Gut microbiome of juvenile coregonid fishes: comparison of sympatric species and their F1 hybrids

Belkova, Natalia; Sidorova, Tuyana; Glyzina, Olga; Yakchnenko, Veronika M.; Sapozhnikova, Yulia; Bukin, Yu. S.; Батурина, О. А.; Суханова, Л. В.

doi:10.1127/fal/2016/0804

Cited by 14 publications

(9 citation statements)

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“…The microbiome of lake Baikal is well-studied by microbiologists. Specifically, metabarcoding works have been performed for the communities of the water column 15–17 , bottom sediments 18–22 , and communities associated with certain baikalian organisms 23,24 . These works have shown that the bacterial biodiversity in the lake is extremely high.…”

Section: Background and Summarymentioning

confidence: 99%

The effect of 16S rRNA region choice on bacterial community metabarcoding results

et al. 2019

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In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.

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Section: Background and Summarymentioning

confidence: 99%

The effect of 16S rRNA region choice on bacterial community metabarcoding results

et al. 2019

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“…S3B). After Mycoplasma , Brevinema was the next greatest contributor to similarity in the AFR habitat (>10%) and has previously been isolated from the lower intestines of rainbow trout ( Oncorhynchus mykiss ) (Ricaud et al ., 2018) as well as whitefishes from the Coregonids (Belkova et al ., 2017). Thus, this taxon may be a common colonizer of the salmonid gut, and because Brevinema species have denitrifying capacity (Yang et al ., 2018), they could contribute to nitrogen metabolism in Arctic char.…”

Section: Discussionmentioning

confidence: 99%

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus)

Element

Engel

Neufeld

et al. 2020

Environmental Microbiology

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Summary Intestinal microbial communities from 362 anadromous Arctic char (Salvelinus alpinus) from the high Arctic Kitikmeot region, Nunavut, Canada, were characterized using high‐throughput 16S rRNA gene sequencing. The resulting bacterial communities were compared across four seasonal habitats that correspond to different stages of annual migration. Arctic char intestinal communities differed by sampling site, salinity and stages of freshwater residence. Although microbiota from fish sampled in brackish water were broadly consistent with taxa seen in other anadromous salmonids, they were enriched with putative psychrophiles, including the nonluminous gut symbiont Photobacterium iliopiscarium that was detected in >90% of intestinal samples from these waters. Microbiota from freshwater‐associated fish were less consistent with results reported for other salmonids, and highly variable, possibly reflecting winter fasting behaviour of these char. We identified microbiota links to age for those fish sampled during the autumn upriver migration, but little impact of the intestinal content and water microbiota on the intestinal community. The strongest driver of intestinal community composition was seasonal habitat, and this finding combined with identification of psychrophiles suggested that water temperature and migratory behaviour are key to understanding the relationship between Arctic char and their symbionts.

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“…Among these 20 microbial genera, eight genera (indicated by asterisks in Table 3) are newly reported as gut microbes of fishes. The remaining 12 genera were previously reported in the gut microflora of freshwater fishes such as Ctenopharyngodon idellus [18], Fundulus heteroclitus [19], Oncorhynchus mykiss [20,21], Danio rerio [22], Carassius auratus [23], Carassius gibelio [24], and Coregonus baicalensis [25]. With the rapid development of modern molecular biotechnology, an increasing number of novel microbial communities and functions have recently been detected in the guts of fishes by using new techniques and methods [7][8][9].…”

Section: New Insights Into the Gut Microbial Communities Of Coral Reementioning

confidence: 99%

Deep Insights into Gut Microbiota in Four Carnivorous Coral Reef Fishes from the South China Sea

et al. 2020

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Investigations of gut microbial diversity among fish to provide baseline data for wild marine fish, especially the carnivorous coral reef fishes of the South China Sea, are lacking. The present study investigated the gut microbiota of four carnivorous coral reef fishes, including Oxycheilinus unifasciatus, Cephalopholis urodeta, Lutjanus kasmira, and Gnathodentex aurolineatus, from the South China Sea for the first time using high-throughput Illumina sequencing. Proteobacteria, Firmicutes, and Bacteroidetes constituted 98% of the gut microbiota of the four fishes, and 20 of the gut microbial genera recovered in this study represent new reports from marine fishes. Comparative analysis indicated that the four fishes shared a similar microbial community, suggesting that diet type (carnivorous) might play a more important role in shaping the gut microbiota of coral reef fishes than the species of fish. Furthermore, the genera Psychrobacter, Escherichia-Shigella, and Vibrio constituted the core microbial community of the four fishes, accounting for 61-91% of the total sequences in each fish. The lack of the genus Epulopiscium in the four fishes was in sharp contrast to what has been found in coral reef fishes from the Red Sea, in which Epulopiscium was shown to be the most dominant gut microbial genus in seven herbivorous coral reef fishes. In addition, while unique gut microbial genera accounted for a small proportion (8-13%) of the total sequences, many such genera were distributed in each coral reef fish species, including several genera (Endozoicomonas, Clostridium, and Staphylococcus) that are frequently found in marine fishes and 11 new reports of gut microbes in marine fishes. The present study expands our knowledge of the diversity and specificity of gut microbes associated with coral reef fishes.

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Gut microbiome of juvenile coregonid fishes: comparison of sympatric species and their F1 hybrids

Cited by 14 publications

References 0 publications

The effect of 16S rRNA region choice on bacterial community metabarcoding results

The effect of 16S rRNA region choice on bacterial community metabarcoding results

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus)

Deep Insights into Gut Microbiota in Four Carnivorous Coral Reef Fishes from the South China Sea

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