Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

Abstract

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes

“…In addition to identification of commensal bacteria typically associated with healthy swine, we identified pathogenic species that can cause illness and physiological changes in the animal’s gastrointestinal tract. These micro-organisms can also be shed into the environment, presenting a potential threat to public health [20, 21]. While other, non-bacterial microbial pathogens can also infect farmed pigs [37, 38], we did not identify a high proportion of non-bacterial DNA in our samples, however eukaryotic pathogen databases are poorly populated and represents an opportunity that could be reassessed in future studies.…”

“…In swine, shotgun metagenome analyses have also been applied to investigate the antimicrobial and heavy metal resistance genes harboured in fattening swine caecal microbiomes, as well as the effect probiotic supplementation has on piglet health [17,18]. While previous studies have shown that caecal microbiomes are diverse and can be correlated with high feed efficiency and utilization [9,19], few studies have utilized the intestinal scraping technique to study micro-organisms directly interacting with the host, particularly in swine [20,21]. In this study, a shotgun metagenome approach was implemented to thoroughly investigate and characterize the pathogenic and commensal bacteria harboured in the swine gut microbiome.…”

Recycling of Citric Acid Waste for Potential Use as Animal Feed through Fermentation with Lactic Acid Bacteria and a Mixture of Fibrolytic Enzymes

“…Lactic acid bacteria are commonly used for the preservation of food and animal feed. Lactic acid bacteria are extensively employed in silage because of their potential to speed up lactic acid formation, lower pH, prevent protein breakdown, minimize dry matter (DM) loss, and improve animal performance [ 11 , 12 , 13 ].…”

“…They also create lactic acid, organic acids, hydrogen peroxide, and bacteriocins [ 11 ]. Finally, the generation of lactic acid during lactic acid fermentation significantly lowers the pH, which appears to inhibit the growth of Gram-negative pathogenic bacteria [ 12 , 13 ]. When forecasting the effectiveness of fermentation and deciding whether to apply bacterial inoculants to silage, the quantity and features of LAB have grown to be a crucial consideration.…”

Alignment-free Phylogenetic Placement and its Applications

“…Given an appropriate selection of reference sequences for the query sequences under consideration, phylogenetic placement is a valuable tool in phylogenetics and metagenomics: The major application of phylogenetic placement has been the identification of short metataxonomic read sequences [470][471][472]. Here, placement results provide information on the identity and evolutionary context of short sequencing reads.…”