The composition of the zebrafish intestinal microbial community varies across development

Stephens, W. Zac; Burns, Adam R.; Stagaman, Keaton; Wong, Sandi; Rawls, John F.; Guillemin, Karen; Bohannan, B. J. M.

doi:10.1038/ismej.2015.140

Cited by 542 publications

(659 citation statements)

References 38 publications

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“…We found that partitions clustered strongly based on whether and how they deviated from the neutral prediction (that is, above, below or within the neutral prediction) across host age (permutational MANOVA r 2 = 0.19, Po0.001; Figure 3a). Thus, the phylogenetic composition of the sub-groups that diverge from neutral patterns remains relatively similar across host development, despite the composition of communities as a whole changing (Stephens et al, 2015). Across age groups, non-neutral partitions of the metacommunity were also much more homogeneous than the neutral partitions, (ANOVA, Po0.01; illustrated by the spread of points in Figure 3a).…”

Section: Resultsmentioning

confidence: 90%

“…For the present study, we used a 16S rRNA gene sequence data set from a previously reported longitudinal study of the developing zebrafish intestinal microbiome (Stephens et al, 2015). A brief description of the study design and sample collection follows, and readers are referred to Stephens et al (2015) for additional details.…”

Section: Zebrafish Microbiota Longitudinal Studymentioning

confidence: 99%

“…A brief description of the study design and sample collection follows, and readers are referred to Stephens et al (2015) for additional details. A population of zebrafish resulting solely from a single mating pair was raised under identical conditions, to minimize both genetic and environmental heterogeneity, and sampled at multiple ages, conventionally measured by days post fertilization (dpf).…”

Section: Zebrafish Microbiota Longitudinal Studymentioning

confidence: 99%

“…16S rDNA sequences from the V4 region of the 16S rRNA gene, subsequent 97% similarity operation taxonomic unit (OTU) tables rarefied to 4250 sequences per sample, and taxonomic classifications were taken directly from Stephens et al (2015).…”

Section: Zebrafish Microbiota Longitudinal Studymentioning

confidence: 99%

“…In this regard, the intestinal microbiota of the zebrafish (Danio rerio) is an ideal experimental system. Zebrafish have historically been used to study vertebrate development, but have also recently emerged as an ideal model for studying interactions between vertebrate hosts and their associated microbial communities (Rawls et al, 2006;Roeselers et al, 2011;Yan et al, 2012;Stephens et al, 2015). This is in large part due to the feasibility of raising a large number of individuals from a single crossing and co-housing them throughout their lifespan in highly controlled environments, thereby minimizing the effects of inter-host variation and ensuring that all individuals are exposed to a shared source pool of microorganisms.…”

Section: Introductionmentioning

confidence: 99%

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Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

et al. 2015

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Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct subgroups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.

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Section: Resultsmentioning

confidence: 90%

Section: Zebrafish Microbiota Longitudinal Studymentioning

confidence: 99%

Section: Zebrafish Microbiota Longitudinal Studymentioning

confidence: 99%

Section: Zebrafish Microbiota Longitudinal Studymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

et al. 2015

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Fasting impairs type 2 helper T cell infiltration in the lung of an eosinophilic asthma mouse model

et al. 2021

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Eosinophilic asthma is a form of bronchial asthma that is caused by the pulmonary infiltration of eosinophils and accounts for approximately half of the patients with severe asthma. Several cell types of the immune system in synergy with the epithelial cells of the lung provoke an inflammatory response in patients with asthma. Recently, the effect of fasting on immune cells and inflammation has attracted considerable attention. Therefore, we examined whether fasting may serve as novel preventive strategy in patients with asthma. In our study, we employed a previously established mouse model of eosinophilic asthma. C57BL/6 mice were inoculated intranasally with interleukin‐33 and ovalbumin (OVA) in order to induce eosinophil infiltration in the lung and subjected to a 48‐h long fasting period directly after or 7 days postinoculation. We used flow cytometry to characterise infiltrated immune cells in the lung and measured the quantity of inflammatory cytokines as well as antigen‐specific immunoglobins (Ig) by ELISA. Our results indicated that fasting lowered the number of eosinophilic pulmonary infiltrates in the eosinophilic asthma model mice. Furthermore, fasting suppressed anti‐OVA IgG1 production. Fasting suppressed Th2 cytokine production by impairing Th2 accumulation in the lung. The findings suggest that fasting may be a novel preventive strategy for eosinophilic asthma.

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Probiotic Treatment Enhances Pre‐feeding Larval Development and Early Survival in Zebrafish Danio rerio

et al. 2022

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The growth and development of healthy culture subjects are essential in increasing productivity in the aquaculture industry. A primary determinant of aquatic animal productivity is the ambient microbial population. If an aquatic animal's microbiome is diverse, with bacteria favoring beneficial over pathogenic species, the health and growth of the animal (i.e., fish or crustacean) can be substantially improved. Embryonic and newly hatched Zebrafish Danio rerio larvae were reared in the presence of (1) water from the broodstock culture tank as a control, (2) a probiotic solution containing 19 strains of live lactic acid bacteria (LAB), or (3) an antibiotic (AB) solution with amoxycillin. Developmental parameters were monitored until 10 d postfertilization. Bacteria present in the water and larvae were cultured and identified by sequencing the V4 hypervariable region of bacterial 16S ribosomal RNA. Probiotic‐treated larvae showed significant increases in every measured morphological parameter and in survival compared to the controls and AB‐treated larvae, including TL, eye development, and swim bladder development before first feeding. Staining with DASPEI (2‐(4‐[dimethylamino]styryl)‐N‐ethylpyridinium iodide) produced fluorescence, revealing increased mitochondrial activity in the gastrointestinal tracts of probiotic‐treated larvae and reflecting advancement of initial metabolic function. Probiotic‐treated larvae showed accelerated yolk absorption, resulting in increased nutrient mobilization and growth. Microbial analyses revealed a greater concentration of bacteria in larvae in response to the probiotic treatment compared to the other two treatments. Species identified in all three treatments included Pseudomonas spp. and Aeromonas spp. (Proteobacteria). The second most diverse and abundant microbiome was seen in controls, whereas AB‐treated larvae had the least diverse microbiome. All treatments revealed the presence of proteobacteria, but an AB‐resistant pathogenic bacterium (Stenotrophomonas maltophilia) was identified in the AB group. These results reveal that the presence of LAB and other bacteria favorably influenced early larval growth, development, digestive function, and survival in Zebrafish even before the onset of feeding.

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The composition of the zebrafish intestinal microbial community varies across development

Cited by 542 publications

References 38 publications

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

Fasting impairs type 2 helper T cell infiltration in the lung of an eosinophilic asthma mouse model

Probiotic Treatment Enhances Pre‐feeding Larval Development and Early Survival in Zebrafish Danio rerio

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