Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

Smith, Chris C. R.; Snowberg, Lisa K.; Caporaso, J. Gregory; Knight, Rob; Bolnick, Daniel I.

doi:10.1038/ismej.2015.64

Cited by 291 publications

(317 citation statements)

References 62 publications

(72 reference statements)

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“…We observed a high variation in sequence number obtained for different samples as described previously [48]. To allow comparison of disparate libraries, normalization of sequence number is achieved by random selection of sequences referred to as rarefaction [49][50][51][52][53][54][55]. The effect of this process on beta diversity has been demonstrated [56][57][58].…”

Section: Discussionmentioning

confidence: 98%

Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England

Sapp

Lewis

Moss

et al. 2016

Forests

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Abstract:Outbreaks of acute oak decline (AOD) have been documented in England from 2006. Both species of native oaks (Quercus robur and Quercus petraea) are affected. To complement isolation efforts for identification of putative causative biotic agents and increase our understanding of bacteria associated with oak tissue, five sites in England were chosen for this study. Samples of outer bark, inner bark, sapwood and heartwood were taken from healthy oak and trees with symptoms at varying stages of the syndrome. Furthermore, larval galleries attributed to infestation with Agrilus biguttatus were included. After DNA extraction and amplification of the V3-V5 fragment of the bacterial 16S rRNA genes by pyrosequencing, the dataset was analyzed to identify patterns in bacterial communities in oak tissue samples with and without AOD symptoms at each site. The composition of bacterial communities differed greatly according to the site from which the samples were obtained. Within each site, the composition of the bacteria associated with symptomatic tissue varied between advanced stages of the syndrome and healthy tissue. Key players in healthy and symptomatic tissue were identified and included members of the Gammaproteobacteria related to Pseudomonas sp. or Brenneria goodwinii and members of the Firmicutes.

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Section: Discussionmentioning

confidence: 98%

Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England

Sapp

Lewis

Moss

et al. 2016

Forests

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“…Bayesian community-level source tracking, a computational approach, was developed to estimate the ratio of the gut microbes potentially obtained from water or prey source in their habitat [21, 37]. However, the contribution of environmental and indigenous gut microbes to gut microbiota in animals facing external environmental change has not been previously investigated.…”

Section: Discussionmentioning

confidence: 99%

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change

Chen

Weng

et al. 2017

PLoS ONE

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Growing evidence points out that the capacity of organisms to acclimate or adapt to new habitat conditions basically depends on their phenomic plasticity attributes, of which their gut commensal microbiota might be an essential impact factor. Especially in aquatic organisms, which are in direct and continual contact with the aquatic environment, the complex and dynamic microbiota have significant effects on health and development. However, an understanding of the relative contribution of internal sorting (host genetic) and colonization (environmental) processes is still unclear. To understand how microbial communities differ in response to rapid environmental change, we surveyed and studied the environmental and gut microbiota of native and habitat-exchanged shrimp (Macrobrachium nipponense) using 16S rRNA amplicon sequencing on the Illumina MiSeq platform. Corresponding with microbial diversity of their living water areas, the divergence in gut microbes of lake-to-river shrimp (CK) increased, while that of river-to-lake shrimp (KC) decreased. Importantly, among the candidate environment specific gut microbes in habitat-exchanged shrimp, over half of reads were associated with the indigenous bacteria in native shrimp gut, yet more candidates presented in CK may reflect the complexity of new environment. Our results suggest that shrimp gut microbiota has high plasticity when its host faces environmental changes, even over short timescales. Further, the changes in external environment might influence the gut microbiome not just by providing environment-associated microbes directly, but also by interfering with the composition of indigenous gut bacteria indirectly.

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“…This somewhat parallel pattern in Streptococcus abundance between the catfish intestinal microbiota and the microbiota of the associated diet samples suggests that diet may have introduced this OTU to the gut microbiota, which could be useful when considering effective routes of probiotic supplementation. Similarly, Smith and coworkers showed that differences in diet-derived microbes associated with the prey items of geographically separate populations of three-spine stickleback partially explained the differences detected in gut microbiota across the various populations [75]. Although when employing sequence based analysis, discerning if OTUs were detected as transient diet-derived microbial DNA artifacts or as viable functioning members of the gut microbiota is difficult and would require further studies.…”

Section: Discussionmentioning

confidence: 99%

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

Peterson²,

et al. 2016

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Aquaculture recently overtook capture fisheries as the largest producer of food fish, but to continue increasing fish production the industry is in search of better methods of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate temporal changes that may occur throughout ontogenetic development of the host. Intestinal microbiota were surveyed with high-throughput DNA sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (dph), while also characterizing the environmental microbes derived from the water supply and the administered diets. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 dph when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 dph. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the species Cetobacterium somerae and Plesiomonas shigelloides showing the highest abundance in the catfish microbiota after 3 dph. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained as a niche habitat, separate from the overall microbial communities present in diets and water-supply. Although, there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Our results have implications for future research related to channel catfish biology and culture, and increase our understanding of ontogenetic effects on the microbiota of teleost fish.

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Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

Cited by 291 publications

References 62 publications

Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England

Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

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