Introduction

As one of the important components of ruminant gastrointestinal tract (GIT) microbiome, archaea are involved in many biological processes, especially methanogenesis. However, the diversity and individual metabolic characteristics of archaea in this habitat remain largely understudied, partly due to the lack of a unified reference genome catalog.

Objectives

This study aimed to construct a unified genome map for taxonomic and functional exploration of ruminant GIT archaea in the future.

Methods

We collected archaeal genomes from public sources and new data of this study. We performed phylogenetic analysis, functional genomics analyses, prophages identification based on the genomes. Using collected genomes as a reference, we conducted metagenomic and metatranscriptomic analyses on rumen fluid samples from 18 dairy cows with different methane (CH₄) production.

Results

We constructed the ruminant GIT archaeal genomes (RGAG) by compiling 405 strain-level (160 species) non-redundant archaeal genomes from more than 10 ruminant species. The functional heterogeneity and methanogenic structure within RGAG was investigated. RGAG possessed 1,124 (99.5 %) unknown microbial biosynthetic gene clusters. A survey of RGAG-borne prophages identified 63 prophages with 122 host-beneficial genes and 18 auxiliary metabolic genes (AMGs). The pipeline for both metagenomics and metatranscriptomics generated in the study revealed the roles of archaeal genomes under-assessed in general analyses of muti-omics. The highly expressed genus Methanosphaera was negatively correlated with CH₄ production.

Conclusion

A unified genome map of ruminant GIT archaea is constructed in the study. Functional genomics indicates that the multifaceted functions of RGAG remains undiscovered. Multi-omics analyses reveals the advantages of metatranscriptomics over metagenomics in studying rumen archaeal communities. Differences in rumen archaeal community structure among cattle with different CH₄ production may reflect the balance between rumen hydrogen production and methanogenesis. Our work provides new understanding of archaeal functions in the ruminant GIT and potential targets for future CH₄ reduction.

中文翻译：

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基于反刍动物胃肠道古细菌基因组图谱的肠道甲烷生产新见解

 介绍

作为反刍动物胃肠道 （GIT） 微生物组的重要组成部分之一，古细菌参与许多生物过程，尤其是甲烷生成。然而，该栖息地中古细菌的多样性和个体代谢特征在很大程度上仍未得到充分研究，部分原因是缺乏统一的参考基因组目录。

 目标

本研究旨在构建统一的基因组图谱，以便将来对反刍动物 GIT 古细菌进行分类学和功能探索。

 方法

我们从公共来源和本研究的新数据中收集了古细菌基因组。我们进行了系统发育分析、功能基因组学分析、基于基因组的噬菌体鉴定。以收集的基因组为参考，我们对 18 头产生不同甲烷 （CH₄） 的奶牛的瘤胃液样本进行了宏基因组学和元转录组学分析。

 结果

我们通过编译来自 10 多个反刍动物物种的 405 个菌株水平 （160 个物种） 非冗余古细菌基因组来构建反刍动物 GIT 古细菌基因组 （RGAG）。研究了 RGAG 内的功能异质性和产甲烷结构。RGAG 拥有 1,124 个 （99.5 %） 未知微生物生物合成基因簇。对 RGAG 携带的原噬菌体的调查确定了 63 个原噬菌体，具有 122 个宿主有益基因和 18 个辅助代谢基因 （AMG）。研究中生成的宏基因组学和元转录组学管道揭示了在多组学的一般分析中被低估的古细菌基因组的作用。高表达属 Methanosphaera 与 CH₄ 的产生呈负相关。

 结论

该研究构建了反刍动物 GIT 古细菌的统一基因组图谱。功能基因组学表明，RGAG 的多方面功能仍未被发现。多组学分析揭示了元转录组学在研究瘤胃古细菌群落方面优于宏基因组学的优势。CH₄ 产量不同牛瘤胃古细菌群落结构的差异可能反映了瘤胃产氢和甲烷生成之间的平衡。我们的工作为反刍动物 GIT 中的古细菌功能以及未来减少 CH₄ 的潜在目标提供了新的理解。