Influenza A H1N1 Induced Disturbance of the Respiratory and Fecal Microbiome of German Landrace Pigs – a Multi-Omics Characterization

Abstract

Here, we used swine as a biomedical model to elucidate the impact of influenza A H1N1 infection on structure and function of the respiratory and gastrointestinal tract microbiome by employing a multi-omics analytical approach. To our knowledge, this is the first study to investigate the temporal development of the porcine microbiome and to provide insights into the functional capacity of the gastrointestinal microbiome during influenza A virus infection.

Application of a maximal-clique based community detection algorithm to gut microbiome data reveals driver microbes during influenza A virus infection

“…In order to test the reproducibility of the proposed workflow, we computed the size of intersection between the microbial families reported to be instrumental in Borey et al ( 2021 ) and Gierse et al ( 2021 ) and the ones found by applying our workflow to these two datasets. The sequences of the first dataset (Borey et al, 2021 ) were downloaded from the NCBI Sequence Read Archive using accession number PRJNA647267 and processed using SHAMAN tool (Volant et al, 2020 ) in order to obtain the OTU abundance matrix and annotation table.…”

“…The sequences of the first dataset (Borey et al, 2021 ) were downloaded from the NCBI Sequence Read Archive using accession number PRJNA647267 and processed using SHAMAN tool (Volant et al, 2020 ) in order to obtain the OTU abundance matrix and annotation table. In case of the second experiment (Gierse et al, 2021 ), We used the sequence data obtained from the fecal samples of healthy and infected cohorts. Supplementary Figures 5A , B show that we achieved descent Jaccard similarity coefficient scores 0.70 and 0.66 for these two datasets, respectively.…”

“…The real data we use is from an influenza infection experiment carried out in pigs at the Department of Experimental Animal Facilities and Biorisk Management of the Friedrich Loeffler Institute within the H1N1pdm09 animal experiment (Schwaiger et al, 2019 ; Gierse et al, 2020 , 2021 ). H1N1 infection was carried out in 19 pigs, three additional animals were used as controls.…”

“…The purpose of the second infection was to trigger the host immune response and explicate the crosstalk between host immune system and gut microbiome. Moreover, it is reported that the presence of influenza A virus matrix protein was observed after the first infection, whereas it was not detected after the second infection, implying a fast recovery of the infected animals (Gierse et al, 2021 ).…”

A high-fat diet disrupts the hepatic and adipose circadian rhythms and modulates the diurnal rhythm of gut microbiota-derived short-chain fatty acids in gestational mice

“…Since the rhythmic patterns of metabolic genes were not entirely regulated by their core clock, we hypothesized that the gut microbiota played a role in modulating the host peripheral circadian clock and downstream genes. Intriguingly, we found that the HF altered the diurnal rhythm of gut microbiota in a diverse manner, which we classified into three categories: (1) phase shift: contrary to the phase-advanced circadian clock in the liver and WAT, the relative abundance of butyric acid-producing family Clostridiaceae_1 was significantly phase-delayed in the HF group compared with the Ctr group ( 50 ); (2) loss rhythmicity: Veillonellaceae and Prevotellaceae have been confirmed to be responsible for producing SCFAs ( 51 , 52 ), and both lost rhythmicity in the HF group; (3) gain rhythmicity: the families Erysipelotrichaceae and Ruminococcaceae both gained rhythmicity in the HF group compared with the Ctr group. The study has revealed that Erysipelotrichaceae accelerated cholesterol accumulation by producing trimethylamine N -oxide, indicating its role in modulating lipid metabolism ( 53 ).…”