Investigating the nutritional profile and bacteriome diversity in Bangladeshi sour yogurt

Tanzina, Afsana Yeasmin; Hoque, M. Nazmul; Mannan, Adnan; Foysal, Javed; Rumi, Meheadi Hasan; Biswas, Sabuj; Bhuiyan, J.A.M. Jahid; Siddiki, Amam Zonaed; Islam, Md. Sirazul; Tay, Chin Yen; Rafiqul, Islam S. M.

doi:10.1016/j.bcab.2022.102451

Cited by 6 publications

(2 citation statements)

References 32 publications

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“…Subsequently, each cycle included denaturation at 95°C for 30 seconds, primer annealing at 55°C for 30 seconds, and elongation at 72°C for 30 seconds. Finally, a final extension step was conducted at 72°C for 5 minutes to complete the process in a thermal cycler (Analytik Jena, Germany) [ 28 ]. The PCR amplicons were observed or visualized using a 1.5% agarose gel.…”

Section: Methodsmentioning

confidence: 99%

Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh

Kawser,

Hoque,

Rahman

et al. 2024

PLoS ONE

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The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.

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Section: Methodsmentioning

confidence: 99%

Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh

Kawser,

Hoque,

Rahman

et al. 2024

PLoS ONE

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show abstract

“…We ampli ed the genomic DNA by targeting the V3 -V4 regions of 16S rRNA gene with 30 µL nal volume containing 3 µL template DNA, 15 µL master mix (BioLabs, USA), 1.5 µL of each V3 -V4 forward (341f: 5′-CCTACGGGNGGCWGCAG-3′) and reverse (785r: 5′-GACTACHVGGGTATCTA ATCC-3′) primers 39 , and 9 µL ddH2O. A 25 cycle of amplicon PCR including initial denaturation at 95°C for 3 min, denaturation at 95°C for 30 s, primer annealing at 55°C for 30 s and elongation at 72°C for 30 s was performed for quanti ed DNA with the nal extension of 5 min at 72°C in a thermal cycler (Analytik Jena, Germany) 40 . The PCR amplicons were visualized in 1.5% agarose gel.…”

Section: Library Preparation Sequencing and Bioinformatics Analysismentioning

confidence: 99%

Unveiling the Gut and Flesh Microbiome Signature and Diversity of the Bangladesh National Fish Hilsa (Tenualosa ilisha)

Hoque,

Kawser,

Rahman

et al. 2023

Preprint

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Fish microbiome science is progressing fast, but it is mostly restricted to farmed or laboratory fish species compared to natural or marine fish populations. The aim of this study was to unveil the gut and flesh microbiome signature and diversity of the anadromous fish, Tenualosa ilisha (hilsa), the national fish of Bangladesh. We analysed 18 samples including 15 gut (intestinal contents) and three flesh samples from 18 individual hilsa fishes collected from three major habitats (e.g., freshwater, brackish water and marine water) of hilsa in Bangladesh through 16S rRNA (V3 – V4 region) gene sequencing-based metagenomics. A total of 325 operational taxonomic units (OTUs) including 67 and 258 in flesh and gut samples, respectively were identified. The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our findings revealed substantial taxonomic variability between sample categories (i.e., gut and flesh; p = 0.0127; Kruskal Wallis test), and habitats (freshwater, brackish water, and marine water; (p = 0.007; Kruskal Wallis test) of the hilsa fishes, indicated by their higher degree of shared microbiota. Of the identified genera, Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, Hafnia etc. were the major bacterial genera detected in hilsa fish. Importantly, we detected six genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella seem to be specific to the hilsa fishes. Our data provided evidence for the existence of both unique and shared bacteriomes with probiotics potentials in the gut and flesh of hilsa fishes, which might be taken into consideration for undertaking future microbiome study in this economically important fish species.

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Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh

Rana,

Hoque,

Rahman

et al. 2024

Environ Monit Assess

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Investigating the nutritional profile and bacteriome diversity in Bangladeshi sour yogurt

Cited by 6 publications

References 32 publications

Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh

Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh

Unveiling the Gut and Flesh Microbiome Signature and Diversity of the Bangladesh National Fish Hilsa (Tenualosa ilisha)

Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh

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