The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids

Abstract

BackgroundSub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown.ResultsWe generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal’s gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes.ConclusionThe reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0590-5) contains supplementary material, which is available to authorized users.

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

“…Our gene-based assembly approach allowed us to greatly expand the known gene catalogue of the vertebrate gut microbiome beyond just the abundant taxa, with a total of >150 million non-redundant coding sequences generated, comprising 88 bacterial and 11 archaeal phyla ( Figure 5). In comparison, recent large-scale metagenome assemblies of the gut microbiome from chickens, pigs, rats, and dogs have generated 7.7, 9.04, 7.7, 5.1, and 1.25 million non-redundant coding sequences, respectively 8,[36][37][38] . It is also illustrative to consider that a recent large-scale metagenome assembly of cattle rumen metagenomes generated 69,678 non-redundant genes involved in carbohydrate metabolism 9 , while our gene collection comprised substantially more CAZy-annotated gene clusters ( n = 87,573), even after collapsing at 50% sequence identity.…”

“…However, such large-scale metagenome assembly-based approaches have not been as extensively applied to most non-human vertebrates. The low amount of metagenome reads classified in some recent studies of the rhinoceros, chicken, cod, and cow gut/rumen microbiome suggests that databases lack much of the genomic diversity in less-studied vertebrates [8][9][10][11] . Indeed, the limited number of studies incorporating metagenome assembly hint at the extensive amounts of as-of-yet novel microbial diversity across the >66,000 vertebrate species on our planet.…”

Sanguinarine metabolism and pharmacokinetics study in vitro and in vivo

“…In China, the extract of M. cordata containing SA was approved as the first traditional Chinese medicine of veterinary drug product which has been proved to possess anti‐inflammatory and growth‐promoting functions (Mei‐Yuan et al, ). Recent metagenome study and the genomic sequence of M. cordata emphasis the importance of this traditional Chinese medicine (Huang et al, ). Due to its biological effects and potential commercial use, research on the pharmacokinetics of SA is necessary in food animals.…”

“…medicine (Huang et al, 2018). Due to its biological effects and potential commercial use, research on the pharmacokinetics of SA is necessary in food animals.…”

Galacto-oligosaccharides modulate the juvenile gut microbiome and innate immunity to improve broiler chicken performance

“…To mitigate the effect of antimicrobial reduction a variety of strategies has been evaluated (8). These include the addition of dietary prebiotic (9,10), phytobiotic dietary additives (11), the incorporation of beneficial enzymes in poultry feed (12), and the administration of live probiotic bacteria in various combinations of the above (7,13). Recent developments in sequencing technologies have led to a greater understanding of mechanisms and effects of these treatments on the gut microbiota and the interaction with host-related functions involved in intestinal health (14,15).…”