DOI: 10.5061/dryad.w9ghx3fvk
title: Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification

description: The acquisition of microbial symbionts enables animals to rapidly adapt to
 and exploit novel ecological niches, thus significantly enhancing the
 evolutionary fitness and success of their hosts. However, the dynamics of
 host-microbe interactions and their evolutionary implications remain
 largely underexplored in marine invertebrates. Crabs of the family
 Sesarmidae (Crustacea: Brachyura) are dominate inhabitants of mangrove
 forests and considered as keystone species there. Their rapid
 diversification, particularly after adopting a plant-feeding lifestyle, is
 believed to have been facilitated by symbiotic gut microbes, enabling
 successful colonization of intertidal and terrestrial environments. To
 investigate the patterns and mechanisms shaping the microbial communities
 and the role of microbes in the evolution of Sesarmidae, we characterized
 and compared the gut microbiome compositions across 43 crab species from
 Sesarmidae and other mangrove-associated families using 16S metabarcoding.
 We found that the gut microbiome assemblages in crabs are primarily
 determined by host identity, with a secondary influence from environmental
 factors such as microhabitat and sampling location, and to a lesser extent
 influenced by biological factors such as sex and gut region. While
 patterns of phylosymbiosis (i.e. when microbial community relationships
 recapitulate the phylogeny of their hosts) were consistently observed in
 all beta-diversity metrics analyzed, the strength of phylosymbiosis varied
 across crab families. This suggests that the bacterial assemblages in each
 family were differentially shaped by different degrees of host filtering
 and/or other evolutionary processes. Notably, Sesarmidae displayed signals
 of cophylogeny with its core gut bacterial genera, which likely play
 crucial functional roles in their hosts by providing lignocellulolytic
 enzymes, essential amino acids and fatty acids supplementation. Our
 results support the hypothesis of microbial contribution to herbivory and
 terrestrialization in mangrove crabs, highlighting the tight association
 and codiversification of the crab holobiont. Benefit-Sharing Statement
 This work provides access to new 16S microbiome data sets obtained from
 the digestive tract of 43 species of crabs, many of which are ecologically
 important species in intertidal and terrestrial environments. Our analyses
 have provided a comprehensive protocol in the study of core microbiome,
 phylosymbiosis and codiversification in non-model organisms, which could
 provide a methodological reference to fuel microbial research on other
 understudied non-model organisms.
description: # Comparative analysis of gut microbiome of mangrove brachyuran crabs
 revealed patterns of phylosymbiosis and diversification ## Description of
 the data and file structure This 16S metabarcoding data set contains a
 total of 441 sequenced gut samples from 224 individuals across 43 crab
 species (10.3 ± 6.5 sample/species). Each individual has a unique id in
 the data set and it gives information about the specimen. For example, in
 **BRA12341F**: **BRA1234** is the voucher code of that individual; **1**
 means it is the first extracted individual under that voucher code (only
 ranging from 1 to 6); **F** means the sameple originates from the hindgut
 of that individual (M = midgut, H = hindgut). ## Code/Software All the
 codes and important intermediate files are available on
 https://github.com/ChandlerTsang/2024_Crab_Gut_Microbiome.