Dataset Information

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run.

ABSTRACT: During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.

SUBMITTER: Emami-Khoyi A

PROVIDER: S-EPMC8001748 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run.

Emami-Khoyi Arsalan A Le Roux Rynhardt R Adair Matthew G MG Monsanto Daniela M DM Main Devon C DC Parbhu Shilpa P SP Schnelle Claudia M CM van der Lingen Carl D CD Jansen van Vuuren Bettine B Teske Peter R PR

Genes 20210304 3

During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, <i>Sardinops sagax</i>, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and ...[more]

PMID: 33806647

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Project description:BackgroundThe fungal microbiome, or mycobiome, is a poorly described component of the gut ecosystem and little is known about its structure and development in children. In South Africa, there have been no culture-independent evaluations of the child gut mycobiota. This study aimed to characterise the gut mycobiota and explore the relationships between fungi and bacteria in the gut microbiome of children from Cape Town communities.MethodsStool samples were collected from children enrolled in the TB-CHAMP clinical trial. Internal transcribed spacer 1 (ITS1) gene sequencing was performed on a total of 115 stool samples using the Illumina MiSeq platform. Differences in fungal diversity and composition in relation to demographic, clinical, and environmental factors were investigated, and correlations between fungi and previously described bacterial populations in the same samples were described.ResultsTaxa from the genera Candida and Saccharomyces were detected in all participants. Differential abundance analysis showed that Candida spp. were significantly more abundant in children younger than 2 years compared to older children. The gut mycobiota was less diverse than the bacterial microbiota of the same participants, consistent with the findings of other human microbiome studies. The variation in richness and evenness of fungi was substantial, even between individuals of the same age. There was significant association between vitamin A supplementation and higher fungal alpha diversity (p = 0.047), and girls were shown to have lower fungal alpha diversity (p = 0.003). Co-occurrence between several bacterial taxa and Candida albicans was observed.ConclusionsThe dominant fungal taxa in our study population were similar to those reported in other paediatric studies; however, it remains difficult to identify the true core gut mycobiota due to the challenges set by the low abundance of gut fungi and the lack of true gut colonising species. The connection between the microbiota, vitamin A supplementation, and growth and immunity warrants exploration, especially in populations at risk for micronutrient deficiencies. While we were able to provide insight into the gut mycobiota of young South African children, further functional studies are necessary to explain the role of the mycobiota and the correlations between bacteria and fungi in human health.

Dataset Information

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run.

Publications

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run.

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