2021年7月29日）与京都基因与基因组百科全书（KEGG，版本v58），使用整合分析流程SqueezeMeta v1.4.0生成了细菌门水平的未标准化读段计数表以及功能特征表；该流程涵盖：使用Prodigal v2.6.3进行开放阅读框（ORF）预测、使用DIAMOND v2.0.8.146完成分类学/功能读段注释、以及使用Bowtie2 v2.3.4.1将读段比对至注释结果。
原始计数表后续通过SQMtools工具进行进一步处理，仅保留细菌读段计数信息，以用于重复研究……