scholarly journals Decision letter: Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature

2018 ◽  
Keyword(s):  
Cold Tolerance ◽  
Genetic Selection ◽  
Microbiome Composition ◽  
Host Genetic ◽  
Selection For ◽  
Response To Temperature

scholarly journals Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Fotini Kokou ◽  
Goor Sasson ◽  
Tali Nitzan ◽  
Adi Doron-Faigenboim ◽  
Sheenan Harpaz ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Genetic Selection ◽  
Breeding Scheme ◽  
Transcriptomic Response ◽  
Temperature Changes ◽  
Microbiome Composition ◽  
Independent Unit ◽  
Host Genetic ◽  
Selection For ◽  
Response To Temperature

The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.

scholarly journals Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Pratima Chapagain ◽  
Donald Walker ◽  
Tim Leeds ◽  
Beth M. Cleveland ◽  
Mohamed Salem
Keyword(s):  
Rainbow Trout ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Genetic Selection ◽  
Rrna Gene ◽  
Genetic Line ◽  
Characteristic Functional ◽  
Fecal Samples ◽  
Host Genetic ◽  
Selection For

Abstract Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial assemblages between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host. Results Tukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, χ2(1) =14.11, p < 0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F1,36 = 4.7, p < 0.05, R2 = 11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples. Conclusion The significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate a possible effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

scholarly journals Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

2020 ◽  
Author(s):  
Pratima Chapagain ◽  
Donald Walker ◽  
Tim Leeds ◽  
Beth M Cleveland ◽  
Mohamed Salem
Keyword(s):  
Rainbow Trout ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Genetic Selection ◽  
Rrna Gene ◽  
Genetic Line ◽  
Characteristic Functional ◽  
Fecal Samples ◽  
Host Genetic ◽  
Selection For

Abstract Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial population between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host. Results Tukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, c2(1) =14.11, p<0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F1,36= 4.7, p<0.05, R2=11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples. Conclusion The significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate an effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

scholarly journals Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout

2020 ◽  
Author(s):  
Pratima Chapagain ◽  
Donald Walker ◽  
Tim Leeds ◽  
Beth M Cleveland ◽  
Mohamed Salem
Keyword(s):  
Rainbow Trout ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Genetic Selection ◽  
Genetic Line ◽  
Characteristic Functional ◽  
Fecal Samples ◽  
Functional Capabilities ◽  
Host Genetic ◽  
Selection For

Abstract Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16srRNA gene. Significant differences in microbial population between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host.Results Tukey’s transformed inverse Simpson indices indicated that ARS-FY-H samples have higher microbial diversity compared to those of the ARS-FY-L (LMM, χ2(1) = 14.11, p < 0.05). The fecal samples showed distinct clusters with significant differences in microbial assemblages between the genetic lines (F1,36= 4.7, p < 0.05, R2 = 11.9%). Further, Tax4Fun analyses predicted characteristic functional capabilities of the microbial communities in the ARS-FY-H and ARS-FY-L samples.Conclusion The significant differences of the microbial assemblages between ARS-FY-H and ARS-FY-L indicate an effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates correlation of the function in improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

scholarly journals Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

2020 ◽  
Author(s):  
Pratima Chapagain ◽  
Donald Walker ◽  
Tim Leeds ◽  
Beth M Cleveland ◽  
Mohamed Salem
Keyword(s):  
Rainbow Trout ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Genetic Selection ◽  
Rrna Gene ◽  
Genetic Line ◽  
Characteristic Functional ◽  
Fecal Samples ◽  
Host Genetic ◽  
Selection For

Abstract Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial population between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host. Results Tukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, c2(1) =14.11, p<0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F1,36= 4.7, p<0.05, R2=11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples. Conclusion The significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate an effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

Genetic selection for nonstructural carbohydrates and its impact on other nutritive attributes of alfalfa ( Medicago sativa ) forage

2021 ◽  
Author(s):  
Annie Claessens ◽  
Marie Bipfubusa ◽  
Caroline Chouinard‐Michaud ◽  
Annick Bertrand ◽  
Gaëtan F. Tremblay ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
Genetic Selection ◽  
Nonstructural Carbohydrates ◽  
Selection For

scholarly journals A gene co-association network regulating gut microbial communities in a Duroc pig population

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Reverter ◽  
Maria Ballester ◽  
Pamela A. Alexandre ◽  
Emilio Mármol-Sánchez ◽  
Antoni Dalmau ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Candidate Genes ◽  
Relative Abundance ◽  
Association Studies ◽  
Single Gene ◽  
Host Genome ◽  
Genome Wide Association Studies ◽  
Vaccine Response ◽  
Microbiome Composition ◽  
Host Genetic

Abstract Background Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical “single-gene-single-trait” approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. Results In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP–P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. Conclusions Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits.

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