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Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments.

ABSTRACT: Intestinal microbiota plays a crucial role in immune development and disease progression in mammals from birth onwards. The gastrointestinal tract of newborn mammals is rapidly colonized by microbes with tremendous biomass and diversity. Understanding how this complex of segmental communities evolves in different gastrointestinal sites over time has great biological significance and medical implications. However, most previous reports examining intestinal microbiota have focused on fecal samples, a strategy that overlooks the spatial microbial dynamics in different intestinal segments. Using intestinal digesta from six intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of newborn piglets, we herein conducted a large-scale 16S rRNA gene sequencing-based study to characterize the segmental dynamics of porcine gut microbiota at eight postnatal intervals (days 1, 7, 14, 21, 28, 35, 120 and 180). A total of 4,465 OTUs were obtained and showed that the six intestinal segments could be divided into three parts; in the duodenum-jejunum section, the most abundant genera included Lactobacillus and Bacteroides; in the ileum, Fusobacterium and Escherichia; and in the cecum-rectum section, Prevotella. Although the microbial communities of the piglets were similar among the six intestinal segments on postnatal day 1, they evolved and quickly differentiated at later intervals. An examination of time-dependent alterations in the dominant microbes revealed that the microbiome in the large intestine was very different from and much more stable than that in the small intestine. The gut microbiota in newborn piglets exhibited apparent temporal and spatial variations in different intestinal segments. The database of gut microbes in piglets could be a referable resource for future studies on mammalian gut microbiome development in early host growth phases.

SUBMITTER: Liu Y

PROVIDER: S-EPMC6400902 | biostudies-other | 2019 Mar

REPOSITORIES: biostudies-other

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Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments.

Liu Ying Y Zheng Zhijun Z Yu Lihuai L Wu Sen S Sun Li L Wu Shenglong S Xu Qian Q Cai Shunfeng S Qin Nan N Bao Wenbin W

Scientific reports 20190305 1

Intestinal microbiota plays a crucial role in immune development and disease progression in mammals from birth onwards. The gastrointestinal tract of newborn mammals is rapidly colonized by microbes with tremendous biomass and diversity. Understanding how this complex of segmental communities evolves in different gastrointestinal sites over time has great biological significance and medical implications. However, most previous reports examining intestinal microbiota have focused on fecal samples ...[more]

PMID: 30837612

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Project description:Background:Most research on galacto-oligosaccharides (GOS) has mainly focused on their prebiotic effects on the hindgut, but their beneficial effects on the small intestine (SI) have received little attention. Since jejunum is the important place to digest and absorb nutrients efficiently, optimal maturation of the jejunum is necessary for maintaining the high growth rate in the neonate. Therefore, this study investigates the effect of the early intervention with GOS on the intestinal development of the jejunum. Methods:A total of 6 litters of neonatal piglets (10 piglets per litter; Duroc × Landrace × Large White) with an average birth weight of 1.55?±?0.05 kg received 1 of 2 treatments based on their assignment to either the control (CON) group or the GOS (GOS) group in each litter. Piglets in the GOS group were orally administrated 10 mL of a GOS solution (reaching 1 g GOS/kg body weight) per day from the age of 1 to 7 d; the piglets in the CON group were treated with the same dose of physiological saline. All piglets were weaned on d 21. On d 8 and 21 of the experimental trial, 1 pig per group from each of the 6 litters was euthanized. Results:The early intervention with GOS increased the average daily gains in the third week (P?<?0.05). Decreased crypt depth was also observed in the jejunum of the piglets on d 21 (P?<?0.05). The early intervention with GOS increased the jejunal lactase activity on d 8, maltase activity and sucrase activity on d 21 (P?<?0.05). In addition, the early intervention with GOS also facilitated the mRNA expression of Sodium glucose co-transporter 1 (SGLT1) on d 8 and the mRNA expression of Glucose transporter type 2 (GLUT2) on d 21 (P?<?0.05). It was further determined that GOS up-regulated the mRNA expression of preproglucagon (GCG), insulin-like growth factor 1 (IGF-1), insulin-like growth factor 1 receptor (IGF-1R) and epidermal growth factor (EGF). GOS also up-regulated the protein expression of glucagon-like peptide-2 (GLP-2) and EGF in the jejunum of the piglets. Furthermore, it was also found that GOS enhanced the protein expression of ZO-1 and occludin on d 8 (P?<?0.05), as well as increased the mRNA expression of TGF-? and decrease the mRNA expression of IL-12 (P?<?0.05). Conclusions:These results indicate that GOS have a positive effect on piglet growth performance in addition to decreasing the crypt depth and enhancing functional development in jejunum of suckling piglets.

Project description:BackgroundMicrobiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we evaluate the accuracy of operational taxonomic unit (OTU) generation, taxonomic classification, alpha- and beta-diversity measures for different settings in QIIME, MOTHUR and a pplacer-based classification pipeline, using a novel software package: DECARD.ResultsIn-silico we generated 100 synthetic bacterial communities approximating human stool microbiomes to be used as a gold-standard for evaluating the colligative performance of microbiome analysis software. Our synthetic data closely matched the composition and complexity of actual healthy human stool microbiomes. Genus-level taxonomic classification was correctly done for only 50.4-74.8% of the source organisms. Miscall rates varied from 11.9 to 23.5%. Species-level classification was less successful, (6.9-18.9% correct); miscall rates were comparable to those of genus-level targets (12.5-26.2%). The degree of miscall varied by clade of organism, pipeline and specific settings used. OTU generation accuracy varied by strategy (closed, de novo or subsampling), reference database, algorithm and software implementation. Shannon diversity estimation accuracy correlated generally with OTU-generation accuracy. Beta-diversity estimates with Double Principle Coordinate Analysis (DPCoA) were more robust against errors introduced in processing than Weighted UniFrac. The settings suggested in the tutorials were among the worst performing in all outcomes tested.ConclusionsEven when using the same classification pipeline, the specific OTU-generation strategy, reference database and downstream analysis methods selection can have a dramatic effect on the accuracy of taxonomic classification, and alpha- and beta-diversity estimation. Even minor changes in settings adversely affected the accuracy of the results, bringing them far from the best-observed result. Thus, specific details of how a pipeline is used (including OTU generation strategy, reference sets, clustering algorithm and specific software implementation) should be specified in the methods section of all microbiome studies. Researchers should evaluate their chosen pipeline and settings to confirm it can adequately answer the research question rather than assuming the tutorial or standard-operating-procedure settings will be adequate or optimal.

Dataset Information

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments.

Publications

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments.

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