Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

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Distinct kin strategies of the legume soybean and the non‐legume balsam by accomplishing different nitrogen acquisition and rhizosphere microbiome composition

The Plant Journal ◽

10.1111/tpj.15656 ◽

2021 ◽

Author(s):

Jie Li ◽

Qingxia Zhao ◽

Weilin Li ◽

Jizheng He ◽

Xingliang Xu

Keyword(s):

Nitrogen Acquisition ◽

Microbiome Composition ◽

Rhizosphere Microbiome

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Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

The ISME Journal ◽

10.1038/ismej.2017.85 ◽

2017 ◽

Vol 11 (10) ◽

pp. 2244-2257 ◽

Cited By ~ 99

Author(s):

Juan E Pérez-Jaramillo ◽

Víctor J Carrión ◽

Mirte Bosse ◽

Luiz F V Ferrão ◽

Mattias de Hollander ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Phenotypic Traits ◽

Microbiome Composition ◽

Rhizosphere Microbiome

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Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

10.1101/736843 ◽

2019 ◽

Cited By ~ 2

Author(s):

Diana J. Rennison ◽

Seth M. Rudman ◽

Dolph Schluter

Keyword(s):

Microbial Communities ◽

Local Adaptation ◽

Biotic Interactions ◽

Ecological Speciation ◽

Microbiome Composition ◽

Interacting Species ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

And Function ◽

Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

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Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species

10.1101/2021.04.27.441490 ◽

2021 ◽

Author(s):

Reilly O. Cooper ◽

Sarah Tjards ◽

Jessica Rischling ◽

David T. Nguyen ◽

Clayton E. Cressler

Keyword(s):

Daphnia Magna ◽

Disease Risk ◽

Control Treatment ◽

Antibiotic Exposure ◽

Community Members ◽

Host Fitness ◽

Microbiome Composition ◽

Single Host ◽

Multigenerational Effects ◽

And Function

AbstractBackgroundChronic antibiotic exposure impacts host health through changes to the microbiome, increasing disease risk and reducing the functional repertoire of community members. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied. However, much less is understood about the multigenerational effects of antibiotic exposure and how the microbiome may recover across host generations.ResultsIn this study, we examined microbiome composition and host fitness across five generations of exposure to a suite of three antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we aimed to examine recovery and resilience of the microbiome. Unexpectedly, we discovered that experimental isolation of single host individuals across generations also exerted a strong effect on microbiome composition, with composition becoming less diverse over generations regardless of treatment. Simultaneously, Daphnia magna body size and cumulative reproduction increased across generations while survival decreased. Though antibiotics did cause substantial changes to microbiome composition, the microbiome generally became similar to the no antibiotic control treatment within one generation of recovery no matter how many prior generations were spent in antibiotics.ConclusionsContrary to results found in vertebrate systems, Daphnia magna microbiome composition recovers quickly after antibiotic exposure. However, our results suggest that the isolation of individual hosts leads to the stochastic extinction of rare taxa in the microbiome, indicating that these taxa are likely maintained via transmission in host populations rather than intrinsic mechanisms. This may explain the intriguing result that microbiome diversity loss increased host fitness.

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820 – Prospective Longitudinal Gut Metagenomic Analysis Suggests Altered Microbiome Composition and Function in Infants Prior to Celiac Disease Onset

Gastroenterology ◽

10.1016/s0016-5085(19)37228-2 ◽

2019 ◽

Vol 156 (6) ◽

pp. S-175

Author(s):

Maureen M. Leonard ◽

Poorani Subramanian ◽

Francesco Valitutti ◽

Gloria Serena ◽

Victoria Kenyon ◽

...

Keyword(s):

Celiac Disease ◽

Disease Onset ◽

Metagenomic Analysis ◽

Microbiome Composition ◽

And Function ◽

Prospective Longitudinal

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Dietary Patterns Differentially Affect Microbiome Composition and Function in a Porcine Model of Obesity-related Metabolic Disorder (OR23-04-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz040.or23-04-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Gloria Solano-Aguilar ◽

Jonathan Shao ◽

Joseph Urban ◽

Sukla Lakshman ◽

Saebyeol Jang ◽

...

Keyword(s):

Dietary Patterns ◽

Dietary Intervention ◽

Diversity Index ◽

Early Stage ◽

Saturated Fat ◽

Post Intervention ◽

Fecal Microbiome ◽

Microbiome Composition ◽

And Function ◽

The Impact

Abstract Objectives To determine the impact of two isocaloric diets containing (38% ,15% and 47% energy from fat, protein and carbohydrate, respectively): Western diet (WD) rich in saturated fat, refined carbohydrate, low in fiber and high in cholesterol, and a heart healthy diet (HHD) rich in unsaturated fat, unrefined carbohydrate, fruits/vegetables, high in fiber and low in cholesterol, on the composition and function of the gut microbiome Methods Thirty-Ossabaw pigs were fed WD or HHD diets with half within each group therapeutically treated with statin (atorvastatin [Lipitor]). The fecal microbiome was analyzed one and six months after dietary intervention by 16S rRNA sequencing and metagenomic function was empirically inferred Results Genus diversity was transiently affected with a reduced Shannon Diversity index one month after feeding the WD or HHD (FDR P < 0.05) with no change between groups at 6 months. Bacterial communities were clustered and separated by diet independent of gender and separated by treatment with statin in the HHD only. Verrucomicrobiaceae (Akkermansia) and Methanobacteriales (Methanobrevibacter) were increased in pigs as early as one month after feeding the HHD, as was Clostridiales and Bifidobacterium (associated with optimal intestinal health). There was an enrichment of Proteobacteria (Succinivibrionaceae, Desulfovibrionaceae) in pigs fed the WD. Additional members of the Firmicutes phylum were detected. Diet-dependent associations (all P < 0.05) were identified between Lachnospiraceae members and early host dyslipidemia, inflammation, and atheromatous lesions in the left anterior descending proximal (LAD) and LAD/Left circumflex (LCX) bifurcation six months post-intervention. Conclusions These data document for the first time a distinctive bacterial profile in Ossabaw pigs with a diet-induced dyslipidemia and early stage atherosclerosis. Taken together these results represent a new model to examine mechanistic pathways of dietary patterns and/or drug interactions and its effect on modulating microbiome in developing atherosclerosis. Funding Sources USDA project 8040-51530-056-00 and Inter Agency USDA Agreement 588-1950-9-001 between BHNRC and Jean Mayer USDA-HNRCA

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