Microbiome dynamics in new-born swine: Comprehensive metagenomic analysis from Day 1 to Day 10 after the birth of piglets.

Microbiome dynamics in new-born swine: Comprehensive metagenomic analysis from Day 1 to Day 10 after birth of piglets. Bacterial infections are among the most frequent causes of death in farms. Among others, Clostridium difficile emerges to be one of the worst pathogens leading to premature death in new-born piglets in swine farms, causing severe diarrhea; this is often managed through therapies that inhibit the toxins’ effects while not removing the bacterial pathogen from the swine intestine. This research, in addition to investigating the abundance of C. difficile in the sows' and piglets' microbiomes in a farm adopting antibiotic vaccines to neutralize the effect of its toxins, delves into the evolution of microorganisms in piglets from 24 to 240 hours after birth. Additionally, a comparative analysis of the microbial composition between piglets and sows at 24, 96, and 240 hours is conducted. This study undertakes a thorough microbiome analysis of pig fecal samples, focusing on sow-piglet pairs from distinct groups to count for 10 mother sows and 3 piglets each. Samples are collected at pivotal time points — 24, 96, and 240 hours after birth - to reveal insights into the microbial landscape. Covariates such as time, diarrhea occurrence, sex, category (sow or piglet sibling), gestation, family, and room are included in the metadata. Sows that are primiparous and pluriparous are indicated, as the formers have been exposed to the gestational area of the farm and where birthing takes place only once. The research employs a robust pipeline, including sample collection, sequencing, and QIIME2-based pre-processing of data. Diversity analyses, encompassing different indices, are adopted to explore microbial compositional variations at different taxonomic levels; finally, differential abundance analysis is performed using the MAASLIN2 package. Results from Alpha diversity analysis unveil significant associations, with time, category, and - at the genus level - diarrheic phenotype. The Beta diversity analysis shows significant microbial distinctions emerging between sows and piglets, with piglets exhibiting a pronounced microbial compositional shift at 24 hours post-birth. Surprisingly, no significant differences arise between microbial compositions at 96 and 240 hours after birth for piglets, indicating stability during this critical developmental phase. At the genus level, there is a noteworthy convergence of piglet microbial compositions towards sow patterns, particularly evident at 48 hours post-birth. However, by 240 hours, a subtle but discernible separation merges again. Similar trends are observed at the species level, although at a less pronounced level. Contrastingly, ASV analysis shows a distinct separation at all considered time points, highlighting a unique microbial pattern that deviates from the observed trends at the genus and species levels. Differential abundance analysis reveals the absence of specific C. difficile-related scenarios but highlights the differential presence of other Clostridium genera, with Clostridium perfringens significantly abundant in samples 24 hours from birth. Additionally, Bacteroides ovatus exhibits a threefold increase in diarrheic samples compared to non-diarrheic samples. This study contributes valuable insights into swine microbiome dynamics, shedding light on microbial variations, stability, and evolution of new-born piglets and sows across 24,96 and 240 hours after birth.