<i>IL23R</i>-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease

Zakrzewski, Martha; Simms, Lisa A.; Brown, Allison; Appleyard, Mark; Irwin, James; Waddell, Nicola; Radford‐Smith, Graham

doi:10.1093/ecco-jcc/jjy188

Cited by 31 publications

(22 citation statements)

References 49 publications

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“…In fact, genetic variants in the IL23R gene have been associated with different susceptibility to fungal infections [ 40 ] and IL-23R deficient mouse was susceptible to systemic infection with C. albicans [ 41 ]. Furthermore, IL-23R had been reported to be involved in the diversity of ileum microbiota in humans [ 42 ]. In the same chromosome, PIK3C3 gene gathered two SNPs associated to Blastocystis abundance.…”

Section: Discussionmentioning

confidence: 99%

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

et al. 2020

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Background: The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results: Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions: Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.

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Section: Discussionmentioning

confidence: 99%

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

et al. 2020

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“…In humans, the family comprises on average 0.01% of the fecal microbiota [21]. Its fine-scale distribution along the human gastrointestinal tract remains to be clarified; but in addition to feces, Christensenellaceae has been detected in human colonic mucosa, ileum, and appendix, and there is also suggestive evidence of airway colonization [21, 56–59]. The family Christensenellaceae is widespread across human populations, and is reported from subjects inhabiting North America [60–62], South America [63, 64], Europe [21, 65], Asia [66, 67], Africa [68–70], and Australia [71].…”

Section: Christensenellaceae Is Ubiquitous Among Humans and Other Animentioning

confidence: 99%

“…The A allele of this variant has been associated with a reduced risk of ileal Crohn’s disease (CD). Within a population of individuals with no signs of CD or other gastrointestinal disorders, a significantly greater relative abundance of Christensenellaceae was detected in the feces of individuals harboring the protective allele (AG genotype) compared to the population with the GG genotype [56]. How the IL23R genotype may affect members of the gut microbiota remains to be clarified.…”

Section: The Christensenellaceae Are Linked To Host Genetic Variationmentioning

confidence: 99%

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health

2019

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The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.

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“…For example, the family Christensenellaceae, which are the most heritable bacteria in the study of Goodrich et al in human, show a heritability of 0.39, while other studies reported an heritability of 0.62 for this family [48,49]. Candidate genes in human that might be associated with Christensenellaceae abundance, such as ILR23 or FUT2,were also identi ed [50,51]. In chicken, studies identi ed differences in microbiota composition between genetic lines, for instance in two chicken lines that differ in their susceptibility to bacterial infections [52] or in two divergent genetic lines for body weight [53].…”

Section: Impact Of the Genetic Line On The Microbiota Compositionmentioning

confidence: 98%

Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken

Cazals¹,

Estellé²,

Bruneau³

et al. 2020

Preprint

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Background Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication through the consumption of contaminated poultry products. Genetic selection of animals more resistant to Salmonella carriage and the modulation of gut microbiota are two promising ways of decreasing individual Salmonella carriage. This study aims to identify the main genetic and microbial factors controlling the individual levels of Salmonella carriage in chickens (Gallus gallus) in controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines, N and 61, were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce the recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition through a 16S rRNA gene high-throughput sequencing approach. Results Results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Out of 617 Operational Taxonomic Units (OTUs), over 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between high and low Salmonella carriers, with 39 differentially abundant OTUs. Finally, via metagenome functional prediction based on 16S data, we identified several metabolic pathways potentially associated to microbiota taxonomic differences (e.g. butyrate metabolism) between high and low carriers. Conclusions Overall, this study demonstrates that the caecal microbiota composition of the N and 61 lines is influenced by the host genetics, which could be one of the reasons why these lines differ for their Salmonella carriage in experimental infection conditions.

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IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease

Cited by 31 publications

References 49 publications

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health

Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken

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