Composition and Metabolic Activities of the Bacterial Community in Shrimp Sauce at the Flavor-Forming Stage of Fermentation As Revealed by Metatranscriptome and 16S rRNA Gene Sequencings

Abstract

The bacterial community and the metabolic activities involved at the flavor-forming stage during the fermentation of shrimp sauce were investigated using metatranscriptome and 16S rRNA gene sequencings. Results showed that the abundance of Tetragenococcus was 95.1%. Tetragenococcus halophilus was identified in 520 of 588 transcripts annotated in the Nr database. Activation of the citrate cycle and oxidative phosphorylation, along with the absence of lactate dehydrogenase gene expression, in T. halophilus suggests that T. halophilus probably underwent aerobic metabolism during shrimp sauce fermentation. The metabolism of amino acids, production of peptidase, and degradation of limonene and pinene were very active in T. halophilus. Carnobacterium, Pseudomonas, Escherichia, Staphylococcus, Bacillus, and Clostridium were also metabolically active, although present in very small populations. Enterococcus, Abiotrophia, Streptococcus, and Lactobacillus were detected in metatranscriptome sequencing, but not in 16S rRNA gene sequencing. Many minor taxa showed no gene expression, suggesting that they were in dormant status.

Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages

“…Shrimp paste is widely consumed as a condiment and used as an ingredient throughout China and the south-east Asian region (1–2). It is normally produced by fermenting small shrimp ( Acetes vulgaris ) with salt at a ratio of 5:1 (shrimp to salt, w/w).…”

Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium

“…The LAB genera Enterococcus, Lactobacillus, Lactococcus , and Streptococcus have been intensively investigated, but lately, other genera including Carnobacterium have also drawn attention since 16S meta-barcoding studies have shown their significance in food (Chaillou et al, 2015; Duan et al, 2016; Fougy et al, 2016; Jääskeläinen et al, 2016). The genus Carnobacterium encompasses 11 species that have been isolated from cold and temperate environments, and from the GI tract of animals as well as from foods of animal origin such as seafood, meat, and dairy products.…”

“…Other species, including C. maltaromaticum and C. divergens , have been found in animal-associated habitats. These two species are the most frequently isolated carnobacteria from various sources (Leisner et al, 2007) and belong to the dominant bacterial communities in meat and fish derived food (Chaillou et al, 2015; Duan et al, 2016; Fougy et al, 2016; Jääskeläinen et al, 2016). These bacteria are therefore very interesting models to investigate the genomic traits responsible for adaptation to animal-associated habitats.…”

Farm and abattoir sources of Carnobacterium species and implications for lamb meat spoilage

“…However, the use of ERIC-PCR was effective at distinguishing C. maltaromaticum from C. inhibens and demonstrating within-species variability in C. maltaromaticum with each ERIC-PCR profile supported by sequencing of the 16S rRNA gene and nearest neighbour homology. From previously published work (Chaillou et al 2015;Duan et al 2016;Fougy et al 2016;J€ a€ askel€ ainen et al 2016) we would have expected to isolate both C. maltaromaticum and C. divergens as these species have been shown to be the dominant bacterial communities in meat-and fish-derived food. However, in this study we did not identify C. divergens in either the farm or carcass samples.…”