A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture

Gilroy, Rachel; Ray, Anuradha; Getino, María; Pursley, Isabella; Horton, Daniel; Alikhan, Nabil-Fareed; Baker, David; Gharbi, Karim; Hall, Neil; Watson, Mick; Adriaenssens, Evelien M.; Foster-Nyarko, Ebenezer; Jarju, Sheikh; Secka, Arss; Antonio, Martín; Oren, Aharon; Chaudhuri, Roy R.; Ragione, Roberto La; Hildebrand, Falk; Pallen, Mark J.

doi:10.21203/rs.3.rs-56027/v3

Cited by 3 publications

(2 citation statements)

References 83 publications

(119 reference statements)

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“…However, in both systems, the bacteria and genes responsible for uric acid breakdown (uricolysis) are unknown. We analyzed metagenome assembled genomes (MAGs) from chicken feces (Gilroy et al, 2020) and the termite hindgut (Herve et al, 2020) and found that many organisms harbor the uric acid gene cluster (subset shown in Figure 9 ). Thus, we find that the uric acid gene cluster is distributed broadly across different ecosystems on the planet and may play an important role in global nitrogen cycling.…”

Section: Discussionmentioning

confidence: 99%

A widely distributed gene cluster compensates for uricase loss in hominids

Liu

Jarman

Low³

et al. 2022

Preprint

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Approximately 15% of US adults have circulating levels of uric acid above its solubility limit, which is causally linked to the disease gout. In most mammals, uric acid elimination is facilitated by the enzyme uricase. However, human uricase is a pseudogene, having been inactivated early in hominid evolution. Though it has long been known that uric acid is eliminated in the gut, the role of the gut microbiota in hyperuricemia has not been studied. Here we identify a widely distributed bacterial gene cluster that encodes a pathway for uric acid degradation. Stable isotope tracing demonstrates that gut bacteria metabolize uric acid to xanthine or short chain fatty acids. Ablation of the microbiota in uricase-deficient mice causes severe hyperuricemia, and anaerobe-targeted antibiotics increase the risk of gout in humans. These data reveal a role for the gut microbiota in uric acid excretion and highlight the potential for microbiome-targeted therapeutics in hyperuricemia.

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Section: Discussionmentioning

confidence: 99%

A widely distributed gene cluster compensates for uricase loss in hominids

Liu

Jarman

Low³

et al. 2022

Preprint

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“…Chicken microbiome studies include mostly 16S rRNA gene amplicon sequencing-based studies, but there have been some metagenomics approaches as well ( Gilroy et al, 2021 ). Microbial compositional results of similar chicken breeds have shown variation that can be attributed to experimental protocol or differences between individual chickens ( Borda-Molina et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species

Jadhav

Han²,

Fasina³

et al. 2022

Front. Physiol.

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The chicken gastrointestinal tract has a diverse microbial community. There is increasing evidence for how this gut microbiome affects specific molecular pathways and the overall physiology, nervous system and behavior of the chicken host organism due to a growing number of studies investigating conditions such as host diet, antibiotics, probiotics, and germ-free and germ-reduced models. Systems-level investigations have revealed a network of microbiome-related interactions between the gut and state of health and behavior in chickens and other animals. While some microbial symbionts are crucial for maintaining stability and normal host physiology, there can also be dysbiosis, disruptions to nutrient flow, and other outcomes of dysregulation and disease. Likewise, alteration of the gut microbiome is found for chickens exhibiting differences in feather pecking (FP) behavior and this alteration is suspected to be responsible for behavioral change. In chickens and other organisms, serotonin is a chief neuromodulator that links gut microbes to the host brain as microbes modulate the serotonin secreted by the host’s own intestinal enterochromaffin cells which can stimulate the central nervous system via the vagus nerve. A substantial part of the serotonergic network is conserved across birds and mammals. Broader investigations of multiple species and subsequent cross-comparisons may help to explore general functionality of this ancient system and its increasingly apparent central role in the gut-brain axis of vertebrates. Dysfunctional behavioral phenotypes from the serotonergic system moreover occur in both birds and mammals with, for example, FP in chickens and depression in humans. Recent studies of the intestine as a major site of serotonin synthesis have been identifying routes by which gut microbial metabolites regulate the chicken serotonergic system. This review in particular highlights the influence of gut microbial metabolite short chain fatty acids (SCFAs) on the serotonergic system. The role of SCFAs in physiological and brain disorders may be considerable because of their ability to cross intestinal as well as the blood-brain barriers, leading to influences on the serotonergic system via binding to receptors and epigenetic modulations. Examinations of these mechanisms may translate into a more general understanding of serotonergic system development within chickens and other avians.

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Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Afonso,

Afonso

2023

Veterinary Sciences

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Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of “semi-quantitative” information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.

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A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture

Cited by 3 publications

References 83 publications

A widely distributed gene cluster compensates for uricase loss in hominids

A widely distributed gene cluster compensates for uricase loss in hominids

Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

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