Gut Locations Research Articles

Clostridium butyricum and carbohydrate active enzymes contribute to the reduced fat deposition in pigs.

Pig gastrointestinal tracts harbor a heterogeneous and dynamic ecosystem populated with trillions of microbes, enhancing the ability of the host to harvest energy from dietary carbohydrates and contributing to host adipogenesis and fatness. However, the microbial community structure and related mechanisms responsible for the differences between the fatty phenotypes and the lean phenotypes of the pigs remained to be comprehensively elucidated. Herein, we first found significant differences in microbial composition and potential functional capacity among different gut locations in Jinhua pigs with distinct fatness phenotypes. Second, we identified that Jinhua pigs with lower fatness exhibited higher levels of short-chain fatty acids in the colon, highlighting their enhanced carbohydrate fermentation capacity. Third, we explored the differences in expressed carbohydrate-active enzyme (CAZyme) in pigs, indicating their involvement in modulating fat storage. Notably, Clostridium butyricummight be a representative bacterial species from Jinhua pigs with lower fatness, and a significantly higher percentage of its genome was dedicated to CAZyme glycoside hydrolase family 13 (GH13). Finally, a subsequent mouse intervention study substantiated the beneficial effects of C. butyricum isolated from experimental pigs, suggesting that it may possess characteristics that promote the utilization of carbohydrates and hinder fat accumulation. Remarkably, when Jinhua pigs were administered C. butyricum, similar alterations in the gut microbiome and host fatness traits were observed, further supporting the potential role of C. butyricum in modulating fatness. Taken together, our findings reveal previously overlooked links between C. butyricum and CAZyme function, providing insight into the basic mechanisms that connect gut microbiome functions to host fatness.

Intestinal Geographical Pattern of Gut Microbiome and Metabolites Identifies Novel Regulators of Graft-Versus-Host Disease

Introduction: The severity of T cell-mediated gastrointestinal graft-versus-host disease (GI-GVHD) correlates with a decrease in the gut microbiome diversity, loss of obligate anaerobic bacteria and alterations in levels of salutary metabolites like short chain fatty acids (SCFAs). However, it is unknown whether the intestinal anatomic geography of the microbiome and its metabolites impacts GI GVHD severity. Herein, we investigate the pattern of the gut microbiome and metabolites from four distinct anatomical sites of intestines after allogeneic stem cell transplant (allo-SCT) via shotgun metagenomics and untargeted mass-spectrometry. Methods: To determine the composition of the gut microbiome and gut metabolites of mice after allo-SCT, we utilized contemporaneous analyses of shotgun metagenomic sequencing and untargeted mass spectrometry on the gut contents of mice 7 or 21 days after major histocompatibility complex (MHC)-disparate BALB/c→C57BL/6 (B6) allogeneic SCT. We investigated the microbial community composition and gut metabolites from four distinct gut locations (terminal ileum, cecum, transverse colon, descending colon) and performed integrative analysis to assess for novel pathways that may regulate GVHD biology. For shotgun metagenomics analyses, reads were depth normalized with BBnorm v.38.96 and assembled per-sample with MEGAHIT v.1.2.9. Prodigal v.2.6.3 was used to find genes in each bin. KofamScan v.1.3.0 was used to assign KEGG ortholog IDs (KO) to translated genes predicted by Prodigal. Community composition profiles were produced with Kraken2 v.2.1.2 and Bracken v.2.6.1. Functional profiles for each sample were determined with the Kraken community composition profiles and Humann3 v.3.0.0, with a GTDB database built with Struo2. Results: Consistent with previous reports from direct stool analyses, our data demonstrated that after allo-SCT, gut microbial diversity is reduced, relative abundance of obligate anaerobes decreases, and relative abundance of facultative anaerobes increases at all the intestinal anatomic sites, but the difference was maximal in ileo-cecal contents. Furthermore, metabolomic analyses reveal a decrease in previously described metabolites such as, SCFAs, bile acids and indoles at these sites. The distinct patterns of change between control and allogeneic samples depended not only on the gut location probed but also correlated with timepoint after transplant (7 days or 21 days) highlighting the importance of probing different gut locations and timepoints. The largest driver of differences between sample groups was (1) gut location (2) time after transplant (3) transplant type. Integrative analyses demonstrated loss of microbial functional genes related to butyrate processing following allo-SCT complementing previous studies that demonstrated reduction in butyrate levels. Further bioinformatic analyses identified novel microbial functional genes and metabolites that may have biological implications. Analyses revealed that after allo-SCT, phenyllactic acid (PLA) levels increased in the transverse colon and distal colon (fig.1). PLA is an anti-microbial compound and has been shown to have immune modulatory properties. Administration of PLA in drinking water of mice after allo-SCT worsened GVHD severity and increased mortality indicating PLA may play a role in inducing dysbiosis and worsening GVHD severity. Conclusion: Contemporaneous analyses of shotgun metagenomic and untargeted mass spectrometry of gut contents after allo-SCT reveal changes in microbial composition and metabolites consistent with previous data from analyses from stool. However, our analysis demonstrates distinct patterns of key metabolites and microbes in between syngeneic and allogeneic depending on gut location and time after transplant. Furthermore, our analyses have identified novel functional genes and metabolites that are implicated in GVHD severity.

Enhancing gut health and performance of grower-finisher pigs: assessing the efficacy of the mixture of microencapsulated essential oils and saponins

Context The livestock industry demands alternative approaches to maintain animal health and productivity without using antimicrobials. Phytogenic feed additives, consisting of plant-derived compounds, offer promising benefits to grower-finisher pigs’ gut microbiota and overall health. Aims This study investigated the impact of essential oils and saponins as phytogenic feed additives on the gut microbiota and productivity of grower-finisher pigs. Methods Four hundred male Large White × Landrace pigs were randomly allocated into control and treatment groups and provided with a basal diet. The treatment group supplemented commercial phytogenic feed additives. Performance data, general health, cumulative mortality, and bodyweight were monitored. Intestinal samples from different gut locations and rectal swab samples were collected for microbiota analysis. Key results No significant difference in weight was observed between the two groups; however, the phytogenic feed additives notably affected gut microbiota. Greater microbial diversity and changes in genera abundance were evident. Campylobacter and Clostridium increased, while beneficial Lactobacillus increased, and Escherichia decreased. The supplemented group demonstrated more consistent growth, with higher minimum weights. Conclusions Phytogenic feed additives have a significant impact on the gut microbiota of grower-finisher pigs. A diverse microbial community and specific changes in genera abundance were observed, indicating the potential role of these additives in modulating gut health. Implications This study emphasises the potential advantages of using phytogenic feed additives to improve the health and productivity of livestock without the use of antibiotics.

101 Fusobacteria,Bacteroidetes, and more! Linking the Microbial Communities in Bovine Liver Abscesses to the Gut

Abstract Liver abscesses (LAs) are a common and important problem in cattle because of their association with decreased growth and production, low carcass quality, and the significant economic losses associated with liver condemnation. Fusobacterium necrophorum has traditionally been considered the primary etiologic agent of LA formation in cattle, but recent evidence has demonstrated that LA microbial communities are far more polymicrobial than previously believed. Here, we characterize microbial communities within multiple LAs from the same animal, provide evidence that some LAs may be seeded from the hindgut, identify biomarkers throughout the gut-liver axis that predict the presence of LAs, and demonstrate the impact of tylosin on microbial communities in the rumen, ileum, and colon. 16S rRNA gene sequencing was used to characterize communities from LA purulent material, as well as from the luminal and epithelia, communities in three gut locations (rumen, ileum, colon) within the same animals. A combination of QIIME2 and phyloseq were used to analyze sequence data, and microbial community composition was compared based on generalized UniFrac distances. Taxa discriminant of LA occurrence were identified using linear discriminant analysis effect size (LEfSe). Despite being the most abundant genus when averaged across all LA communities, Fusobacterium spp. was not the predominant taxa in the majority of LAs. In fact, members of Bacteriodetes (largely Bacteroides, Porphyromonas) were the predominant taxa in more than one-half of all LA communities. Importantly, multiple LAs from the same animal had remarkably similar community structure, and multiple taxa including Bifidobacterium spp., widely considered beneficial to gut barrier function in humans, were differentially abundant in both the foregut and hindgut between cattle that did and did not have LAs. Further, tylosin had little impact on the diversity and composition of microbial communities within LAs but did alter communities in the rumen and small intestine. In particular, members of the family Lachnospiraceae were more abundant in the rumen and hindgut of animals given tylosin. Together, these results provide additional evidence challenging the traditional theory of LA etiology (that bacterial translocation occurs exclusively from the rumen) and provides evidence that barrier dysfunction in the gut may be the underlying cause of LA formation.

Efficient genetic editing of human intestinal organoids using ribonucleoprotein-based CRISPR.

Organoids, combined with genetic editing strategies, have the potential to offer rapid and efficient investigation of gene function in many models of human disease. However, to date, the editing efficiency of organoids with the use of non-viral electroporation methods has only been up to 30%, with implications for the subsequent need for selection, including turnaround time and exhaustion or adaptation of the organoid population. Here, we describe an efficient method for intestinal organoid editing using a ribonucleoprotein-based CRISPR approach. Editing efficiencies of up to 98% in target genes were robustly achieved across different gut anatomical locations and developmental timepoints from multiple patient samples with no observed off-target editing. The method allowed us to study the effect of loss of the tumour suppressor gene PTEN in normal human intestinal cells. Analysis of PTEN-deficient organoids defined phenotypes that likely relate to its tumour suppressive function in vivo, such as a proliferative advantage and increased organoid budding. Transcriptional profiling revealed differential expression of genes in pathways commonly known to be associated with PTEN loss, including mTORC1 activation.

Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice.

Inflammatory bowel diseases (IBDs) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective and affordable for managing symptoms. Glucosinolate compounds are highly concentrated in broccoli sprouts, especially glucoraphanin (GLR), and can be metabolized by certain mammalian gut bacteria into anti-inflammatory isothiocyanates, such as sulforaphane. Gut microbiota exhibit biogeographic patterns, but it is unknown if colitis alters these or whether the location of glucoraphanin-metabolizing bacteria affects anti-inflammatory benefits. We fed specific pathogen-free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 34-day experiment to simulate chronic, relapsing ulcerative colitis (UC). We monitored body weight, fecal characteristics, lipocalin, serum cytokines, and bacterial communities from the luminal- and mucosal-associated populations in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet with DSS treatment performed better than mice fed the control diet with DSS, and had significantly more weight gain, lower Disease Activity Index scores, lower plasma lipocalin and proinflammatory cytokines, and higher bacterial richness in all gut locations. Bacterial communities were assorted by gut location but were more homogenous across locations in the control diet + DSS mice. Importantly, our results showed that broccoli sprout feeding abrogated the effects of DSS on gut microbiota, as bacterial richness and biogeography were similar between mice receiving broccoli sprouts with and without DSS. Collectively, these results support the protective effect of steamed broccoli sprouts against dysbiosis and colitis induced by DSS. IMPORTANCE Evaluating bacterial communities across different locations in the gut provides a greater insight than fecal samples alone and provides an additional metric by which to evaluate beneficial host-microbe interactions. Here, we show that 10% steamed broccoli sprouts in the diet protects mice from the negative effects of dextran sodium sulfate-induced colitis, that colitis erases biogeographic patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. Mice fed the broccoli sprout diet during colitis performed better than mice fed the control diet while receiving DSS. The identification of accessible dietary components and concentrations that help maintain and correct the gut microbiome may provide universal and equitable approaches to IBD prevention and recovery, and broccoli sprouts represent a promising strategy.

Comparative genomics and phenotypic studies to determine site-specificity of Escherichia coli in the lower gastrointestinal tract of humans

ABSTRACT Escherichia coli (E. coli) is an important commensal in the human gut; however, it is unknown whether strains show site-specificity in the lower gut. To investigate this, we assessed genotypic and phenotypic differences in 37 clone pairs (two strains with very similar multiple locus variable-number-tandem-repeat analysis [MLVA] profiles) of E. coli isolated from mucosal biopsies of two different gut locations (terminal ileum and rectum). The clone pairs varied at the genomic level; single nucleotide polymorphisms (SNPs) were common, multiple nucleotide polymorphisms (MNPs) were observed but less common, and few indels (insertions and deletions) were detected. The variation was higher in clone pairs that are associated with non-human-associated sequence types (ST) compared to human-associated STs, such as ST95, ST131, and ST73. No gene(s) with non-synonymous mutations were found to be commonly associated with either the terminal ileum or the rectal strains. At the phenotypic level, we identified the metabolic signatures for some STs. Rectum strains of some STs showed consistently higher metabolic activity with particular carbon sources. Clone pairs belonging to specific STs showed distinct growth patterns under different pH conditions. Overall, this study showed that E. coli may exhibit genomic and phenotypic variability at different locations in the gut. Although genomics did not reveal significant information suggesting the site-specificity of strains, some phenotypic studies have suggested that strains may display site-specificity in the lower gut. These results provide insights into the nature and adaptation of E. coli in the lower gut of humans. To the best of our knowledge, no study has investigated or demonstrated the site-specificity of commensal E. coli in the human gut.

Extensive identification of serum metabolites related to microbes in different gut locations and evaluating their associations with porcine fatness.

Gut microbiota plays important roles in host metabolism. Whether and how much the gut microbiota in different gut locations contributes to the variations of host serum metabolites are largely unknown, because it is difficult to obtain microbial samples from different gut locations on a large population scale. Here, we quantified the gut microbial compositions using 16S rRNA gene sequencing for 1070 samples collected from the ileum, cecum and faeces of 544 F6 pigs from a mosaic pig population. Untargeted metabolome measurements determined serum metabolome profiles. We found 1671, 12,985 and 103,250 significant correlations between circulating serum metabolites and bacterial ASVs in the ileum, cecum, and faeces samples. We detected nine serum metabolites showing significant correlations with gut bacteria in more than one gut location. However, most metabolite-microbiota pairwise associations were gut location-specific. Targeted metabolome analysis revealed that CDCA, taurine, L-leucine and N-acetyl-L-alanine can be used as biomarkers to predictporcine fatness. Enriched taxa in fat pigs, for example Prevotella and Lawsonia intracellularis were positively associated with L-leucine, while enriched taxa in lean pigs, such as Clostridium butyricum, were negatively associated with L-leucine and CDCA, but positively associated with taurine and N-acetyl-L-alanine. These results suggested that the contributions of gut microbiota in each gut location to the variations of serum metabolites showed spatial heterogeneity.

Dachengqi Decoction alleviates intestinal inflammation in ovalbumin-induced asthma by reducing group 2 innate lymphoid cells in a microbiota-dependent manner.

Dachengqi Decoction (DCQD) as a classic traditional Chinese medicine has been reported to be effective in treating asthma, but its mechanism remains unknown. This study aimed to reveal the mechanisms of DCQD on the intestinal complications of asthma mediated by group 2 innate lymphoid cells (ILC2) and intestinal microbiota. Ovalbumin (OVA) was used to construct asthmatic murine models. IgE, cytokines (e.g., IL-4, IL-5), fecal water content, colonic length, histopathologic appearance, and gut microbiota were evaluated in asthmatic mice treated with DCQD. Finally, we administered DCQD to antibiotic-treated asthmatic mice to measure the ILC2 in the small intestine and colon. DCQD decreased pulmonary IgE, IL-4, and IL-5 levels in asthmatic mice. The fecal water content, the colonic length weight loss, and the epithelial damage of jejunum, ileum, and colon of asthmatic mice were ameliorated by DCQD. Meanwhile, DCQD greatly improved intestinal dysbiosis by enriching Allobaculum, Romboutsia and Turicibacter in the whole intestine, and Lactobacillus gasseri only in the colon. However, DCQD caused less abundant Faecalibaculum and Lactobacillus vaginalis in the small intestine of asthmatic mice. A higher ILC2 proportion in different gut segments of asthmatic mice was reversed by DCQD. Finally, significant correlations appeared between DCQD-mediated specific bacteria and cytokines (e.g., IL-4, IL-5) or ILC2. These findings indicate that DCQD alleviated the concurrent intestinal inflammation in OVA-induced asthma by decreasing the excessive accumulation of intestinal ILC2 in a microbiota-dependent manner across different gut locations.

Membrane filtration processing of infant milk formula alters protein digestion in young pigs

Reducing heat treatment (HT) during processing of infant milk formula (IMF) is desirable to produce a product that more closely resembles breast milk. By employing membrane filtration (MEM), we produced an IMF (60:40 whey to casein ratio) at pilot scale (250 kg). MEM-IMF had a significantly higher content of native whey (59.9 %) compared to HT-IMF (4.5 %) (p < 0.001). Pigs, at 28 days old, were blocked by sex, weight and litter origin and assigned to one of two treatments (n = 14/treatment): (1) starter diet containing 35 % of HT-IMF powder or (2) starter diet containing 35 % of MEM-IMF powder for 28 days. Body weight and feed intake were recorded weekly. Pigs at day 28 post weaning were sacrificed 180 min after their final feeding, for the collection of gastric, duodenal, jejunum and ileal contents (n = 10/treatment). MEM-IMF diet resulted in more water-soluble proteins and higher levels of protein hydrolysis in the digesta at various gut locations compared to HT-IMF (p < 0.05). In the jejunal digesta, a higher concentration of free amino acids were present post MEM-IMF consumption (247 ± 15 µmol g−1 of protein in digesta) compared to HT-IMF (205 ± 21 µmol g−1 of protein). Overall, average daily weight gain, average dairy feed intake and feed conversion efficiency were similar for pigs fed either MEM-IMF or HT-IMF diets, but differences and trends to difference of these indicators were determined in particular intervention periods. In conclusion, reducing heat treatment during processing of IMF influenced protein digestion and revealed minor effects on growth parameters providing in vivo evidence that babies who are fed with IMF processed by MEM are likely to have different protein digestion kinetics but minimal effect on overall growth trajectories as babies fed IMF processed by traditional thermal processing.

Uncovering the biogeography of the microbial commmunity and its association with nutrient metabolism in the intestinal tract using a pig model.

The gut microbiota is a complex ecosystem that is essential for the metabolism, immunity and health of the host. The gut microbiota also plays a critical role in nutrient absorption and metabolism, and nutrients can influence the growth and composition of the gut microbiota. To gain a better understanding of the relationship between the gut microbial composition and nutrient metabolism, we used a pig model by collecting the contents of the different intestinal locations from six pigs to investigate microbial composition in different intestinal locations based on 16S rRNA gene sequencing and the concentrations of short-chain fatty acids (SCFAs), amino acids, fat, and crude ash in different intestinal locations using gas chromatography and chemical analysis. The results showed that the richness and diversity of intestinal microbial communities gradually increased from the small intestine to the large intestine. The relative abundance of Proteobacteria was higher in the jejunum and ileum, whereas the proportion of Firmicutes was higher in the cecum and colon. The concentrations of SCFAs were higher in the cecum and colon (P < 0.05). The concentrations of amino acids were higher in the small intestine than in the large intestine, while the amino acid content was significantly higher in the ascending colon than in the transverse colon and descending colon. The correlation analysis revealed that Ruminococcaceae UCG-005, Coriobacteriaceae_uncultured, [Eubacterium] hallii group, Mogibacterium and Lachnospiraceae AC2044 group had a higher positive correlation with SCFAs, crude ash and fat but had a negative correlation with amino acids in different gut locations of pigs. These findings may serve as fundamental data for using nutrient metabolism to regulate human and animal gut microbes and health and provide guidance for exploring host-microbe bidirectional interaction mechanisms and driving pathways.

The Microbiome in Osteoarthritis: a Narrative Review of Recent Human and Animal Model Literature.

The microbiome has recently emerged as a powerful contributor to health and illness in chronic, systemic disorders. Furthermore, new microbiome niches beyond traditional gut locations are frequently being described. Over the past 5years, numerous pivotal studies have demonstrated associations between changes in various microbiome niches and the development of osteoarthritis (OA). Herein, we review the most impactful recent literature, including microbiome associations with disease and the potential therapeutic value of microbiome manipulation. The gut microbiome of human OA patients is enriched in specific bacterial clades, most notably Streptococcus, which correlates with OA pain, Firmicutes, and others. Most studies have focused on knee OA, although one publication demonstrated positive associations with 3 gut microbiome clades in hand OA. OA can be easily distinguished from RA by evaluating differences in oral microbiome composition. Most studies have also demonstrated a reduction in richness of the gut microbiome (alpha diversity) associated with OA. Several studies have identified bacterial signatures within human knee and hip cartilage, synovial fluid, and synovial tissue and have described changes in these patterns occurring with the development of OA. In animal models of OA, high-fat diet-induced obesity has been the most well-studied OA risk factor associated with changes in the microbiome, with numerous bacterial clades changed within the gut microbiome and associated with OA. Also in animal models, various oral supplementations, including dietary fiber, probiotics including Lactobacillus species, and cecal microbiome transplantation have all shown improvements in OA histopathology or cartilage healing. Microbiome changes are strongly associated with the OA disease process and with individual OA risk factors related to both the gut microbiome and the microbial DNA patterns in the joint. Microbiome-directed interventions have the potential to prevent or reduce the progression of OA. Future studies should investigate the mechanistic underpinnings of these microbiome associations and further define the therapeutic potential of microbiome augmentation.

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance

BackgroundAntimicrobial resistance (AMR) has been regarded as a major threat to global health. Pigs are considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of large-scale quantitative data on the distribution of ARGs in the pig production industry. The bacterial species integrated ARGs in the gut microbiome have not been clarified.ResultsIn the present study, we used deep metagenomic sequencing data of 451 samples from 425 pigs including wild boars, Tibetan pigs, and commercial or cross-bred experimental pigs under different rearing modes, to comprehensively survey the diversity and distribution of ARGs and detect the bacteria integrated in these ARGs. We identified a total of 1295 open reading frames (ORFs) recognized as antimicrobial resistance protein-coding genes. The ORFs were clustered into 349 unique types of ARGs, and these could be further classified into 69 drug resistance classes. Tetracycline resistance was most enriched in pig feces. Pigs raised on commercial farms had a significantly higher AMR level than pigs under semi-free ranging conditions or wild boars. We tracked the changes in the composition of ARGs at different growth stages and gut locations. There were 30 drug resistance classes showing significantly different abundances in pigs between 25 and 240 days of age. The richness of ARGs and 41 drug resistance classes were significantly different between cecum lumen and feces in pigs from commercial farms, but not in wild boars. We identified 24 bacterial species that existed in almost all tested samples (core bacteria) and were integrated 128 ARGs in their genomes. However, only nine ARGs of these 128 ARGs were core ARGs, suggesting that most of the ARGs in these bacterial species might be acquired rather than constitutive. We selected three subsets of ARGs as indicators for evaluating the pollution level of ARGs in samples with high accuracy (r = 0.73~0.89).ConclusionsThis study provides a primary overview of ARG profiles in various farms under different rearing modes, and the data serve as a reference for optimizing the use of antimicrobials and evaluating the risk of pollution by ARGs in pig farms.5YKgi5ZLgAPxFHnKjiANNtVideo abstract

Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes versicolor).

Simple SummaryThe different gut sections potentially provide different habitats for gut microbiota. We found that Bacteroidetes, Firmicutes, and Proteobacteria were the three primary phyla in gut microbiota of C. versicolor. The relative abundance of dominant phyla Bacteroidetes and Firmicutes exhibited an increasing trend from the small intestine to the large intestine, and there was a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the hindgut, and some metabolic pathways were higher in the hindgut. Our results reveal the variations of gut microbiota composition and metabolic pathways in different parts of the lizards’ intestine.Vertebrates maintain complex symbiotic relationships with microbiota living within their gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and their gut microbiota. However, this understanding is limited in lizards and the spatial heterogeneity and co-occurrence patterns of gut microbiota inside the gastrointestinal tracts of a host and variations of microbial community among samples remain poorly understood. To address this issue and provide a guide for gut microbiota sampling from lizards, we investigated the bacteria in three gut locations of the oriental garden lizard (Calotes versicolor) and the data were analyzed for bacterial composition by 16S ribosomal RNA (16S rRNA) gene amplicon sequencing. We found the relative abundance of the dominant phyla exhibited an increasing trend from the small intestine to the large intestine, and phyla Firmicutes, Bacteroidetes and Proteobacteria were the three primary phyla in the gut microbiota of C. versicolor. There were a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the sample from the hindgut. The secondary bile acid biosynthesis, glycosaminoglycan degradation, sphingolipid metabolism and lysosome were significantly higher in the hindgut than that in the small intestine. Taken together our results indicate variations of gut microbiota composition and metabolic pathway in different parts of the oriental garden lizard.

Lipids and organic acids in three gut locations affect feed efficiency of commercial pigs as revealed by LC\u2013MS-based metabolomics

Feed efficiency (FE) is an important economic indicator in pig production. Improving the FE of commercial pigs is an important strategy for minimizing pig production costs and providing sustainability to the pig industry. In this study, nontargeted LC–MS metabolomics was performed on the contents of the three intestine segments (ileum, cecum and colon) of high-FE and low-FE pigs to explore the effects of small-molecule metabolites in pig intestine on pig FE. A total of 225 Duroc × (Landrace × Yorkshire) pigs in the 30–100 kg stage were sorted based on FE, and 20 pigs with extreme phenotypes were selected, with 10 in each group. A total of 749 metabolites were identified, of which 15, 38 and 11 differed between high-FE and low-FE pigs in ileum, cecum and colon, respectively. These candidate biomarkers mainly comprised lipids and organic acids, which could partially explain the FE difference between the two groups. Among the identified differential metabolites, the lipids are mainly involved in combatting inflammation and oxidation in the ileum and cecum and in bile acid metabolism and vitamin D absorption in the cecum. A difference in organic acids was mainly observed in the hindgut, which is involved in the metabolism of amino acids and fatty acids. This comprehensive study provides new insight into the biochemical mechanisms associated with pig FE.

Expression of Transient Receptor Potential Ankyrin 1 and Transient Receptor Potential Vanilloid 1 in the Gut of the Peri-Weaning Pig Is Strongly Dependent on Age and Intestinal Site.

Simple SummaryWeaning is a critical event for the piglet, contributing to aberrant gut function and resulting in reduced barrier function and retarded protein digestion. The gut is able to “sense” nutrients and release gut hormones to regulate digestive processes. To that end, various gastrointestinal cell types possess transient receptor potential channels that are involved in regulating gastric motility and secretion. Herbal compounds, currently used in pig nutrition as antibiotic alternatives, are able to activate these channels and could potentially aid digestion. However, these channels have not been characterized in the gut of the pig and their ability to release gut hormones has never been explored. This study’s objective was to characterize TRPA1 and TRPV1 in the pig’s gut and explore their potential to modulate gastric function. A gene expression study was performed on tissues obtained from different locations in the guts of piglets of varying age. Moreover, the ability to secrete peptide hormones was investigated by characterizing them on enteroendocrine cells. Both channels were found to be expressed in the mucosa of the porcine gut, strongly dependent on age and location. Moreover, the endocrine nature of both channels was confirmed, indicating their possible role in gut hormone release and the regulation of gastric emptying.Transient receptor potential (TRP) channels contribute to sensory transduction in the body, agonized by a variety of stimuli, such as phytochemicals, and they are predominantly distributed in afferent neurons. Evidence indicates their expression in non-neuronal cells, demonstrating their ability to modulate gastrointestinal function. Targeting TRP channels could potentially be used to regulate gastrointestinal secretion and motility, yet their expression in the pig is unknown. This study investigated TRPA1 and TRPV1 expression in different gut locations of piglets of varying age. Colocalization with enteroendocrine cells was established by immunohistochemistry. Both channels were expressed in the gut mucosa. TRPV1 mRNA abundance increased gradually in the stomach and small intestine with age, most notably in the distal small intestine. In contrast, TRPA1 exhibited sustained expression across ages and locations, with the exception of higher expression in the pylorus at weaning. Immunohistochemistry confirmed the endocrine nature of both channels, showing the highest frequency of colocalization in enteroendocrine cells for TRPA1. Specific co-localization on GLP-1 immunoreactive cells indicated their possible role in GLP-1 release and the concomitant intestinal feedback mechanism. Our results indicate that TRPA1 and TRPV1 could play a role in gut enteroendocrine activity. Moreover, age and location in the gut significantly affected gene expression.

Weaning affects the glycosidase activity towards phenolic glycosides in the gut of piglets.

Phenolic compounds in pig diets, originating either from feed ingredients or additives, may occur as glycosides, that is conjugated to sugar moieties. Upon ingestion, their bioavailability and functionality depend on hydrolysis of the glycosidic bond by endogenous or microbial glycosidases. Hence, it is essential to map the glycosidase activities towards phenolic glycosides present along gut. Therefore, the activity of three key glycosidases, that is α-glucosidase (αGLU), β-glucosidase (βGLU) and β-galactosidase (βGAL), was quantified in small intestinal mucosa and digesta of piglets at different gastrointestinal sites (stomach, three parts of small intestine, caecum and colon) and at different ages around weaning (10days before and 0, 2, 5, 14 and 28days after weaning). Activity assays were performed with p-nitrophenyl glycosides at neutral pH. The αGLU activities in mucosa and digesta were low (overall means 1.4 and 60U respectively) as compared to βGLU (15.2 and 199U) and βGAL (23.4 and 298U; p<.001). Moreover, αGLU activity in mucosa was unaffected by age. Conversely, βGLU and βGAL activities dropped significantly after weaning. Minimal levels, ranging between 18% and 54% of the pre-weaning values, were reached at 5days post-weaning. Similarly, in small intestinal digesta, reductions from 60% up to 90% were observed for the three enzyme activities on day five post-weaning as compared to pre-weaning levels. In caecal contents, activities were lowest at 14days post-weaning, while in stomach and colon no clear weaning-induced effects were observed. Our data suggest that weaning affects the glycosidase activity in mucosa (mainly endogenous origin) and digesta (primarily bacterial origin) with the most pronounced effects occurring 5days post-weaning. Moreover, differences in activities exist between different glycosidases and between gut locations. These insights can facilitate the prediction of the fate of existing and newly synthetized glycosides after oral ingestion in piglets.

Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency.

Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.

Characterization of the microbiome along the gastrointestinal tracts of semi-artificially reared bar-headed geese (Anser indicus).

As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, compositions and predicted functions of semi-artificially reared bar-headed geese by sampling five different gut locations (the oropharynxs, crops, gizzards, ceca, and cloacae) along the gastrointestinal tracts of three individuals. Alpha diversity analyses showed that the gizzards had the richest species diversity and that the ceca had the least. Beta diversity analyses showed that the cecal samples formed their own cluster, while samples from the oropharynxs, crops, gizzards, and cloacae overlapped with each other. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria constituted the top five dominant phyla among all five gastrointestinal sections. At the genus level, a total of 10 genera with proportions above 2.5% were found to be significantly different among the gastrointestinal sections. Furthermore, 53 genera were detected in all gastrointestinal sections of bar-headed geese. PICRUSt data also predicted a group of microbial functions overrepresented in the different segments of the gastrointestinal tracts. Understanding the microbiota along the bar-headed geese gastrointestinal tracts is essential for future microbiological study of this bird and may contribute to the development of geese husbandry.

Subsets of mononuclear phagocytes are enriched in the inflamed colons of patients with IBD

BackgroundMyeloid cells, especially mononuclear phagocytes, which include monocytes, macrophages and dendritic cells (DC), play vital roles in innate immunity, and in the initiation and maintenance of adaptive immunity. While T cell-associated activation pathways and cytokines have been identified and evaluated in inflammatory bowel disease (IBD) patients (Neurath, Nat Rev Gastroenterol Hepatol 14:269–78, 1989), the role of mononuclear phagocytes are less understood. Recent reports support the crucial role of DC subsets in the development of acute colitis models (Arimura et al., Mucosal Immunol 10:957–70, 2017), and suggest they may contribute to the pathogenesis of ulcerative colitis (UC) by inducing Th1/Th2/Th17 responses (Matsuno et al., Inflamm Bowel Dis 23:1524–34, 2017).ResultsWe performed in silico analysis and evaluated the enrichment of immune cells, with a focus on mononuclear phagocytes in IBD patient colonic biopsies. Samples were from different gut locations, with different levels of disease severity, and with treatment response to current therapies. We observe enrichment of monocytes, M1 macrophages, activated DCs (aDCs) and plasmacytoid dendritic cells (pDCs) in inflamed tissues from various gut locations. This enrichment correlates with disease severity. Additionally, the same mononuclear phagocytes subsets are among the top enriched cell types in both infliximab and vedolizumab treatment non-responder samples. We further investigated the enrichment of selected DC and monocyte subsets based on gene signatures derived from a DC- and monocyte-focused single cell RNA-seq (scRNA-seq) study (Villani et al., Science 356:eaah4573, 2017), and verified enrichment in both inflamed tissues and those with treatment resistance. Moreover, we validated an increased mononuclear phagocyte subset abundance in a Dextran Sulphate Sodium (DSS) induced colitis model in C57Bl/6 mice representative of chronic inflammation.ConclusionsWe conducted an extensive analysis of immune cell populations in IBD patient colonic samples and identified enriched subsets of monocytes, macrophages and dendritic cells in inflamed tissues. Understanding how they interact with other immune cells and other cells in the colonic microenvironment such as epithelial and stromal cells will help us to delineate disease pathogenesis.