Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention.

Chunlong Mu,Yong Su,Yuxiang Yang,Erwin G Zoetendal,Weiyun Zhu

doi:10.3389/fmicb.2017.00797

Abstract

Early-life antibiotic interventions can change the predisposition to disease by disturbing the gut microbiota. However, the impact of antibiotics on gut microbiota in the gastrointestinal tract is not completely understood, although antibiotic-induced alterations in the distal gut have been reported. Here, employing a piglet model, the microbial composition was analyzed by high-throughput 16S rRNA gene sequencing and PICRUSt predictions of metagenome function. The present study showed clear spatial variation of microbial communities in the stomach and intestine, and found that the administration of antibiotics (a mixture of olaquindox, oxytetracycline calcium, kitasamycin) in early life caused markedly differential alterations in the compartmentalized microbiota, with major alterations in their spatial variation in the lumen of the stomach and small intestine. In piglets fed an antibiotic-free diet, most of the variation in microbial communities was concentrated in gut segments and niches (lumen/mucosa). The microbial diversity was higher in the lumen of stomach and duodenum than that in ileum. The early-life antibiotic intervention decreased the abundance of some Lactobacillus species and increased the abundance of potentially pathogenic Streptococcus suis in the lumen of the stomach and small intestine. Interestingly, the intervention increased the abundance of Treponema only in the colonic lumen and that of Faecalibacterium only in the ileal mucosa. Furthermore, the antibiotic intervention exerted location-specific effects on the functional potential involved in the phosphotransferase system (decreased sucrose phosphotransferase in the stomach) and antibiotic-resistance genes (increased in the colon). These results point to an early-life antibiotic-induced dramatic and location-specific shift in the gut microbiota, with profound impact in the foregut and less impact in the hindgut. Collectively, these findings provide new insights into the membership of the microbiota along the gastrointestinal tract of piglets and highlight the importance of considering the foregut microbiota in health management of piglets at early life.

Highlights

Gut microbiota are important to the metabolism and health of their hosts
The antibiotic intervention significantly increased the relative abundance of Treponema and decreased the relative abundance of Prevotella compared with the control group (q < 0.05, Figure 4A). These results suggested that the effects of the antibiotics on the microbial composition in the lumen varied between gut locations
By high-throughput sequencing of 16S rRNA genes, we analyzed the impact of an early-life antibiotic intervention on microbial community diversity and functions in the gastrointestinal tract (GIT) of piglets

Summary

Introduction

Gut microbiota are important to the metabolism and health of their hosts. The composition and distribution of the microbiota of the intestine of pigs have been extensively investigated (Kim and Isaacson, 2015). Our previous studies found that the cultured luminal and mucosal microbes from porcine gut had different role in amino acid metabolism (Yang Y.X. et al, 2014). These suggest that microbiota from different intestinal compartments and niches have different functional roles. It is widely regarded that compared to the microbial numbers in the colon (1011–1012 CFU/mL), stomach and small intestine have relatively low numbers of bacteria, with 101–103 CFU/mL in the lumen of stomach and duodenum, and 104–107 CFU/mL in the lumen of jejunum and ileum (O’Hara and Shanahan, 2006). To gain further insight into the distribution of gut microbiota, it is crucial to understand the spatial variation in microbiota across the stomach to intestine

Methods

Discussion

Conclusion