Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine

Abstract

Background: Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine.

Aims/methods: This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics.

Results and discussion: We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea.

Conclusions/take home message: Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.

Keywords: 16S rRNA gene sequencing; intestinal tract microbiome; metaproteomics; metatranscriptomics; methanogenesis; methanogenic archaea.

Figure 1

Alpha diversity parameters and community composition of the porcine intestinal tract (naïve and infected individuals summarized). Boxplots with total number of ASVs (A) and percentage of archaeal ASVs (B) between sample types. Barplots with total prokaryotic (bacterial and archaeal) community composition (C) and archaeal community composition (D). Color-coding represents the phylum affiliation, with Firmicutes in blue color grades, Bacteroidetes in green, Euryarchaeota in brown and Spirochaetes in yellow. Bacterial genera below 1% relative abundance were excluded and all present archaeal genera remained in the dataset.

Figure 2

Temporal dynamics of archaeal phylotypes in feces of healthy and Influenza A virus-infected swine. Bubble plot of the 12 most abundant ASVs and corresponding Blast output to species level with highest sequence identity with Mb. = Methanobrevibacter and Ms. = Methanosphaera, and on family level with Methanomethylophilaceae. Bubble size indicates the absolute amount of archaeal read counts per million sequences (archaea and bacteria).

Figure 3

Temporal and longitudinal development of the archaeal community composition in swine feces and intestinal samples. Nonmetric multidimensional scaling (nMDS) plots, based on Bray-Curtis dissimilarities of the archaeal community composition over 31 days in feces on ASV-level [(A), n = 19] and of different intestinal locations and feces from the individuals [(B), n = 6]. Treatment in (A) and (B) is represented by the colors blue (healthy) and red (H1N1-infected). Sample type in (B) is represented by the shape and polygon areas highlighting the location-specific clustering. The ileal data points are located on the right, while the colonal and fecal data points are clustered on the left of the plot.

Figure 4

Overview of methane metabolism-related mRNA transcripts for the family Methanobacteriaceae (left) and a heatmap detailing the enzymatic distribution for the predominant archaeal genera Methanobrevibacter and Methanosphaera (right).