AUTHOR=Meene Alexander , Gierse Laurin , Schwaiger Theresa , Karte Claudia , Schröder Charlotte , Höper Dirk , Wang Haitao , Groß Verena , Wünsche Christine , Mücke Pierre , Kreikemeyer Bernd , Beer Martin , Becher Dörte , Mettenleiter Thomas C. , Riedel Katharina , Urich Tim 

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

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1250140

DOI=10.3389/fmicb.2023.1250140

ISSN=1664-302X

ABSTRACT=<sec id="sec1"><title>Background</title><p>Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine.</p></sec><sec id="sec2"><title>Aims/Methods</title><p>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.</p></sec><sec id="sec3"><title>Results and discussion</title><p>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 <italic>Methanobrevibacter</italic> and <italic>Methanosphaera</italic>. 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 <italic>Methanobrevibacter</italic> and <italic>Methanosphaera</italic> 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.</p></sec><sec id="sec4"><title>Conclusions/Take home message</title><p>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.</p></sec>