Dietary Bile Salt Types Influence the Composition of Biliary Bile Acids and Gut Microbiota in Grass Carp

Lipid metabolism can influence host’s health. There is increasing evidence for interplay between two key regulating factors in lipid metabolism: bile acids (BAs) and gut microbiota. However, very little is known about how types of different diet-supplemented bile salts (BS) influence this interaction in vivo. We sought to explore these relationships using grass carp (Ctenopharyngodon idellus), which often suffers functional disorder of liver and gallbladder. We studied fluctuations of BAs in the gall and changes of microbial communities in the gut in response to seven different diets: five different BS, chelating BS agent, and control. The BS comprised two primary BS [sodium taurochololate (TCAS) and sodium taurochenodeoxycholate (TCDCAS)], sodium tauroursodeoxycholate (TUDCAS), and two secondary BS [sodium taurodeoxycholate (TDCAS) and sodium taurolithocholate (TLCAS)]. Supplementation of primary BS caused a more significant fluctuation of biliary BAs than secondary BS, and TCAS caused a more prominent increase than TCDCAS and TUDCAS. For the gut microbiota, primary BS tended to increase their diversity and induce community succession, secondary BS resulted in a higher firmicutes/bacteroidetes ratio, while TUDCAS had no significant effects. Changes of the gut microbiota triggered by different types of BS caused alteration in BAs biotransformation. Two-obesity-associated families, Lachnospiraceae and Ruminococcaceae were positively correlated with biliary cholic acid (CA), taurochenodeoxycholic acid (TCDCA), and deoxycholic acid (DCA). As both primary and secondary BS resulted in increased synthesis of toxic secondary Bas by the gut microbiota, future studies should pay closer attention to gut microbiota when considering BA treatment

Blunt Snout Bream (Megalobrama amblycephala) MyD88 and TRAF6: Characterisation, Comparative Homology Modelling and Expression

MyD88 and TRAF6 play an essential role in the innate immune response in most animals. This study reports the full-length MaMyD88 and MaTRAF6 genes identified from the blunt snout bream (Megalobrama amblycephala) transcriptome profile. MaMyD88 is 2501 base pairs (bp) long, encoding a putative protein of 284 amino acids (aa), including the N-terminal DEATH domain of 78 aa and the C-terminal TIR domain of 138 aa. MaTRAF6 is 2252 bp long, encoding a putative protein of 542 aa, including the N-terminal low-complexity region, RING domain (40 aa), a coiled-coil region (64 aa) and C-terminal MATH domain (147 aa). Coding regions of MaMyD88 and MaTRAF6 genomic sequences consisted of five and six exons, respectively. Physicochemical and functional characteristics of the proteins were analysed. Alpha helices were dominant in the secondary structure of the proteins. Homology models of the MaMyD88 and MaTRAF6 domains were constructed applying the comparative modelling method. RT-qPCR was used to analyse the expression of MaMyD88 and MaTRAF6 mRNA transcripts in response to Aeromonas hydrophila challenge. Both genes were highly upregulated in the liver, spleen and kidney during the first 24 h after the challenge. While MyD88 and TRAF6 have been reported in various aquatic species, this is the first report and characterisation of these genes in blunt snout bream. This research also provides evidence of the important roles of these two genes in the blunt snout bream innate immune system

Population size may shape the accumulation of functional mutations following domestication

Abstract Background Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. Results Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . Conclusions Our results confirm the classical population genetics theory prediction and highlight the important role of species’ N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process

Mitochondrial genome sequences retrieved from GenBank for this study.

<p>Mitochondrial genome sequences retrieved from GenBank for this study.</p

Mitochondrial genome sequences retrieved from GenBank for this study.

<p>Mitochondrial genome sequences retrieved from GenBank for this study.</p

Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda)

<div><p>Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers. To help resolve their phylogenetic relationships, the complete mitogenomes of eight Chinese viviparid snails, <i>Viviparus chui</i>, <i>Cipangopaludina chinensis</i>, <i>C</i>. <i>ussuriensis</i>, <i>C</i>. <i>dianchiensis</i> (endangered), <i>Margarya melanioides</i> (endangered), <i>M</i>. <i>monodi</i> (critically endangered), <i>Bellamya quadrata</i> and <i>B</i>. <i>aeruginosa</i>, were sequenced and compared to almost all of the available caenogastropod mitogenomes. Viviparidae possess the largest mitogenomes (16 392 to 18 544 bp), exhibit the highest A+T bias (72.5% on average), and some exhibit unique gene orders (a rearrangement of the standard MYCWQGE box), among the Caenogastropoda. Apart from the Vermetidae family and Cerithioidea superfamily, which possessed unique gene orders, the remaining studied caenogastropod mitogenomes exhibited highly conserved gene order, with minimal variations. Maximum likelihood and Bayesian inference analyses, used to reconstruct the phylogenetic relationships among 49 almost complete (all 37 genes) caenogastropod mitogenomes, produced almost identical tree topologies. Viviparidae were divided into three clades: a) <i>Margarya</i> and <i>Cipangopaludina</i> (except <i>C</i>. <i>ussuriensis</i>), b) <i>Bellamya</i> and <i>C</i>. <i>ussuriensis</i>, c) <i>Viviparus chui</i>. Our results present evidence that some <i>Cipangopaludina</i> species (<i>dianchiensis</i> and <i>cathayensis</i>) should be renamed into the senior genus <i>Margarya</i>. The phylogenetic resolution obtained in this study is insufficient to fully resolve the relationships within the ‘b’ clade, but if <i>C</i>. <i>chinensis</i> proves to be a valid representative of the genus, <i>C</i>. <i>ussuriensis</i> may have to be reassigned a different genus (possibly <i>Bellamya</i>, or even a new genus). Non-monophyly also remains pervasive among the higher (above the family-level) Caenogastropod taxonomic classes. Gene order distance matrix produced a different phylogenetic signal from the nucleotide sequences, which indicates a limited usability of this approach for inferring caenogastropod phylogenies. As phenotypic homoplasy appears to be widespread among some viviparid genera, in order to effectively protect the rapidly diminishing endemic Viviparid populations in China, further detailed molecular phylogenetic studies are urgently needed to resolve the taxonomic status of several species.</p></div

Sampling and specimen details.

<p>Sampling and specimen details.</p

Phylogenetic relationships and gene order.

<p>Phylogenetic relationships among the majority of the available caenogastropod mitogenomic sequences (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181699#pone.0181699.t002" target="_blank">Table 2</a>) based on nucleotide sequences of all 37 genes. <i>Haliotis rubra</i> and <i>Pleuropoma jana</i> were used as outgroups. Numbers on the nodes correspond to ML bootstrap support (left, expressed as 0–100) and BI posterior probabilities (right, expressed as 0–1.0). Only values below 100/1.0 are depicted. Gene order is shown next to each sequence.</p

La Charente

04 mai 18921892/05/04 (A21,N7932)-1892/05/04.Appartient à l’ensemble documentaire : PoitouCh