Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference

Zhang, Meiling; Sun, Yanfa; Liu, Yukun; Qiao, Fang; Chen, Liqiao; Liu, Wen Tso; Du, Zhen‐Yu; Li, Erchao

doi:10.1016/j.aquaculture.2015.12.014

Cited by 185 publications

(129 citation statements)

References 42 publications

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“…Zhang et al . () also identified differences in the GI microbiome of Nile tilapia acclimated to freshwater and water at 24 psu (practical salinity units), with those reared in freshwater harbouring greater abundances of Actinobacteria vs seawater‐reared fish which harboured more Fusobacteria. These findings indicate that the bacterial communities of the gut of fishes must be adapted to tolerate the same conditions as the host organism.…”

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 92%

“…; Zhang et al . ). However, understanding the influence of variables such as salinity in the wild is hampered by covariation of other environmental parameters and host taxonomy (Sullam et al .…”

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 97%

“…Fishes live in dynamic environments where conditions such as temperature, hydrostatic pressure and salinity are highly variable (Zhang et al . ). The intestine, a major osmoregulatory organ in fishes, adapts to osmolality in seawater and is involved in gene expression for salinity acclimation (Wong et al .…”

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 97%

“…() examined the allochthonous microbiome of Nile tilapia and identified Firmicutes as the primary phylum, and Zhang et al . () identified the most frequent phyla to be Actinobacteria, Bacteroidetes and Proteobacteria in tilapia reared in saline water, suggesting these proportions are different depending on rearing conditions. Between‐study comparisons suggest that aspects of study design largely influence lower level taxa as there are few similarities in dominant microbiome members among studies.…”

Section: Gut Microbiome Of Economically Significant Speciesmentioning

confidence: 99%

“…; Zhang et al . ), but how these processes impact the gut microbiome is still poorly understood. Sullam et al .…”

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 99%

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Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

et al. 2017

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Summary The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next‐generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host–microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.

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Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 92%

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 97%

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 97%

Section: Gut Microbiome Of Economically Significant Speciesmentioning

confidence: 99%

“…; Zhang et al . ), but how these processes impact the gut microbiome is still poorly understood. Sullam et al .…”

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 99%

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Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

et al. 2017

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Systematic literature review identifying bacterial constituents in the core intestinal microbiome of rainbow trout (Oncorhynchus mykiss)

Hines,

Marshall,

Smith

et al. 2023

Aquaculture Fish & Fisheries

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Fish aquaculture has become the fastest growing sector in global food production. Thus, ensuring the sustainability of aquaculture practices is of the utmost importance. Studies in higher vertebrates (i.e. mammals) have demonstrated the role of the host microbiome in physiological processes from nutrient acquisition to pathogen protection. Therefore, analysis of fish microbiomes is an important factor to consider with regard to overall animal health and welfare. Rainbow trout (Oncorhynchus mykiss) are an economically valued fish cultured worldwide. Several studies have identified microbial constituents inhabiting the intestinal tract of rainbow trout. To better elucidate some of the core constituents of the rainbow trout intestinal microbiome, this systematic literature review analysed the relative abundance results from 25 articles published on the rainbow trout intestinal microbiome from 2017 to 2021. Bacteria classified within the phyla Firmicutes and Proteobacteria were observed in every study. At the family level, Lactobacillaceae was consistently observed. Additionally, bacteria in the Actinobacteria, Bacteroides, and Tenericutes phyla were identified in at least 50% of the studies. Interestingly, Mycoplasma spp. were occasionally the most dominant organisms present in the microbiome. Overall, the results here identify bacteria that are commonly found members of the rainbow trout intestinal microbiome.

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Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis

Härer

Rennison

2022

Ecology and Evolution

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Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities (‘multivarvector’). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.

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Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference

Cited by 185 publications

References 42 publications

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

Systematic literature review identifying bacterial constituents in the core intestinal microbiome of rainbow trout (Oncorhynchus mykiss)

Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis

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