| 1. |
- Singh, Abhijeet, et al.
(author)
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High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.
- 2020
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 11
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Journal article (peer-reviewed)abstract
- The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline "AcetoScan" presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.
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| 2. |
- Singh, Aprajita, et al.
(author)
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Yarrowia lipolytica yeast as a dietary supplement for rainbow trout (Oncorhynchus mykiss) : Effects on gut microbiota, health and immunity
- 2024
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In: Aquaculture. - : Elsevier. - 0044-8486 .- 1873-5622. ; 590
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Journal article (peer-reviewed)abstract
- This study evaluated the effect of whole and autolysed Yarrowia lipolytica CBS 7504 strain on growth performance, gut immunity and gut microbiota composition in juvenile rainbow trout (Oncorhynchus mykiss). Fish were fed diets containing 2% and 5% whole or autolysed Y. lipolytica (WY and AY) in a 45-day trial, with a no-yeast diet as control. Log2 fold change analysis of Y. lipolytica diets showed relative change in abundance and association of certain microbial taxa with respect to control such as a correlation between the relative abundance of Desulfovibrionaceae in diets with WY. Moreover, diets at 5% and 2% levels demonstrated a synergistic association with relative levels of Sphingobacteriaceae and Rhodobacteraceae, respectively. However, the overall analyses showed little/no impact of Y. lipolytica supplementation on overall intestinal microbial composition, growth parameters and body indices. Gene expression analysis of the intestine revealed significant elevation in expression of immune-related genes of the complement pathway (c3 and c-type lectin), membrane receptor pathway (tlr2 and tlr5), mucosal innate immune pathway (muc-2), cytokines (tnf-α) and adaptive immune pathway (igt and cd4) in 5% WY. In conclusion, it can be inferred that dietary Y. lipolytica can be a useful functional feed supplement for rainbow trout when used as whole yeast at a 5% inclusion level since it can modulate gut microbial communities and act as a potential immunostimulant for the host.
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