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The gastrointestinal (GI) tract harbors a diverse population of microorganisms. While much work has been focused on the characterization of the bacterial community, very little is known about the fungal community, or mycobiota, in different animal species and chickens in particular. Here, we characterized the biogeography of the mycobiota along the GI tract of day 28 broiler chicks and further examined its possible shift in response to bacitracin methylene disalicylate (BMD), a commonly used in-feed antibiotic, through Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes. Out of 124 samples sequenced, we identified a total of 468 unique fungal features that belong to four phyla and 125 genera in the GI tract. Ascomycota and Basidiomycota represented 90% to 99% of the intestinal mycobiota, with three genera, i.e., Microascus, Trichosporon, and Aspergillus , accounting for over 80% of the total fungal population in most GI segments. Furthermore, these fungal genera were dominated by Scopulariopsis brevicaulis ( Scopulariopsis is the anamorph form of Microascus ), Trichosporon asahii , and two Aspergillus species. We also revealed that the mycobiota are more diverse in the upper than lower GI tract. The cecal mycobiota transitioned from being S. brevicaulis dominant on day 14 to T. asahii dominant on day 28. Furthermore, 2-week feeding of 55 mg/kg BMD tended to reduce the cecal mycobiota α-diversity. Taken together, we provided a comprehensive biogeographic view and succession pattern of the chicken intestinal mycobiota and its influence by BMD. A better understanding of intestinal mycobiota may lead to the development of novel strategies to improve animal health and productivity. IMPORTANCE The intestinal microbiota is critical to host physiology, metabolism, and health. However, the fungal community has been often overlooked. Recent studies in humans have highlighted the importance of the mycobiota in obesity and disease, making it imperative that we increase our understanding of the fungal community. The significance of this study is that we revealed the spatial and temporal changes of the mycobiota in the GI tract of the chicken, a nonmammalian species. To our surprise, the chicken intestinal mycobiota is dominated by a limited number of fungal species, in contrast to the presence of hundreds of bacterial taxa in the bacteriome. Additionally, the chicken intestinal fungal community is more diverse in the upper than the lower GI tract, while the bacterial community shows an opposite pattern. Collectively, this study lays an important foundation for future work on the chicken intestinal mycobiome and its possible manipulation to enhance animal performance and disease resistance., (Copyright © 2020 American Society for Microbiology.)

The intestinal microbiome is critically important in shaping a variety of host physiological responses. However, it remains elusive on how gut microbiota impacts overall growth and more specifically, adipogenesis. Using the pig as an animal model, we compared the differences in bacterial community structure throughout the intestinal tract in two breeds (Landrace and Jinhua) of pigs with distinct phenotypes. The Landrace is a commercial purebred and the Jinhua is a Chinese indigenous, slow-growing breed with high propensity for fat deposition. Using 16S rRNA gene sequencing, we revealed that the bacterial communities are more diverse in the duodenum, jejunum, and cecum of Jinhua pigs than in those of Landrace pigs, whereas the ileal and colonic microbiota show a similar complexity between the two breeds. Furthermore, a number of bacterial taxa differentially exist in Jinhua and Landrace pigs throughout the entire intestinal tract, with the jejunal and ileal microbiome showing the greatest contrast. Functional prediction of the bacterial community suggested increased fatty acid biosynthesis in Jinghua pigs, which could partially explain their adiposity phenotype. Further studies are warranted to experimentally verify the relative contribution of each enriched bacterial species and their effect on adipogenesis and animal growth.

Digestive enzyme activity is involved in the regulation of growth performance because digestive enzymes function to improve the feed efficiency by digestion and in turn to modulate the process of nutrient metabolism. The objective of this study was to investigate the differences of the digestive enzyme activities and expression of nutrient transporters in the intestinal tract between Jinhua and Landrace pigs and to explore the potential breed-specificity in digestion and absorption. The pancreas segments and the digesta and mucosa of the duodenum, jejunum, and ileum were collected from 10 Jinhua pigs and Landrace pigs, respectively. The activities of trypsin, chymotrypsin, amylase, maltase, sucrase, and lipase were measured and the expression levels of PepT1 , GLUT2 , SGLT1 , FABP1 , FABP2 , and FABP4 were examined. Results showed that the trypsin activity in the pancreas of Jinhua pigs was higher than that in Landrace pigs, but was lower in the small intestine, except for in the jejunal mucosa. The chymotrypsin activity in the small intestine of Jinhua pigs was higher than that in Landrace pigs, except for in jejunal mucosa and contents. Compared with Landrace pigs, the amylase and maltase activity in the small intestine of Jinhua pigs was lower, except for in ileal mucosa. The sucrase activity in the small intestine of Jinhua pigs was also lower than Landrace pigs, except for in jejunal mucosa. Furthermore, the lipase activity in the small intestine of Jinhua pigs was higher than that in Landrace pigs. The mRNA levels of PepT1 and GLUT2 in duodenal, jejunal and ileal mucosa showed no difference between Jinhua and Landrace pigs, whereas SGLT1 in ileal mucosa was lower in Jinhua pigs. The mRNA levels of FABP1 , FABP2 and FABP4 in the small intestinal mucosa of Jinhua pigs were higher than in Landrace pigs. These findings indicate that there is a certain difference in the digestibility and absorption of nutrients in small intestine of Jinhua and Landrace pigs, partially resulting in their differences in growth development and fat deposition. [ABSTRACT FROM AUTHOR]

Defensins are a class of antimicrobial peptides in vertebrates that function as the first line of innate immunity with potent antimicrobial and immunomodulatory activities. Fourteen defensins, namely, avian β-defensin 1 to 14 (AvBD1-14), have been identified in chickens. Before characterizing the role of AvBDs in innate immunity during the early development of chickens, we collected tissue segments from the liver, spleen, and gastrointestinal (GI) tract including the esophagus, crop, proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and colon from broilers at days 1, 3, 7, 14, and 28. After RNA isolation and reverse transcription, we determined the expression levels of the 14 AvBD genes in these tissues during the first 28 days after hatching by real-time PCR. The results suggested the AvBDs were widely expressed in the chicken liver, spleen, and gastrointestinal (GI) tract. Interestingly, we did not detect AvBD11 expressed in the GI tract, even in the liver and spleen. Additionally, AvBDs were differentially expressed in the chicken GI tract. AvBD5 and AvBD14 were expressed most abundantly in the proximal GI tract, especially the esophagus and crop. Moreover, AvBD5, AvBD7, AvBD9, and AvBD14 were expressed in an inverted-V pattern with the peak being the observed expression at days 3, 7, or 14 in the chicken spleen, esophagus, duodenum, and cecum. Other AvBDs presented biphasic or inverted-V expression patterns in different tissues. The expression levels of all detected AvBDs were strengthened after hatching rather than decreasing steadily. Therefore, AvBDs were found to be expressed widely in the chicken liver, spleen, and GI tract and their expression levels were primarily up regulated during the early development of chicken, implying the potential essential roles of AvBDs in early innate defense and infection resistance of chickens. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The yellow catfish (Pelteobagrus fulvidraco) is an important economic freshwater aquaculture species in Asia. However, little is known about its immune response to bacterial pathogen infection. Here, two cytokines, the proinflammatory cytokine interleukin-8 (IL-8) and the anti-inflammatory cytokine interleukin-10 (IL-10), were identified and characterized in the yellow catfish for the first time. We found that the full length of the IL-8 cDNA was 784 bp and contained an open reading frame (ORF) of 336 bp, while the IL-10 gene was 973 bp in length with a 549 bp of ORF. In addition, both the IL-8 and the IL-10 had similar tissue-specific expression patterns. They were more abundant in the spleen and lowest expressed in the liver. Furthermore, IL-10 but not IL-8 was significantly upregulated in the intestine of yellow catfish by feed supplementation of Clostridium butyricum (CB). More importantly, the expression levels of intestinal IL-10 and IL-8 were up- and downregulated by pathogen Aeromonas punctata stimuli with the presence of CB, respectively. Collectively, these results suggest that IL-10 and IL-8 mediate important roles in the immunity of yellow catfish, and feed supplementation of CB may able to reduce the intestinal inflammation caused by bacteria infections through regulating the expression of IL-10 and IL-8. [ABSTRACT FROM AUTHOR]

Simple Summary: Enterotype (ET) is defined based on different gut microbial community composition. It has been considered as a critical factor strongly associated with the porcine feed efficiency and growth characteristic. However, little is known about whether the ET clustering depends on the pig breeds and the effects of the different enterotypes on the butyrate metabolism in pigs. Therefore, we studied Jinhua pig's enterotype by using 16S rRNA high throughput sequencing, and then analyzed the interaction between enterotype and butyrate production. Results showed that we identified three ETs driven by discriminative genera dominated by Lactobacillus, Clostridium sensu stricto 1, and Bacteroides, respectively. Significant differences in the fecal contents of butyrate production and butyrate-producing bacteria were observed among ETs. These findings present a first overview of the enterotypes clustering in Jinhua pigs and provide new insights into the relationship between the different ETs and intestinal butyrate production. Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p < 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p < 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p < 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p < 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig's phenotypic performance and nutrient metabolism. [ABSTRACT FROM AUTHOR]

[Display omitted] • DON-induced gut toxicity is partly mediated by gut microbiota. • L. murinus is a potential probiotic against DON. • L. murinus and its EVs effectively alleviated DON-induced intestinal barrier disorder. • LmEVs upregulate TLR2 to promote M2 macrophage polarization to protect the gut barrier. Deoxynivalenol (DON) is a common environmental pollutant that poses a serious health risk to humans worldwide. This study was aim to explore whether gut microbiota is involved in DON-induced intestinal toxicity as well as to reveal effect of probiotics derived from gut microbiota in protecting intestinal barrier and to elucidate mechanism. We found that DON caused disturbed gut microbiota, particularly Lactobacillus murinus (L. murinus) deficiency. DON enhanced M1 macrophage polarization and decreased tight junction protein expression. Microbiota transplantation experiments showed that transfer of DON-disrupted microbiota to healthy mice resulted in delivery of DON-induced intestinal toxicity. Besides, DON lost its damaging effect on macrophage and intestinal barrier in antibiotic-treated mice. Further intervention experiments revealed that L. murinus induce macrophage conversion from M1 to M2 phenotype through secreted extracellular vesicles (EVs) to alleviate DON-induced intestinal barrier disruption. Mechanistically, EVs activate TLR2 to promote M2 macrophage polarization and release IL-10, which in turn enhances intestinal barrier function. Upon successful translation of its efficacy into clinical practice, EVs created from L. murinus could be a novel possible treatment strategy for DON-induced gut disease. [ABSTRACT FROM AUTHOR]

Many studies have shown the efficacy of phage therapy in reducing intestinal pathogens. However, phage-based probiotic treatment is poorly studied in view of effects on the gut microbiota and intestinal inflammation. In this study, a lytic or a temperate phage (each at 4 ×108 PFU per day) or a streptomycin solution (40 mg per day) were administered to mice via drinking water for 31 days. Subsequently, mice were challenged with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). S. Typhimurium does not serve as the host bacterium and is not lysed by both phages. For intestinal inflammation evaluation, mice were given one dose of streptomycin for 24 h before the S. Typhimurium challenge. High-throughput sequencing analysis revealed that the phylum Firmicutes became the most abundant in mice pretreated with phages. The alpha diversity of gut bacteria was higher in phage treated than in streptomycin treated mice. Moreover, pretreatment with the lytic and the temperate phage before the S. Typhimurium challenge increased two beneficial genera, Lactobacillus and Bifidobacterium. According to the pathological analysis of ileum, cecum, and serum, temperate or lytic gut phage pretreatment of mice markedly reduced intestinal inflammation, concomitant with lower serum concentration of lipopolysaccharides (LPS) and diamine oxidase (DAO). The oral pretreatments of mice (ST, Lyt, Lys, SM) generally caused an increased expression of IL-1β, TNF-α, IFN-γ, IL-4, and IL-10 compared to the matching control. However, in mice pretreated with the lytic phage, the mRNA expression for the pro-inflammatory cytokine TNF-α was not significantly higher than that of the control group. No significant differences were detected for peripheral blood B lymphocytes, CD3 +T cells, and the CD4 + /CD8 + ratio in mice pretreated with the lytic and lysogenic phage. This study demonstrated that even lytic phages not targeting the pathogenic serovar Salmonella Typhimurium alleviated intestinal dysbiosis and inflammation in challenged mice. [ABSTRACT FROM AUTHOR]