Stool phospholipid signature is altered by diet and tumors

Fecal microbial and metabolic characteristics of swine from birth to market

Introduction

Recently, the research on pig intestinal microbiota has become a hot topic in the field of animal husbandry. There are few articles describing the dynamic changes of porcine fecal microbiota and metabolites at different time points from birth to market.

Methods

In the present study, 381 fecal samples were collected from 633 commercial pigs at 7 time points, including the 1st day, the 10th day, the 25th day, the 45th day, the 70th day, the 120th day, and the 180th day after the birth of swine, were used for microbiome analysis by Illumina MiSeq sequencing methods while 131 fecal samples from 3 time points, the 10th day, the 25th day, and 70th day after birth, were used for metabolome analysis by LC-MS methods.

Results

For the microbiome analysis, the fecal microbial richness increased over time from day 1 to 180 and the β-diversity of fecal microbiota was separated significantly at different time points. Firmicutes were the main phyla from day 10 to 180, followed by Bacteroides. The abundance of Lactobacillus increased significantly on day 120 compared with the previous 4 time points. From day 120 to day 180, the main porcine fecal microbes were Lactobacillus, Clostridium_sensu_stricto_1, Terrisporobacter and Streptococcus. Clostridium_sensu_stricto_1 and Terrisporobacter increased over time, while Lactobacillus, Escherichia-Shigella, Lachnoclostridium decreased with the time according to the heatmap, which showed the increase or decrease in microbial abundance over time. For the metabolome analysis, the PLS-DA plot could clearly distinguish porcine fecal metabolites on day 10, 25, and 70. The most different metabolic pathways of the 3 time points were Tryptophan metabolism, Sphingolipid signaling pathway, Protein digestion and absorption. Some metabolites increased significantly over time, such as Sucrose, L-Arginine, Indole, 2,3-Pyridinedicarboxylic acid and so on, while D-Maltose, L-2-Aminoadipic acid, 2,6-diaminohexanoic acid, L-Proline were opposite. The correlation between fecal metabolites and microbiota revealed that the microbes with an increasing trend were positively correlated with the metabolites affecting the tryptophan metabolic pathway from the overall trend, while the microbes with a decreasing trend were opposite. In addition, the microbes with an increasing trend were negatively correlated with the metabolites affecting the lysine pathway.

Discussion

In conclusion, this study elucidated the dynamic changes of porcine fecal microbiota and metabolites at different stages from birth to market, which may provide a reference for a comprehensive understanding of the intestinal health status of pigs at different growth stages.

Identification of Independent and Shared Metabolic Responses to High-Fiber and Antibiotic Treatments in Fecal Metabolome of Grow-Finish Pigs

Feeding high-fiber (HF) coproducts to grow–finish pigs as a cost-saving practice could compromise growth performance, while the inclusion of antibiotic growth promoters (AGPs) may improve it. The hindgut is a shared site of actions between fiber and AGPs. However, whether the metabolic interactions between them could occur in the digestive tract of pigs and then become detectable in feces have not been well-examined. In this study, wheat middling (WM), a HF coproduct, and bacitracin, a peptide antibiotic (AB), were fed to 128 grow–finish pigs for 98 days following a 2 × 2 factorial design, including antibiotic-free (AF) + low fiber (LF); AF + HF; AB + LF, and AB + HF, for growth and metabolic responses. The growth performance of the pigs was compromised by HF feedings but not by AB. A metabolomic analysis of fecal samples collected on day 28 of feeding showed that WM elicited comprehensive metabolic changes, especially in amino acids, fatty acids, and their microbial metabolites, while bacitracin caused selective metabolic changes, including in secondary bile acids. Limited metabolic interactions occurred between fiber and AB treatments. Moreover, the correlations between individual fecal metabolites and growth support the usage of fecal metabolome as a source of biomarkers for monitoring and predicting the metabolic performance of grow–finish pigs.

Development of an Assay to Determine the Amount of Ca-Fatty Acid Soaps in Feces

BACKGROUND

The quantification of fecal Ca-fatty acid soaps is important to understand how fatty acids behave in the gastrointestinal tract.

OBJECTIVE

As current methods to extract Ca-fatty acid soaps from feces give low recoveries an accurate assay to determine the amount of fatty acid soaps in feces was developed.

METHOD

Ca-fatty acid soaps are determined indirectly after non-soap fatty acid compounds have been extracted from the feces. Synthetic Ca-fatty acid soaps of different chain lengths (C12-C18) and degree of saturation (C18:0-C18:2) were incubated with several solvents to find the solvents that least-solubilize the Ca-fatty acid soaps. A three-step extraction was devised using extractions with hexane, hexane-isopropanol and water either at room temperature or at 60°C, 37°C, or 80°C, respectively. Feces were spiked with free fatty acids, Ca-fatty acid soaps, Na-fatty acid salts, and phospholipids.

RESULTS

All of the free fatty acids and phospholipids and almost all of the Na-fatty acid salts were removed and 98% of Ca-lauric acid soap, 99% of Ca-stearic acid soap, and 93% of oleic acid soap were recovered.

CONCLUSIONS

The method is suitable for determining fatty acids in the form of Ca-fatty acid soaps in feces.

HIGHLIGHTS

New method to determine fecal Ca-fatty acid soaps. Consistent and high recovery of fatty acid-soaps.

Unique inducible filamentous motility identified in pathogenic Bacillus cereus group species

Active migration across semi-solid surfaces is important for bacterial success by facilitating colonization of unoccupied niches and is often associated with altered virulence and antibiotic resistance profiles. We isolated an atmospheric contaminant, subsequently identified as a new strain of Bacillus mobilis, which showed a unique, robust, rapid, and inducible filamentous surface motility. This flagella-independent migration was characterized by formation of elongated cells at the expanding edge and was induced when cells were inoculated onto lawns of metabolically inactive Campylobacter jejuni cells, autoclaved bacterial biomass, adsorbed milk, and adsorbed blood atop hard agar plates. Phosphatidylcholine (PC), bacterial membrane components, and sterile human fecal extracts were also sufficient to induce filamentous expansion. Screening of eight other Bacillus spp. showed that filamentous motility was conserved amongst B. cereus group species to varying degrees. RNA-Seq of elongated expanding cells collected from adsorbed milk and PC lawns versus control rod-shaped cells revealed dysregulation of genes involved in metabolism and membrane transport, sporulation, quorum sensing, antibiotic synthesis, and virulence (e.g., hblA/B/C/D and plcR). These findings characterize the robustness and ecological significance of filamentous surface motility in B. cereus group species and lay the foundation for understanding the biological role it may play during environment and host colonization.

Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State

BACKGROUND

The onset of ulcerative colitis (UC) is associated with alterations in lipid metabolism and a disruption of the balance between pro- and anti-inflammatory molecules. Only a few studies describe the mucosal lipid biosignatures during active UC. Moreover, the dynamics of lipid metabolism in the remission state is poorly defined. Therefore, this study aims to characterize mucosal lipid profiles in treatment-naïve UC patients and deep remission UC patients compared with healthy subjects.

METHODS

Treatment-naïve UC patients (n = 21), UC patients in deep remission (n = 12), and healthy volunteers (n = 14) were recruited. The state of deep remission was defined by histological and immunological remission defined by a normalized TNF-α gene expression. Mucosa biopsies were collected by colonoscopy. Lipid analysis was performed by means of ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS-MS). In total, 220 lipids from 11 lipid classes were identified.

RESULTS

The relative concentration of 122 and 36 lipids was altered in UC treatment-naïve patients and UC remission patients, respectively, compared with healthy controls. The highest number of significant variations was in the phosphatidylcholine (PC), ceramide (Cer), and sphingomyelin (SM) composition. Multivariate analysis revealed discrimination among the study groups based on the lipid profile. Furthermore, changes in phosphatidylethanolamine(38:3), Cer(d18:1/24:0), and Cer(d18:1/24:2) were most distinctive between the groups.

CONCLUSION

This study revealed a discriminant mucosal lipid composition pattern between treatment-naïve UC patients, deep remission UC patients, and healthy controls. We report several distinctive lipids, which might be involved in the inflammatory response in UC, and could reflect the disease state.

Complex Network of NKT Cell Subsets Controls Immune Homeostasis in Liver and Gut

The liver-gut immune axis is enriched in several innate immune cells, including innate-like unconventional and adaptive T cells that are thought to be involved in the maintenance of tolerance to gut-derived antigens and, at the same time, enable effective immunity against microbes. Two subsets of lipid-reactive CD1d-restricted natural killer T (NKT) cells, invariant NKT (iNKT) and type II NKT cells present in both mice and humans. NKT cells play an important role in regulation of inflammation in the liver and gut due to their innate-like properties of rapid secretion of a myriad of pro-inflammatory and anti-inflammatory cytokines and their ability to influence other innate cells as well as adaptive T and B cells. Notably, a bi-directional interactive network between NKT cells and gut commensal microbiota plays a crucial role in this process. Here, we briefly review recent studies related to the cross-regulation of both NKT cell subsets and how their interactions with other immune cells and parenchymal cells, including hepatocytes and enterocytes, control inflammatory diseases in the liver, such as alcoholic and non-alcoholic steatohepatitis, as well as inflammation in the gut. Overwhelming experimental data suggest that while iNKT cells are pathogenic, type II NKT cells are protective in the liver. Since CD1d-dependent pathways are highly conserved from mice to humans, a detailed cellular and molecular understanding of these immune regulatory pathways will have major implications for the development of novel therapeutics against inflammatory diseases of liver and gut.

Development of suspension cell culture model to mimic circulating tumor cells

Circulating tumor cells (CTCs) are essential for the establishment of distant metastasis. Numerous studies have characterized CTCs as metastatic precursors; however, the molecular nature of CTCs has not been completely revealed yet due to the low number of CTCs in the blood stream. As an alternative approach, we developed a long-term suspension cell culture model using human breast cancer cell lines to mimic CTCs. We found that more than 40 passaged suspension cells acquired the ability to enhance metastasis like cancer stem cells. To identify molecular changes acquired during the suspension cell culture, we analyzed metabolic and lipidomic profiles as well as transcriptome in MDA-MB-468 suspension cells. Glutamate and leucine levels increased in suspension cells, and cholesterol synthesis pathway was altered. The inhibition of glutamate metabolic pathway decreased the proliferation of suspension cells compared to that of adherent cells. In the lipidomic profile, PC species containing long chain and polyunsaturated fatty acids increased in suspension cells and these species could be authentic and specific biomarkers for highly metastatic cancers. As this CTC-mimicking suspension cell culture model may easily apply to various types of cancer, we suggest this model as a great tool to develop therapeutic targets and drugs to eradicate metastatic cancer cells.

Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn’s disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and the microbiological profiles were significantly different between IBD and healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, Flavobacterium, and Oscillospira decreased. Various metabolites including biogenic amines, amino acids, lipids, were significantly increased in IBD, while others, such as two B group vitamins, were decreased in IBD compared to healthy subjects. This study underlines the potential role of an inter-omics approach in understanding the metabolic pathways involved in IBD. The combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and patients with IBD.

Diet as a Trigger or Therapy for Inflammatory Bowel Diseases

The most common question asked by patients with inflammatory bowel disease (IBD) is, "Doctor, what should I eat?" Findings from epidemiology studies have indicated that diets high in animal fat and low in fruits and vegetables are the most common pattern associated with an increased risk of IBD. Low levels of vitamin D also appear to be a risk factor for IBD. In murine models, diets high in fat, especially saturated animal fats, also increase inflammation, whereas supplementation with omega 3 long-chain fatty acids protect against intestinal inflammation. Unfortunately, omega 3 supplements have not been shown to decrease the risk of relapse in patients with Crohn's disease. Dietary intervention studies have shown that enteral therapy, with defined formula diets, helps children with Crohn's disease and reduces inflammation and dysbiosis. Although fiber supplements have not been shown definitively to benefit patients with IBD, soluble fiber is the best way to generate short-chain fatty acids such as butyrate, which has anti-inflammatory effects. Addition of vitamin D and curcumin has been shown to increase the efficacy of IBD therapy. There is compelling evidence from animal models that emulsifiers in processed foods increase risk for IBD. We discuss current knowledge about popular diets, including the specific carbohydrate diet and diet low in fermentable oligo-, di-, and monosaccharides and polyols. We present findings from clinical and basic science studies to help gastroenterologists navigate diet as it relates to the management of IBD.

Choline Deficiency Causes Colonic Type II Natural Killer T (NKT) Cell Loss and Alleviates Murine Colitis under Type I NKT Cell Deficiency

Serum levels of choline and its derivatives are lower in patients with inflammatory bowel disease (IBD) than in healthy individuals. However, the effect of choline deficiency on the severity of colitis has not been investigated. In the present study, we investigated the role of choline deficiency in dextran sulfate sodium (DSS)-induced colitis in mice. Methionine-choline-deficient (MCD) diet lowered the levels of type II natural killer T (NKT) cells in the colonic lamina propria, peritoneal cavity, and mesenteric lymph nodes, and increased the levels of type II NKT cells in the livers of wild-type B6 mice compared with that in mice fed a control (CTR) diet. The gene expression pattern of the chemokine receptor CXCR6, which promotes NKT cell accumulation, varied between colon and liver in a manner dependent on the changes in the type II NKT cell levels. To examine the role of type II NKT cells in colitis under choline-deficient conditions, we assessed the severity of DSS-induced colitis in type I NKT cell-deficient (Jα18^-/-) or type I and type II NKT cell-deficient (CD1d^-/-) mice fed the MCD or CTR diets. The MCD diet led to amelioration of inflammation, decreases in interferon (IFN)-γ and interleukin (IL)-4 secretion, and a decrease in the number of IFN-γ and IL-4-producing NKT cells in Jα18^-/- mice but not in CD1d^-/- mice. Finally, adaptive transfer of lymphocytes with type II NKT cells exacerbated DSS-induced colitis in Jα18^-/- mice with MCD diet. These results suggest that choline deficiency causes proinflammatory type II NKT cell loss and alleviates DSS-induced colitis. Thus, inflammation in DSS-induced colitis under choline deficiency is caused by type II NKT cell-dependent mechanisms, including decreased type II NKT cell and proinflammatory cytokine levels.

Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view

The recent characterization of the gut microbiome of traditional rural and foraging societies allowed us to appreciate the essential co-adaptive role of the microbiome in complementing our physiology, opening up significant questions on how the microbiota changes that have occurred in industrialized urban populations may have altered the microbiota-host co-metabolic network, contributing to the growing list of Western diseases. Here, we applied a targeted metabolomics approach to profile the fecal metabolome of the Hadza of Tanzania, one of the world's few remaining foraging populations, and compared them to the profiles of urban living Italians, as representative of people in the post-industrialized West. Data analysis shows that during the rainy season, when the diet is primarily plant-based, Hadza are characterized by a distinctive enrichment in hexoses, glycerophospholipids, sphingolipids, and acylcarnitines, while deplete in the most common natural amino acids and derivatives. Complementary to the documented unique metagenomic features of their gut microbiome, our findings on the Hadza metabolome lend support to the notion of an alternate microbiome configuration befitting of a nomadic forager lifestyle, which helps maintain metabolic homeostasis through an overall scarcity of inflammatory factors, which are instead highly represented in the Italian metabolome.

Intestinal Epithelial Toll-Like Receptor 4 Signaling Affects Epithelial Function and Colonic Microbiota and Promotes a Risk for Transmissible Colitis

Evidence obtained from gene knockout studies supports the role of Toll-like receptor 4 (TLR4) in intestinal inflammation and microbiota recognition. Increased epithelial TLR4 expression is observed in patients with inflammatory bowel disease. However, little is known of the effect of increased TLR4 signaling on intestinal homeostasis. Here, we examined the effect of increased TLR4 signaling on epithelial function and microbiota by using transgenic villin-TLR4 mice that overexpress TLR4 in the intestinal epithelium. Our results revealed that villin-TLR4 mice are characterized by increases in the density of mucosa-associated bacteria and bacterial translocation. Furthermore, increased epithelial TLR4 signaling was associated with an impaired epithelial barrier, altered expression of antimicrobial peptide genes, and altered epithelial cell differentiation. The composition of the colonic luminal and mucosa-associated microbiota differed between villin-TLR4 and wild-type (WT) littermates. Interestingly, WT mice cohoused with villin-TLR4 mice displayed greater susceptibility to acute colitis than singly housed WT mice did. The results of this study suggest that epithelial TLR4 expression shapes the microbiota and affects the functional properties of the epithelium. The changes in the microbiota induced by increased epithelial TLR4 signaling are transmissible and exacerbate dextran sodium sulfate-induced colitis. Together, our findings imply that host innate immune signaling can modulate intestinal bacteria and ultimately the host's susceptibility to colitis.