Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes

Over the course of human evolution, shifts in dietary practices such as meat-eating and cooking, have resulted in reduced fiber intake, a trend that has been exaggerated more recently in industrialized populations. Reduced fiber consumption is associated with a loss of gut microbial taxa that degrade fiber, particularly butyrate. Therefore, this dietary shift in humans may have altered the abundance of microbial genes involved in butyrate production. This study uses a gene-targeted alignment approach to quantify the abundance of butyrate production pathway genes from published wild nonhuman primate and human gut metagenomes. Surprisingly, humans have higher diversity and relative abundances of butyrate production pathways compared with all groups of nonhuman primates except cercopithecoids. Industrialized populations of humans also differ only slightly in butyrate pathway abundance from nonindustrialized populations. This apparent resilience of butyrate production pathways to shifts in human diet across both evolutionary and modern populations may signal an evolutionary shift in host–microbe interactions in humans that increased SCFA production. Such a shift could have contributed to meeting the increased energy requirements of humans relative to nonhuman primates.     

Colonic Lesions,Cytokine Profiles,and Gut Microbiota in Plasminogen-Deficient Mice

Plasminogen-deficient (FVB/NPan-plg^tm1Jld, plg^tm1Jld) mice, which are widely used as a wound-healing model, are prone to spontaneous rectal prolapses. The aims of this study were 1) to evaluate the fecal microbiome of plg^tm1Jld mice for features that might contribute to the development of rectal prolapses and colonic inflammation and 2) to assess the relevance of the inflammatory phenotype to the variability in wound healing in this model. The plg^tm1Jld mice exhibited delayed wound healing, and they could be divided into 3 distinct groups that differed according to the time until wound closure. Colonic lesions in plg^tm1Jld mice, which were characterized by necrotizing ulcerations and cystically dilated glands, were restricted to the intermediate and distal parts of the colon. The cytokine profile was indicative of chronic tissue damage, but the genetic modification did not change the composition of the gut microbiota, and none of the clinical or biochemical parameters correlated with the gut microbiota composition.Several studies using plasminogen-deficient (plg^tmJld) mice have demonstrated that plasminogen, the proenzyme of plasmin, can degrade fibrin and other extracellular matrix proteins.⁴⁴ Plasminogen is essential for wound healing in skin,⁴⁰ which begins with inflammation, followed by epithelial proliferation, and thereafter tissue remodeling. Because the migrating keratinocytes of plg^tm1Jld mice have a decreased ability to dissect the platelet-rich fibrin matrix, they exhibit severely impaired wound healing.^15,40 In addition, plasmin mediates various pathologic processes, such as tumor growth and cancer metastasis,⁸ and therapeutic intervention related to plasminogen has shown encouraging results in experimental tumors.³¹ Therefore, one important application of these mice is the induction of wound healing to study basic mechanistic functions of plasmin, such as the clearance of the extracellular matrix and activation of tumor growth factors.³¹Spontaneous rectal prolapse and colonic ulceration in plg^tm1Jld mice compromise studies using these mice by leading to loss of body weight (wasting disease)⁶ and wellbeing-related, early study termination.⁶ Like other inflammatory conditions, rectal prolapse and chronic colonic inflammation might affect wound healing and contribute to the wide interindividual variation in the wound-healing processes of plg^tm1Jld mice.^28,40The development of rectal prolapses and colonic ulcerations in plg^tm1Jld mice reportedly is due to vascular occlusion.⁶ This pathologic condition is alleviated by superimposing fibrinogen deficiency on plasminogen deficiency, suggesting that fibrin is the primary substrate for plasmin.^7,15 The wide variation in effective tissue remodeling during the wound healing of plasminogen-deficient mice remains unexplained.Wound healing depends to a large extent on cells and factors of the immune system.^3,53 We previously have shown that disease development in mouse models for various inflammatory conditions, including type 1 diabetes,^17-19,35 type 2 diabetes,^4,13,42 atopic dermatitis³⁰ and inflammatory bowel disease,²⁰ is influenced by the composition of gut microbiota. Therefore, gut inflammation can be presumed to interfere with wound healing and thus may increase the uncontrolled interindividual variation in these models. In addition, gut inflammatory conditions in humans, such as inflammatory bowel disease⁴³ and irritable bowel syndrome,²³ are linked to dysbiosis in the intestine. In mice deficient in IL10 or IL2 and in rats carrying HLA-B27,⁵² inflammatory bowel disease can be alleviated by germ-free status^10,49,52 or ampicillin.²⁰ However, the possible role of the gut microbiome in rectal prolapse, colonic lesions, and wound healing in plasminogen-deficient mice has not previously been assessed.The aims of the current study were 1) to evaluate the fecal microbiome of plg^tm1Jld mice and their unaffected WT littermates for features that might contribute to their rectal prolapse and colonic inflammation phenotypes and 2) to assess the relevance of the inflammatory phenotype to the variability in wound healing in this model.     

Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana,USA

We used high throughput pyrosequencing to characterize stomach and gut content microbiomes of Crassostrea virginica, the Easter oyster, obtained from two sites, one in Barataria Bay (Hackberry Bay) and the other in Terrebonne Bay (Lake Caillou), Louisiana, USA. Stomach microbiomes in oysters from Hackberry Bay were overwhelmingly dominated by Mollicutes most closely related to Mycoplasma; a more rich community dominated by Planctomyctes occurred in Lake Caillou oyster stomachs. Gut communities for oysters from both sites differed from stomach communities, and harbored a relatively diverse assemblage of phylotypes. Phylotypes most closely related to Shewanella and a Chloroflexi strain dominated the Lake Caillou and Hackberry Bay gut microbiota, respectively. While many members of the stomach and gut microbiomes appeared to be transients or opportunists, a putative core microbiome was identified based on phylotypes that occurred in all stomach or gut samples only. The putative core stomach microbiome comprised 5 OTUs in 3 phyla, while the putative core gut microbiome contained 44 OTUs in 12 phyla. These results collectively revealed novel microbial communities within the oyster digestive system, the functions of the oyster microbiome are largely unknown. A comparison of microbiomes from Louisiana oysters with bacterial communities reported for other marine invertebrates and fish indicated that molluscan microbiomes were more similar to each other than to microbiomes of polychaetes, decapods and fish.     

Altered lipid properties of the stratum corneum in Canine Atopic Dermatitis

Skin barrier disruption plays a role in the pathogenesis of atopic dermatitis (AD) in humans. However, little is known about skin barrier (dys-) function in Canine Atopic Dermatitis. The properties of lipids located in the outermost layer of the skin, the stratum corneum (SC) are considered to be important for the barrier. In the present study the lipid composition and lipid organization of the SC of AD dogs and control dogs were examined. The lipid composition of lesional AD skin as compared to control skin, showed a reduced free fatty acid level and a decreased ratio of ceramide[NS] C44/C34, in which C44 and C34 are the total numbers of carbon atoms of the sphingosine (S) and non-hydroxy (N) acyl chains. As a consequence of the observed changes in lipid composition in AD lesional skin the lamellar organization of lipids altered and a shift from orthorhombic to hexagonal lipid packing was monitored. Simultaneously an increased conformational disordering occurred. These changes are expected to compromise the integrity of the skin barrier. The C44/C34 chain length ratio of ceramide[NS] also showed a decreasing nonlinear relationship with the AD severity score (CADESI). Taken together, canine atopic skin showed alterations in SC lipid properties, similar to the changes observed in atopic dermatitis in humans, that correlated with a disruption of the skin barrier. Hence lipids play an important role in the pathogenesis of Canine Atopic Dermatitis.     

Granulocytes Impose a Tight Bottleneck upon the Gut Luminal Pathogen Population during Salmonella Typhimurium Colitis

Topological, chemical and immunological barriers are thought to limit infection by enteropathogenic bacteria. However, in many cases these barriers and their consequences for the infection process remain incompletely understood. Here, we employed a mouse model for Salmonella colitis and a mixed inoculum approach to identify barriers limiting the gut luminal pathogen population. Mice were infected via the oral route with wild type S. Typhimurium (S. Tm) and/or mixtures of phenotypically identical but differentially tagged S. Tm strains (“WITS”, wild-type isogenic tagged strains), which can be individually tracked by quantitative real-time PCR. WITS dilution experiments identified a substantial loss in tag/genetic diversity within the gut luminal S. Tm population by days 2–4 post infection. The diversity-loss was not attributable to overgrowth by S. Tm mutants, but required inflammation, Gr-1⁺ cells (mainly neutrophilic granulocytes) and most likely NADPH-oxidase-mediated defense, but not iNOS. Mathematical modelling indicated that inflammation inflicts a bottleneck transiently restricting the gut luminal S. Tm population to approximately 6000 cells and plating experiments verified a transient, inflammation- and Gr-1⁺ cell-dependent dip in the gut luminal S. Tm population at day 2 post infection. We conclude that granulocytes, an important clinical hallmark of S. Tm-induced inflammation, impose a drastic bottleneck upon the pathogen population. This extends the current view of inflammation-fuelled gut-luminal Salmonella growth by establishing the host response in the intestinal lumen as a double-edged sword, fostering and diminishing colonization in a dynamic equilibrium. Our work identifies a potent immune defense against gut infection and reveals a potential Achilles'' heel of the infection process which might be targeted for therapy.     

Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice

Mutation of the adenomatous polyposis coli (APC gene), an early event in the adenoma-carcinoma sequence, is present in 70-80% of sporadic human colorectal adenomas and carcinomas. To test the hypothesis that mutation of the APC gene alters microbial interactions with host intestinal mucosa prior to the development of polyposis, culture-independent methods (targeted qPCR assays and Illumina sequencing of the 16S rRNA gene V1V2 hypervariable region) were used to compare the intestinal microbial composition of 30 six-week old C57BL/6 APC^Min/+ and 30 congenic wild type (WT) mice. The results demonstrate that similar to 12-14 week old APC^Min/+ mice with intestinal neoplasia, 6 week old APC^Min/+ mice with no detectable neoplasia, exhibit an increased relative abundance of Bacteroidetes spp in the colon. Parallel mouse RNA sequence analysis, conducted on a subset of proximal colonic RNA samples (6 APC^Min/+, 6 WT) revealed 130 differentially expressed genes (DEGs, fold change ≥ 2, FDR <0.05). Hierarchical clustering of the DEGs was carried out by using 1-r dissimilarity measurement, where r stands for the Pearson correlation, and Ward minimum variance linkage, in order to reduce the number of input variables. When the cluster centroids (medians) were included along with APC genotype as input variables in a negative binomial (NB) regression model, four of seven mouse gene clusters, in addition to APC genotype, were significantly associated with the increased relative abundance of Bacteroidetes spp. Three of the four clusters include several downregulated genes encoding immunoglobulin variable regions and non-protein coding RNAs. These results support the concept that mutation of the APC gene alters colonic-microbial interactions prior to polyposis. It remains to be determined whether interventions directed at ameliorating dysbiosis in APC^Min/+mice, such as through probiotics, prebiotics or antibiotics, could reduce tumor formation.     

Analysis of Gut Microbiota in Patients with Breast Cancer and Benign Breast Lesions

Breast cancer (BC) and benign breast lesions (BBLs) are common diseases in women worldwide. The gut microbiota plays a vital role in regulating breast diseases’ formation, progression, and therapy response. Hence, we explored the structure and function of gut microflora in patients with BC and BBLs. A cohort of 66 subjects was enrolled in the study. Twenty-six subjects had BC, 20 subjects had BBLs, and 20 matched healthy controls. High throughput 16S ribosomal RNA (16S rRNA) gene sequencing technology was used to determine the microbial community structure. Compared with healthy individuals, BC patients had significantly lower alpha diversity indices (Sobs index, p = 0.019; Chao1 index, p = 0.033). Sobs and Chao1 indices were also lower in patients with BBLs than healthy individuals, without statistical significance (p = 0.279, p = 0.314, respectively). Both unweighted and weighted UniFrac analysis showed that beta diversity differed significantly among the three groups (p = 3.376e–14, p < 0.001, respectively). Compared with healthy individuals, the levels of Porphyromonas and Peptoniphilus were higher in BC patients (p = 0.004, p = 0.007, respectively), whereas Escherichia and Lactobacillus were more enriched in the benign breast lesion group (p < 0.001, p = 0.011, respectively). Our study indicates that patients with BC and BBLs may undergo significant changes in intestinal microbiota. These findings can help elucidate the role of intestinal flora in BC and BBLs patients. Open in a separate window     

The Gastrointestinal Tract as a Potential Infection Reservoir of Digital Dermatitis-Associated Treponemes in Beef Cattle and Sheep

Digital dermatitis (DD) is an important cause of lameness in dairy cattle worldwide. It has now been reported in beef cattle and also sheep (contagious ovine digital dermatitis [CODD]). Three Treponema phylogroups are consistently isolated from lesions, Treponema medium-like, Treponema phagedenis-like, and Treponema pedis. The gastrointestinal (GI) tract and feces are suggested sites of treponemal infection in dairy cattle; however, isolation of DD-associated treponemes from these areas has previously failed. This study surveyed gingival tissues, rectal tissues, and feces of beef cattle and sheep for the molecular presence (PCR) and isolation of the three cultivable DD-treponeme phylogroups. Of the sheep gingival (n = 40) and rectal (n = 40) tissues, 1/40 gingival tissues was positive for DD-associated treponemes (T. pedis), as were 3/40 rectal tissues (one containing T. medium-like and two containing T. pedis). No DD-associated treponeme DNA was amplified from beef cattle rectal tissues (n = 40); however, 4/40 beef gingival tissues were positive for DD-associated treponemes (all containing T. phagedenis-like). A T. phagedenis-like DD-associated treponeme was isolated from the rectal tissue of a CODD symptomatic sheep. Beef cattle (n = 41) and sheep (n = 79) feces failed to amplify DD-associated Treponema DNA. Twenty-two treponemes were isolated from sheep feces; however, upon phylogenetic analysis, these clustered with the considered nonpathogenic treponemes. This study detected DD-associated treponemes in the GI tract tissues of sheep and beef cattle and successfully isolated a DD-associated treponeme from ruminant rectal tissue. This gives evidence that the GI tract is an important infection reservoir of DD-associated treponemes in multiple DD-infected species.     

Pollen as a chronometer and sediment tracer,Burrinjuck Reservoir,Australia

Pollen analysis is widely used to reconstruct vegetation and land use histories, but can also provide sedimentological information. At Burrinjuck Reservoir, in south-eastern Australia, annual grass pollen peaks are used to distinguish each year's sediment, even when there are no visible laminations. In conjunction with other dating methods, this allows the determination of year by year influxes of all sediment components. Pollen grains in the Burrinjuck sediments are shown to be predominantly waterborne so that they can be used to trace sediment to its source in particular vegetation stands. Pollen concentration and the proportion of damaged pollen might also distinguish sediment eroded from topsoils and that from subsoils. Pollen analysis can thus be used to locate specific erosion events in both time and space.     

Bovine liver dihydropyrimidine amidohydrolase: purification, properties, and characterization as a zinc metalloenzyme

Beef liver dihydropyrimidine amidohydrolase has been purified to homogeneity using both an electrophoretic and a hydrophobic chromatographic method. The enzyme is a tetramer with a molecular weight of 226,000 g mol-1, a subunit molecular weight of 56,500 g mol-1, and contains 4 mol of tightly bound (Ks greater than or equal to 1.33 X 10(9) M-1) Zn2+ per mole of active enzyme. The enzyme appears to be a true Zn2+ metalloenzyme because there exists a direct proportionality between enrichment of Zn2+ and active enzyme during purification, there is an almost quantitative relationship between the loss of both enzyme activity and Zn2+ during 8-hydroxyquinoline-5-sulfonic acid treatment to form apoenzyme, Zn2+ and Co2+ reactivate dipicolinic acid-inhibited enzyme, and saturating concentrations of a substrate, dihydrothymine, protect against 8-hydroxyquinoline-5-sulfonic acid inhibition. EDTA does not inhibit the enzyme; however, 8-hydroxyquinoline-5-sulfonic acid, o-phenanthroline, and 2,6-dipicolinic acid cause a time-dependent loss in activity which follows pseudo-first-order kinetics. Analysis of the resulting kinetic data for these three chelators indicates that the reaction pathway involves the formation of an enzyme-Zn2+-chelator ternary complex which then dissociates to form apoenzyme and a Zn2+-chelator complex. Like other Zn2+ metalloenzymes, the enzyme is inhibited by a number of substituted sulfonamides. In the case of p-nitrobenzenesulfonamide, this inhibition is competitive in nature. Using the purified enzyme, kinetic constants were determined for a variety of dihydropyrimidines, ureidocarboxylic acids, and hydantoin substrates. Normal hyperbolic kinetics were observed for the hydrolysis of the cyclic compounds, but the cyclization of the ureidoacids showed biphasic kinetics and different values of Km can be estimated at either high or low concentrations of these substrates.     

Single Nucleotide Polymorphisms in IL8 and TLR4 Genes as Candidates for Digital Dermatitis Resistance/Susceptibility in Holstein Cattle

Relatedness between single nucleotide polymorphisms in IL8 and TLR4 genes and digital dermatitis resistance/susceptibility was investigated in seventy Holstein dairy cows. Animals were assigned into two groups, affected group (n?=?35) and resistant group (n?=?35) based on clinical signs and previous history of farm clinical records. Blood samples were collected for DNA extraction to ampliy fragments of 267-bp and 382-bp for IL8 and TLR4 genes, respectively. PCR-DNA sequencing revealed three SNPs in each of IL8 and TLR4 genes. The identified SNPs associated with digital dermatitis resistance were C94T, A220G, and T262A for IL8 and C118T for TLR4. However, the G349C and C355A SNPs in TLR4 gene were associated with digital dermatitis susceptibility. Chi-square analysis for comparison the distribution of all identified SNPs in both IL8 and TLR4 genes between resistant and affected animals showed no significant variation among the identified SNPs in IL8 gene. Meanwhile, there was a significant variation in case of TLR4 gene. As a pilot study, the present results revealed that identified SNPs in IL8 and TLR4 genes can be used as a genetic marker and predisposing factor for resistance/susceptibility to digital dermatitis in dairy cows. However, TLR4 gene may be a potential candidate for such disease.     

Adipocytes as a Link Between Gut Microbiota-Derived Flagellin and Hepatocyte Fat Accumulation

While the role of both elevated levels of circulating bacterial cell wall components and adipose tissue in hepatic fat accumulation has been recognized, it has not been considered that the bacterial components-recognizing adipose tissue receptors contribute to the hepatic fat content. In this study we found that the expression of adipose tissue bacterial flagellin (FLG)-recognizing Toll-like receptor (TLR) 5 associated with liver fat content (r = 0.699, p = 0.003) and insulin sensitivity (r = -0.529, p = 0.016) in humans (n = 23). No such associations were found for lipopolysaccharides (LPS)-recognizing TLR4. To study the underlying molecular mechanisms of these associations, human HepG2 hepatoma cells were exposed in vitro to the conditioned culture media derived from FLG or LPS-challenged human adipocytes. The adipocyte-mediated effects were also compared to the effects of direct HepG2 exposure to FLG and LPS. We found that the media derived from FLG-treated adipocytes stimulated fat accumulation in HepG2 cells, whereas either media derived from LPS-treated adipocytes or direct FLG or LPS exposure did not. This is likely due to that FLG-treatment of adipocytes increased lipolysis and secretion of glycerol, which is known to serve a substrate for triglyceride synthesis in hepatocytes. Similarly, only FLG-media significantly decreased insulin signaling-related Akt phosphorylation, IRS1 expression and mitochondrial respiratory chain ATP5A. In conclusion, our results suggest that the FLG-induced TLR5 activation in adipocytes increases glycerol secretion from adipocytes and decreases insulin signaling and mitochondrial functions, and increases fat accumulation in hepatocytes. These mechanisms could, at least partly, explain the adipose tissue TLR5 expression associated with liver fat content in humans.