The Role of Host Genetic Signatures on Root–Microbe Interactions in the Rhizosphere and Endosphere

Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation

The ISME Journal ◽

10.1038/s41396-019-0529-2 ◽

2019 ◽

Vol 14 (1) ◽

pp. 302-317 ◽

Cited By ~ 7

Author(s):

Peixin Fan ◽

Beilei Bian ◽

Lin Teng ◽

Corwin D. Nelson ◽

J. Driver ◽

...

Keyword(s):

Genetic Variation ◽

Gut Microbiota ◽

Bos Taurus ◽

Bos Indicus ◽

Nucleotide Polymorphisms ◽

Paternal Genome ◽

Host Genetics ◽

Microbe Interactions ◽

Host Genetic

Abstract Multiple synergistic factors affect the development and composition of mammalian gut microbiota, but effects of host genetics remain unclear. To illuminate the role of host genetics on gut microbiota, we employed animals with a graduated spectrum of genetic variation with minimal environmental influences. We bred 228 calves with linearly varying breed composition from 100% Angus (Bos taurus) to 100% Brahman (Bos indicus), as a proxy for genetic variation, and then raised the offspring in the same environment with identical diets. We hypothesized each breed would harbor distinct gut microbiota due to genetic influence. We found that the gut microbiota of preweaning calves at 3 months old is significantly affected by host genetics, profoundly by paternal genome. We also demonstrate that single nucleotide polymorphisms in host mucin-encoding genes, critical for gut mucosal health, are significantly correlated with both breed composition and mucin-degrading gut bacteria. We further demonstrate host genetics indirectly changes gut microbiota composition via microbe–microbe interactions. These findings indicate a strong contribution by host genetics in shaping the gut microbiota during early life stages, shedding light on impact of animal breeding on gut microbiota, which is associated with animal growth and health.

Download Full-text

Avian influenza virus with pandemic potential: Suspected role of microbe/microbe and host/microbe interactions in change, adaptive evolution and host range shift

Microbial Ecology in Health and Disease ◽

10.3402/mehd.v17i4.7769 ◽

2005 ◽

Vol 17 (4) ◽

Author(s):

Boris A. Shenderov

Keyword(s):

Influenza Virus ◽

Avian Influenza ◽

Avian Influenza Virus ◽

Host Range ◽

Adaptive Evolution ◽

Range Shift ◽

Microbe Interactions ◽

Host Microbe Interactions

Download Full-text

Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

10.1101/2020.07.28.226019 ◽

2020 ◽

Author(s):

Qiulong Yan ◽

Yu Wang ◽

Xiuli Chen ◽

Hao Jin ◽

Guangyang Wang ◽

...

Keyword(s):

Ethnic Origin ◽

Chinese Adults ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Dna And Rna ◽

Bacterial Microbiome ◽

Chinese Cohort ◽

Host Genetic

AbstractBackgroundTrillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated.Methods and ResultsHere, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.ConclusionsThis study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

Download Full-text

Genetic diversity of Collaborative Cross mice controls viral replication, clinical severity and brain pathology induced by Zika virus infection, independently of Oas1b

10.1101/677484 ◽

2019 ◽

Cited By ~ 3

Author(s):

Caroline Manet ◽

Etienne Simon-Lorière ◽

Grégory Jouvion ◽

David Hardy ◽

Matthieu Prot ◽

...

Keyword(s):

Genetic Diversity ◽

Viral Load ◽

Viral Replication ◽

Clinical Severity ◽

Brain Pathology ◽

Zikv Infection ◽

Infected Cells ◽

Host Genetic ◽

Host Genes

ABSTRACTThe explosive spread of Zika virus (ZIKV) has been associated with major variations in severe disease and congenital afflictions among infected populations, suggesting an influence of host genes. We investigated how genome-wide variants could impact susceptibility to ZIKV infection in mice. We first describe that the susceptibility of Ifnar1 knockout mice is largely influenced by their genetic background. We then show that the broad genetic diversity of Collaborative Cross mice, which receptor to type I interferon (IFNAR) was blocked by anti-IFNAR antibody, expressed phenotypes ranging from complete resistance to severe symptoms and death with large variations in the peak and rate of decrease of plasma viral load, in brain viral load, in brain histopathology and in viral replication rate in infected cells. Differences of susceptibility between CC strains were correlated between Zika, Dengue and West Nile viruses. We identified highly susceptible and resistant mouse strains as new models to investigate the mechanisms of human ZIKV disease and other flavivirus infections. Genetic analyses revealed that phenotypic variations are driven by multiple genes with small effects, reflecting the complexity of ZIKV disease susceptibility in human population. Notably, our results rule out a role of the Oas1b gene in the susceptibility to ZIKV. Altogether, this study emphasizes the role of host genes in the pathogeny of ZIKV infection and lays the foundation for further genetic and mechanistic studies.IMPORTANCEIn recent outbreaks, ZIKV has infected millions of people and induced rare but potentially severe complications, including Guillain-Barré syndrome and encephalitis in adults. While several viral sequence variants were proposed to enhance the pathogenicity of ZIKV, the influence of host genetic variants in the clinical heterogeneity remains mostly unexplored. We have addressed this question using a mouse panel which models the genetic diversity of human population and a ZIKV strain from a recent clinical isolate. Through a combination of in vitro and in vivo approaches, we demonstrate that multiple host genetic variants determine viral replication in infected cells, and clinical severity, kinetics of blood viral load and brain pathology in mice. We describe new mouse models expressing high susceptibility or resistance to ZIKV and to other flaviviruses. These models will facilitate the identification and mechanistic characterization of host genes that influence ZIKV pathogenesis.

Download Full-text

Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence

10.1101/2021.11.13.468422 ◽

2021 ◽

Author(s):

Curtis M Lively ◽

Julie Xu ◽

Frida Ben-Ami

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Infection Prevalence ◽

Strong Positive Correlation ◽

Frequency Dependent ◽

Frequency Dependent Selection ◽

Host Diversity ◽

Host Genetic ◽

Host Parasite

Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.

Download Full-text