Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves.

Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus, Lachnospira, and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.

Early inoculation with caecal fermentation broth alters small intestine morphology, gene expression of tight junction proteins in the ileum, and the caecal metabolomic profiling of broilers.

BACKGROUND: The establishment of stable microbiota in early life is beneficial to the individual. Changes in the intestinal environment during early life play a crucial role in modulating the gut microbiota. Therefore, early intervention to change the intestinal environment can be regarded as a new regulation strategy for the growth and health of poultry. However, the effects of intestinal environmental changes on host physiology and metabolism are rarely reported. This study was conducted to investigate the effects of early inoculation with caecal fermentation broth on small intestine morphology, gene expression of tight junction proteins in the ileum, and cecum microbial metabolism of broilers. RESULTS: Our data showed that early inoculation with caecal fermentation broth could improve intestine morphology. The small intestine villus height was significantly increased (P < 0.05) in the intervened broilers compared to the control group, especially on day 28. A similar result was observed in the ratio of villus height to crypt depth (P < 0.05). Meanwhile, we found early inoculation significantly increased (P < 0.05) the expression levels of zonula occludens-1 (ZO1) on days 14 and 28, claudin-1 (CLDN1) on day 28, whereas the gene expression of claudin-2 (CLDN2) was significantly decreased (P < 0.05) on days 14 and 28. Gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) technology was further implemented to systematically evaluate the microbial metabolite profiles. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) displayed a distinct trend towards separation between the fermentation broth group (F group) and the control group (C group). The differentially expressed metabolites were identified, and they were mainly functionally enriched in beta-alanine metabolism and biosynthesis of unsaturated fatty acids. In addition, 1,3-diaminopropane was selected as a key biomarker that responded to early inoculation with caecal fermentation broth. CONCLUSIONS: These results provide insight into intestinal metabolomics and confirm that early inoculation with caecal fermentation broth can be used as a potential strategy to improve intestinal health of broilers.