Undibacterium danionis sp. nov. isolated from a zebrafish (Danio rerio)

Kämpfer, Peter; Irgang, Rute; Busse, Hans Jürgen; Poblete‐Morales, Matías; Kleinhagauer, Tanita; Glaeser, Stefanie P.; Avendaño‐Herrera, Rubén

doi:10.1099/ijsem.0.001244

Cited by 18 publications

(9 citation statements)

References 26 publications

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“…Undibacterium is a genus of typically aquatic bacteria and has been found in various sources of freshwater environments [64,65]. Additionally, Undibacterium has been described in the intestinal microbiota of shrimp, zebrafish, and bats [66][67][68]. Several species affiliated with the genus Undibacterium reportedly produce various fatty acids and polar lipids [64,65].…”

Section: Discussionmentioning

confidence: 99%

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

Zhang

Lin

et al. 2021

Microorganisms

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The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia–Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia–Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

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Section: Discussionmentioning

confidence: 99%

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

Zhang

Lin

et al. 2021

Microorganisms

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“…Of these six, only a single genus, Undibacterium, was present in all adult samples of both skin and gill. Undibacterium species have been isolated from other fishes and may play a role in biofilm degradation (70)(71)(72)(73). Given that they were not detected in embryonic or water samples, skates likely acquire Undibacterium through horizontal transfer from an unknown source or drastically enrich this genus from starting levels below the limit of detection.…”

Section: Discussionmentioning

confidence: 99%

Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

Mika

Okamoto

Shubin

et al. 2020

Preprint

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Microbial transmission from parent to offspring is hypothesized to be universal in vertebrates. However, evidence for this is limited as many clades remain unexamined. Chondrichthyes, as one of the earliest–branching vertebrate lineages, provide an opportunity to investigate the phylogenetic breadth of this hypothesis. To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, Leucoraja erinacea, at six points during ontogeny. We identify site-specific microbiomes dominated by the bacterial phyla Proteobacteria and Bacteroidetes, a composition similar to, but distinct from, that of other chondrichthyans. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Our study is the first exploration of the chondrichthyan microbiome throughout ontogeny and provides the first evidence of vertical transmission in this group, which may be the primary mechanism for the signature of phylosymbiosis previously observed in elasmobranchs.

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“…Undibacterium is a genus of typically aquatic bacteria, isolated from various sources of freshwater, e.g., drinking water, purified water, waterfalls, freshwater streams, freshwater shrimp culture ponds and also from permafrost soil (Kämpfer et al, 2007; Eder et al, 2011; Liu et al, 2013; Kim et al, 2014; Sheu et al., 2014a; Sheu et al., 2014b; Du et al., 2015; Nguyen, Lee & Kim, 2015; Chen et al., 2017). In addition, it was isolated from shrimp intestines (Rungrassamee et al, 2014) and from zebrafish Danio rerio (Kämpfer et al, 2016). The genus Undibacterium has been described in host-associated symbiotic microbial communities (Jani & Briggs, 2014) and 132 sequences of Undibacterium have been deposited in GenBank.…”

Section: Discussionmentioning

confidence: 99%

Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene

Mioduchowska

Czyż

Gołdyn

et al. 2018

PeerJ

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Bacterial endosymbionts of aquatic invertebrates remain poorly studied. This is at least partly due to a lack of suitable techniques and primers for their identification. We designed a pair of non-degenerate primers which enabled us to amplify a fragment of ca. 500 bp of the 16S rRNA gene from various known bacterial endosymbiont species. By using this approach, we identified four bacterial endosymbionts, two endoparasites and one uncultured bacterium in seven, taxonomically diverse, freshwater crustacean hosts from temporary waters across a wide geographical area. The overall efficiency of our new WOLBSL and WOLBSR primers for amplification of the bacterial 16S rRNA gene was 100%. However, if different bacterial species from one sample were amplified simultaneously, sequences were illegible, despite a good quality of PCR products. Therefore, we suggest using our primers at the first stage of bacterial endosymbiont identification. Subsequently, genus specific primers are recommended. Overall, in the era of next-generation sequencing our method can be used as a first simple and low-cost approach to identify potential microbial symbionts associated with freshwater crustaceans using simple Sanger sequencing. The potential to detected bacterial symbionts in various invertebrate hosts in such a way will facilitate studies on host-symbiont interactions and coevolution.

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Undibacterium danionis sp. nov. isolated from a zebrafish (Danio rerio)

Cited by 18 publications

References 26 publications

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene

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