The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.

Feilong Deng,Yunjuan Peng,Yushan Li,Hua Li,Samantha Howe,Ying Li,Jiangchao Zhao,Hua Yang,Yingping Xiao,Xiaoyuan Wei,Xiaofan Wang

doi:10.3390/ani11072139

Abstract

Simple SummaryArchaea is identified as the key link in the interaction between gut microbiota and host metabo-lism. Studies on human and mice have reported archaea, especially methanogenic archaea, makes an important impact on the energy harvesting capacity of the host by improving fermentation. But, in pigs, the metabolic potential of archaea at different production stages are still largely unknown. Herein, we re-analyzed 276 metagenomic samples to explore the diversity, composi-tion, and potential functions of archaea in pigs. The results showed significant regional variations in archaeal composition. Furthermore, the Metacyc pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, and archaea may be involved in carbohydrate metabolism and de novo synthesis of some kinds of essential amino acid. Overall, metagenomic re-analysis revealed that the composition and functional potential of archaea in the swine gut and suggested that archaea may make an important function in pigs.Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

Highlights

IntroductionBefore Dr Carl Woese and his colleagues separated archaea
Before Dr Carl Woese and his colleagues separated archaea from the bacteria domain based on phylogenetic analysis of ribosomal RNA sequences, archaea were considered a subgroup of bacteria [1]
A few studies have in examined are an essential class of gut microorganisms humans archaeal and anicomposition by sequencing methods; most studies only focused on mals, they have been neglected for many years

Summary

Introduction

Before Dr Carl Woese and his colleagues separated archaea At that time) from the bacteria domain based on phylogenetic analysis of ribosomal RNA sequences, archaea were considered a subgroup of bacteria [1]. To highlight the differences between archaea and bacteria, Dr Carl Woese formally proposed the name of “Archaea”. With the advancement of research technologies and tools, a large number of novel archaea and their characteristics have been discovered. Archaea have highly diverse energy sources and unique metabolic characteristics and cell physiology, making it possible for them to live in various extreme environments, such as extreme temperature [3], high-salt [4], extreme alkaline [5], or acidic environments [6]. As a “young” group with unique natural capabilities and biological characteristics, archaea have attracted increasing research interest in the past decade

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