Effect of Dietary Oxalate on the Gut Microbiota of the Mammalian Herbivore Neotoma albigula

Miller, Aaron W.; Oakeson, Kelly F.; Dale, Colin; Dearing, M. Denise

doi:10.1128/aem.00216-16

Cited by 42 publications

(48 citation statements)

References 53 publications

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“…In a previous study, 116 OTUs from the gut microbiota of N. albigula exhibited a significant increase in relative abundance with oxalate consumption, whereas only one OTU significantly decreased in relative abundance [42]. For SDR in the current study, dietary oxalate likewise affected specific taxa within the gut microbiota in both the transplant and no-transplant groups.…”

Section: Discussionmentioning

confidence: 45%

“…For SDR in the current study, dietary oxalate likewise affected specific taxa within the gut microbiota in both the transplant and no-transplant groups. In the transplant group, this was manifested as an increase in frequency of several donor taxa including 22 that exhibited a significant increase in the Miller et al [42] experiment. For the no-transplant group, only two of the OTUs that exhibited a significant increase in frequency were found in the group of 116 OTUs from the previous study (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, Neotoma albigula is capable of degrading >90% of the dietary oxalate ingested by N. albigula at levels up to 9% dietary oxalate by dry weight [41]. Moreover, N. albigula maintains this highly effective oxalate-degrading microbiota even after 6 months on a low (0.2 %) oxalate diet [42]. Thus, this pair of species makes an excellent model to examine the effect of fecal transplants on oxalate degradation.…”

Section: Introductionmentioning

confidence: 99%

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Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation

et al. 2016

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Gut microbes are essential for the degradation of dietary oxalate, and this function may play a role in decreasing the incidence of kidney stones. However, many oxalate-degrading bacteria are susceptible to antibiotics and the use of oxalate-degrading probiotics has only led to an ephemeral reduction in urinary oxalate. The objective of the current study was to determine the efficacy of using whole-community microbial transplants from a wild mammalian herbivore, Neotoma albigula, to increase oxalate degradation over the long term in the laboratory rat, Rattus norvegicus. We quantified the change in total oxalate degradation in lab rats immediately after microbial transplants and at 2- and 9-month intervals following microbial transplants. Additionally, we tracked the fecal microbiota of the lab rats, with and without microbial transplants, using high-throughput Illumina sequencing of a hyper-variable region of the 16S rRNA gene. Microbial transplants resulted in a significant increase in oxalate degradation, an effect that persisted 9 months after the initial transplants. Functional persistence was corroborated by the transfer, and persistence of a group of bacteria previously correlated with oxalate consumption in N. albigula, including an anaerobic bacterium from the genus Oxalobacter known for its ability to use oxalate as a sole carbon source. The results of this study indicate that whole-community microbial transplants are an effective means for the persistent colonization of oxalate-degrading bacteria in the mammalian gut.

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Section: Discussionmentioning

confidence: 45%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation

et al. 2016

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“…We used our modeling strategy to estimate microbial community dynamics from 16S rDNA time-series data collected from the white-throated woodrat, Neotoma albigula (Miller et al, 2016). These animals were experimentally fed varying amounts of oxalate, a naturally occurring plant secondary compound that has been demonstrated to have toxic effects on a broad range of herbivores (e.g.…”

Section: Application Of Model To Oxalate Degradation In Neotoma Albigulamentioning

confidence: 99%

Modeling time-series data from microbial communities

Ridenhour

Brooker

Williams

et al. 2016

Preprint

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As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (e.g. skin, soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open, thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but given the 'big data' nature of these studies, there are currently no methods capable of utilizing the breadth of the data to infer ecological interactions from these longitudinal data.We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that 1) takes advantage of the fact that the data are time series; 2) constrains estimates to allow for the possibility of many more interactions than data; and 3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.

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“…Many other hosts utilize their microbiome to detoxify harmful chemicals. The woodrat microbiome degrades terpenes, enabling the woodrat to live in a specialized dietary niche [82][83][84][85][86] . Bark beetles 87 , pine weevils 88 , and coffee berry borers 89 also use their microbiomes to detoxify plant secondary compounds in specialized niches.…”

Section: Hosts Leverage Locally Adapted Microbesmentioning

confidence: 99%

Can the microbiome influence host evolutionary trajectories?

Henry

Bruijning

Forsberg

et al. 2019

Preprint

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The microbiome shapes many traits in hosts, but we still do not understand how it influences host evolution. To impact host evolution, the microbiome must be heritable and have phenotypic effects on the host. However, the complex inheritance and context-dependence of the microbiome challenges traditional models of organismal evolution. Here, we take a multifaceted approach to identify conditions in which the microbiome influences host evolutionary trajectories. We explore quantitative genetic models to highlight how microbial inheritance and phenotypic effects can modulate host evolutionary responses to selection. We synthesize the literature across diverse taxa to find common scenarios of microbiome driven host evolution. First, hosts may leverage locally adapted microbes, increasing survivorship in stressful environments. Second, microbial variation may increase host phenotypic variation, enabling exploration of novel fitness landscapes. We further illustrate these effects by performing a meta-analysis of artificial selection in Drosophila, finding that bacterial diversity also frequently responds to host selection. We conclude by outlining key avenues of research and experimental procedures to improve our understanding of the complex interplay between hosts and microbiomes. By synthesizing perspectives through multiple conceptual and analytical approaches, we show how microbiomes can influence the evolutionary trajectories of hosts.

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Effect of Dietary Oxalate on the Gut Microbiota of the Mammalian Herbivore Neotoma albigula

Cited by 42 publications

References 53 publications

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation

Modeling time-series data from microbial communities

Can the microbiome influence host evolutionary trajectories?

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