The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms

Environmental Microbiology

Yoshizawa

Sun

et al. 2019

Summary The taxonomy of marine and non‐marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean‐to‐land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non‐marine adaptive genes. This included various Na+‐dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non‐marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low‐affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non‐marine bacteria. Strikingly, the central metabolism Na+‐translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+‐translocating counterpart was repeatedly gained in non‐marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non‐marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non‐marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

Section: Resultsmentioning

confidence: 99%

Repeated evolutionary transitions of flavobacteria from marine to non‐marine habitats

Environmental Microbiology

Yoshizawa

Sun

et al. 2019

“…Instead, several ASVs were found to be signi cantly enriched in the skin of antibiotic treated sh, particularly Tenacibaculum. This is a concern, as this genus encompasses numerous pathogenic species which have the capacity to cause serious ulcerative disease (tenacibaculosis) in a wide range of marine sh species [67][68][69]. In other sh, treatment with antibiotics has also been shown to have negative effects that extend across the mucosal surfaces.…”

Section: Discussionmentioning

confidence: 99%

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

Legrand

Catalano

Wos‐Oxley

et al. 2020

Preprint

Background The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish ( Seriola lalandi ) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. Results Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish – an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more ‘normal’ (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. Conclusion As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.

“…For C. angulata, the detected Arcobacter and Tenacibaculum spp. are known pathogens that are reported to have caused considerable economic losses in marine fish and mollusc aquaculture (54)(55)(56). Moreover, the hemolymph of the three invertebrates also harbors some potential probiotics, which may protect the host against pathogen infection through the production of antimicrobials or antibiotics (17).…”

Section: Discussionmentioning

confidence: 99%

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method

Sun

et al. 2018

Appl Environ Microbiol

Symbiotic microorganisms have been found in the hemolymph (blood) of many aquatic invertebrates, such as crabs, shrimps and oysters. Hemolymph is a critical site in host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies using selective media (e.g., TCBS, 2216E, and LB) for enumerating and isolating microbial cells. However, doubts remain about the "true" representation of the microbial abundance and diversity of symbiotic microorganisms in hemolymph, particularly for uncultivable microorganisms which are believed to be more abundant than the cultured. To explore this, we developed a culture-independent cell extraction method for separating microbial cells from the hemolymph of three aquatic invertebrates (, , and) involving filtration through a 5-μm mesh filter membrane (the Filtration Method). A combination of the Filtration Method with fluorescence microscopy and high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. More than 2.6 × 10 cells/mL of microbial cells dominated by and, and, and and, were detected in the hemolymph of ,, and , respectively. A parallel study for investigating the hemolymph microbiome by comparing the Filtration Method and a culture-dependent method (the Plate Count Method), showed significantly higher microbial abundances (between 26 and 369-folds difference; P<0.05) and less biased community structures of the Filtration Method than those of the Plate Count Method. Furthermore, hemolymph of the three invertebrates harbored many potential pathogens, including ,, and Finally, the Filtration Method provides a solution that improves understanding of the metabolic functions of uncultivable hemolymph microorganisms (e.g., metagenomics) devoid of host hemocytes contamination. Microorganisms are found in invertebrates' hemolymph, a critical site in host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies. However, doubts remain about the "true" representation of hemolymph microbiome. This study developed a culture-independent cell extraction method that could separate microbial cells from the hemolymph of three aquatic invertebrates (, , and) based on filtration through a 5-μm mesh filter membrane (the Filtration Method). A combination of the Filtration Method with fluorescence microscopy and high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. Our results demonstrate that the hemolymph of aquatic invertebrates harbors a much higher microbial abundance and distinct microbial community composition than previously estimated. Furthermore, this work provides a less biased solution for studying the metabolic functions of uncultivable hemolymph microbiota devoid of host hemocytes contamination.