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The development of alternative in vitro culture methods has increased in the last decade as three-dimensional organoids of various tissues, including those of the small and large intestines. Due to their multicellular composition, organoids offer advantages over traditionally used immortalized or primary cell lines. However, organoids must be accurate models of their tissues of origin. This study compared gene expression profiles with respect to markers of specific cell types (stem cells, enterocytes, goblet, and enteroendocrine cells) and barrier maturation (tight junctions) of colonoid and enteroid cultures with their tissues of origin and colonoids with enteroids. Colonoids derived from three healthy pigs formed multilobed structures with a monolayer of cells similar to the crypt structures in colonic tissue. Colonoid and enteroid gene expression signatures were more similar to those found for the tissues of their origin than to each other. However, relative to their derived tissues, organoids had increased gene expression levels of stem cell markers Sox9 and Lgr5 encoding sex-determining region Y-box 9 and leucine-rich repeat-containing G protein-coupled rector 5, respectively. In contrast, expression levels of Occl and Zo1 encoding occludin and zonula occludens 1, respectively, were decreased. Expression levels of the cell lineage markers Atoh1, Cga, and Muc2 encoding atonal homolog 1, chromogranin A, and mucin 2, respectively, were decreased in colonoids, whereas Sglt1 and Apn encoding sodium-glucose transporter 1 and aminopeptidase A, respectively, were decreased in enteroids. These results indicate colonoid and enteroid cultures were predominantly comprised of undifferentiated cell types with decreased barrier maturation relative to their tissues of origin.

The genetic architecture of dark cutting was investigated with a case-control genome-wide association study on two groups of beef cattle analyzed separately and together (combined group). Groups I (n = 64) and II (n = 150) were genotyped using the 70K GeneSeek Genomic Profiler for Beef Cattle-HD and the 50K Illumina BovineSNP50v2 BeadChip, respectively. Dark cutting was analyzed as a binary trait (case versus control) using logistic regression in an additive model implemented in PLINK version 1.9. Significant loci were not identified when correcting for multiple testing (false discovery rate), suggesting that the trait is not controlled by genes with big effects, or the sample size was not large enough to detect these major genes. Regions harbouring single-nucleotide polymorphisms (SNPs) with a raw p

Significance Mammalian central synapses of diverse functions contribute to highly complex brain organization, but the molecular basis of synaptic diversity remains open. This is because current synapse proteomics are restricted to the “average” composition of abundant synaptic proteins. Here, we demonstrate a subcellular proteomic workflow that can identify and quantify the deep proteome of synaptic vesicles, including previously missing proteins present in a small percentage of central synapses. This synaptic vesicle proteome revealed many proteins of physiological and pathological relevance, particularly in the low-abundance range, thus providing a resource for future investigations on diversified synaptic functions and neuronal dysfunctions., Current proteomic studies clarified canonical synaptic proteins that are common to many types of synapses. However, proteins of diversified functions in a subset of synapses are largely hidden because of their low abundance or structural similarities to abundant proteins. To overcome this limitation, we have developed an “ultra-definition” (UD) subcellular proteomic workflow. Using purified synaptic vesicle (SV) fraction from rat brain, we identified 1,466 proteins, three times more than reported previously. This refined proteome includes all canonical SV proteins, as well as numerous proteins of low abundance, many of which were hitherto undetected. Comparison of UD quantifications between SV and synaptosomal fractions has enabled us to distinguish SV-resident proteins from potential SV-visitor proteins. We found 134 SV residents, of which 86 are present in an average copy number per SV of less than one, including vesicular transporters of nonubiquitous neurotransmitters in the brain. We provide a fully annotated resource of all categorized SV-resident and potential SV-visitor proteins, which can be utilized to drive novel functional studies, as we characterized here Aak1 as a regulator of synaptic transmission. Moreover, proteins in the SV fraction are associated with more than 200 distinct brain diseases. Remarkably, a majority of these proteins was found in the low-abundance proteome range, highlighting its pathological significance. Our deep SV proteome will provide a fundamental resource for a variety of future investigations on the function of synapses in health and disease.

There is emerging evidence that an unhealthy dietary pattern may increase the risk of developing depression or anxiety, whereas a healthy dietary pattern may decrease it. This nascent research suggests that dietary interventions could help prevent, or be an alternative or adjunct therapy for, depression and anxiety. The relation, however, is complex, affected by many confounding variables, and is also likely to be bidirectional, with dietary choices being affected by stress and depression. This complexity is reflected in the data, with sometimes conflicting results among studies. As the research evolves, all characteristics of the relation need to be considered to ensure that we obtain a full understanding, which can potentially be translated into clinical practice. A parallel and fast-growing body of research shows that the gut microbiota is linked with the brain in a bidirectional relation, commonly termed the microbiome–gut–brain axis. Preclinical evidence suggests that this axis plays a key role in the regulation of brain function and behavior. In this review we discuss possible reasons for the conflicting results in diet–mood research, and present examples of areas of the diet–mood relation in which the gut microbiota is likely to be involved, potentially explaining some of the conflicting results from diet and depression studies. We argue that because diet is one of the most significant factors that affects human gut microbiota structure and function, nutritional intervention studies need to consider the gut microbiota as an essential piece of the puzzle.

CYBASC proteins are ascorbate (AscH-) reducible, diheme b containing membrane integral cytochrome b561 proteins (cytb561), which are proposed to be involved in AscH- recycling and facilitation of i...

The food we consume and its interactions with the host and their gut microbiota affect normal gut function and health. Functional gut disorders (FGDs), including irritable bowel syndrome (IBS), can result from negative effects of these interactions, leading to a reduced quality of life. Certain foods exacerbate or reduce the severity and prevalence of FGD symptoms. IBS can be used as a model of perturbation from normal gut function with which to study the impact of foods and diets on the severity and symptoms of FGDs and understand how critical processes and biochemical mechanisms contribute to this impact. Analyzing the complex interactions between food, host, and microbial metabolites gives insights into the pathways and processes occurring in the gut which contribute to FGDs. The following review is a critical discussion of the literature regarding metabolic pathways and dietary interventions relevant to FGDs. Many metabolites, for example bile acids, SCFAs, vitamins, amino acids, and neurotransmitters, can be altered by dietary intake, and could be valuable for identifying perturbations in metabolic pathways that distinguish a “normal, healthy” gut from a “dysfunctional, unhealthy” gut. Dietary interventions for reducing symptoms of FGDs are becoming more prevalent, but studies investigating the underlying mechanisms linked to host, microbiome, and metabolite interactions are less common. Therefore, we aim to evaluate the recent literature to assist with further progression of research in this field.

Effects of residual feed intake (RFI) and genetic group on growth, carcass, and meat quality characteristics of bovine longissimus lumborum (LL), triceps brachii (TB), semimembranosus (SM), and gluteus medius (GM) muscles were investigated using 72 purebred Angus, purebred Charolais, and Angus crossbred steers (n = 24 per genetic group) classified as either high (inefficient) or low (efficient) RFI (n = 12 high and low RFI steers within genetic group). There was no RFI effect (P > 0.05) on growth, carcass, and meat quality measurements except high RFI steers had the highest dry matter intake (P

Background Human health depends on a population of microorganisms that inhabit the gut and contribute to homeostasis of the host, including nutrition, immunity and metabolism. Many of the organisms are interactive and mutually dependent, where the end-products for one organism become the fuel for another through substrate and metabolic cross-feeding. To optimise the gut microbiota using diet, the composition and functionality of the gut microbiota, including these interacting networks, must be understood. Microbial composition and functionality is affected by the structure of the energy input, which is primarily dietary fibre for the gut microbiota. The structure of dietary fibre has been reviewed by carbohydrate chemists, but knowledge of how dietary fibre structure affects the gut microbiota is limited. Scope and approach The hierarchical structures of dietary fibre are reviewed, encompassing macrostructure, mesostructure and molecular structure, and how they are affected by food processing and digestion. These factors are considered in relation to their affects on microbial composition and functionality, to provide insight on the interactions between diet, the microbiota, and human health. Key findings and conclusions Food processing and digestion affect food structure, primarily through the removal of some soluble fractions and increased solubilisation of insoluble fractions. The provision of insoluble carbohydrates to the colon appears important for the sustenance of ‘keystone’ species that play a crucial role in stabilising the gut community. Further work is needed at the microbial strain level to understand the impact of increasing fibre solubility. This should be done in studies using well-characterised carbohydrates that consider the impact of food processing and digestion.

The bacterial production of acetate via reductive acetogenesis along the Wood–Ljungdahl metabolic pathway is an important source of this molecule in several environments, ranging from industrial bioreactors to the human gastrointestinal tract. Here, we contributed to the study of reductive acetogens by considering mathematical modelling techniques for the prediction of bacterial growth and acetate production. We found that the incorporation of a hydrogen uptake concentration threshold into the models improves their predictions and we calculated this threshold as 86.2 mM (95% confidence interval 6.1–132.6 mM). Monod kinetics and first-order kinetics models, with the inclusion of two candidate threshold terms or reversible Michaelis–Menten kinetics, were compared to experimental data and the optimal formulation for predicting both growth and metabolism was found. The models were then used to compare the efficacy of two growth media for acetogens. We found that the recently described general acetogen medium was superior to the DSMZ medium in terms of unbiased estimation of acetogen growth and investigated the contribution of yeast extract concentration to acetate production and bacterial growth in culture. The models and their predictions will be useful to those studying both industrially and environmentally relevant reductive acetogenesis and allow for straightforward adaptation to similar cases with different organisms.

The microbiological, physical, chemical, and immunological barriers of the gastrointestinal tract (GIT) begin developing in utero and finish maturing postnatally. Maturation of these barriers is essential for the proper functioning of the GIT. Maturation, particularly of the immunological barrier, involves stimulation by bacteria. Segmented filamentous bacteria (SFB) which are anaerobic, spore-forming commensals have been linked to immune activation. The presence and changes in SFB abundance have been positively correlated to immune markers (cytokines and immunoglobulins) in the rat ileum and stool samples, pre- and post-weaning. The abundance of SFB in infant stool increases from 6 months, peaks around 12 months and plateaus 25 months post-weaning. Changes in SFB abundance at these times correlate positively and negatively with the production of interleukin 17 (IL 17) and immunoglobulin A (IgA), respectively, indicating involvement in immune function and maturation. Additionally, the peak in SFB abundance when a human milk diet was complemented by solid foods hints at a diet effect. SFB genome analysis revealed enzymes involved in metabolic pathways for survival, growth and development, host mucosal attachment and substrate acquisition. This narrative review discusses the current knowledge of SFB and their suggested effects on the small intestine immune system. Referencing the published genomes of rat and mouse SFB, the use of food substrates to modulate SFB abundance is proposed while considering their effects on other microbes. Changes in the immune response caused by the interaction of food substrate with SFB may provide insight into their role in infant immunological barrier maturation.

Background & Aims Single immunoglobulin interleukin-1–related receptor (SIGIRR) is a major inhibitor of Toll-like receptor signaling. Our laboratory identified a novel SIGIRR stop mutation (p.Y168X) in an infant who died of severe necrotizing enterocolitis (NEC). Herein, we investigated the mechanisms by which SIGIRR mutations induce Toll-like receptor hyper-responsiveness in the neonatal gut, disrupting postnatal intestinal adaptation. Methods Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 was used to generate transgenic mice encoding the SIGIRR p.Y168X mutation. Ileal lysates, mouse intestinal epithelial cell (IEC) lysates, and intestinal sections were used to assess inflammation, signal transducer and activator of transcription 3 (STAT3) phosphorylation, microRNA (miRNA), and interleukin-1–related–associated kinase 1 (IRAK1) expression. Western blot, quantitative reverse-transcription polymerase chain reaction(qRT-PCR), and luciferase assays were performed to investigate SIGIRR–STAT3 signaling in human intestinal epithelial cells (HIEC) expressing wild-type or SIGIRR (p.Y168X) plasmids. Results SigirrTg mice showed increased intestinal inflammation and nuclear factor-κB activation concomitant with decreased IEC expression of miR-146a and miR-155. Mechanistic studies in HIECs showed that although SIGIRR induced STAT3-mediated expression of miR-146a and miR-155, the p.Y168X mutation disrupted SIGIRR-mediated STAT3-dependent miRNA expression. Chromatin immunoprecipitation and luciferase assays showed that SIGIRR activation of STAT3-induced miRNA expression is dependent on IRAK1. Both in HIECs and in the mouse intestine, decreased expression of miR-146a observed with the p.Y168X mutation increased expression of IRAK1, a protein whose down-regulation is important for postnatal gut adaptation. Conclusions Our results uncover a novel pathway (SIGIRR–STAT3–miRNA–IRAK1 repression) by which SIGIRR regulates postnatal intestine adaptation, which is disrupted by a SIGIRR mutation identified in human NEC. These data provide new insights into how human genetic mutations in SIGIRR identified in NEC result in loss of postnatal intestinal immune tolerance., Graphical abstract

Coolia Meunier 1919 from benthic assemblages of Hawai'i and Guam were isolated and clonal cultures were established from single cells. Cultures were identified to species-level based on 28S rRNA and ITS-5.8S rRNA genes and tested for toxicity. In Hawai'i, two strains of C. malayensis were isolated. In Guam, a high biodiversity was identified: four strains of C. malayensis, one strain of C. palmyrensis, one strain of C. tropicalis, one strain of C. canariensis phylogroup III, and two strains forming a new phylogroup (phylogroup IV) of nontoxic C. canariensis. Morphology of the new C. canariensis phylogroup was described using light microscopy and scanning electron microscopy. Mass cultures and methanol extracts of representative cultures (C. malayensis, C. palmyrensis, C. canariensis, C. tropicalis) from Guam were prepared for liquid chromatography-mass spectrometry analysis. Chemical analyses revealed yessotoxin analogue C56H78O18S2 is produced by C. malayensis, C. canariensis phylogroup IV and C. palmyrensis, but other analogues, C57H80O18S2 and C58H86O18S2, were only found in C. malayensis (Okinawa) and C. canariensis phylogroup IV. Individual toxin profiles were also different over time for an Okinawa strain of C. malayensis (NIES-3637), highlighting intra and inter-species variation in Yessotoxin-analogue expression. Biological activity was tested using Artemia bioassay and toxicity was observed in Guam and Okinawa strains of C. malayensis. Strong support of four distinct clades within the C. canariensis species complex was recovered in phylogenetic analyses, despite morphological similarities.

Human breast milk is the optimal source of nutrients for growing infants. However, many circumstances can arise which preclude breast milk feeding, leading to the use of infant formula, including during the weaning period. Many diet-related effects are modulated by the gut microbiome. Therefore, we investigated the effect of human milk (HM) or infant formula (IF) on the gut microbiota in weanling rats. The gut microbiota of weanling male Sprague–Dawley rats fed HM or IF for 28 days was analysed by shotgun metagenome sequencing. Caecal contents were analysed by liquid chromatography–mass spectrometry metabolomics. Numerous genera within the Proteobacteria phylum were relatively more abundant in the ileum, caecum, and colon of rats fed HM, including ileal Escherichia (HM = 9.6% ± 4.3 SEM; IF = 0.9% ± 0.3 SEM; P = 0.03). Other taxa that differed between HM- and IF-fed rats included Prevotella and Ruminococcus. Overall, more differences were observed in the ileum than the caecum and colon between rats fed HM and IF. For the rats fed IF, in the ileum, the relative abundance of Bifidobacterium was higher (HM = 1.7% ± 0.7 SEM; IF = 5.0% ± 1.5 SEM; P = 0.04) with gene functions related to carbohydrate and amino acid metabolism also decreased. In the caecum, metabolic features such as bile acids were elevated while amino sugars were also decreased. Our results show that HM and IF composition differences are reflected in the gut microbiome composition and function in both the small and large intestines.

Background Cytokines, chemokines, C-reactive proteins (CRP) and ferritin are known inflammatory markers. However, cytokines such as interleukin (IL-1β), (IL-6) and tumour necrosis factor (TNF-α) have been reported to interfere with both the bone resorption and bone formation processes. Similarly, immune cell cytokines are known to contribute to inflammation of the adipose tissue especially with obesity. IL-10 but not IL-33 has been linked to lower ferritin levels and anemia. In this study, we hypothesized that specific cytokine levels in the plasma of women with low bone mineral density (BMD) would be higher than those in the plasma of healthy women due to the actions of elevated levels of pro-inflammatory cytokines in inducing osteoclast formation and differentiation during senescence. Results Levels of cytokines (IFNα2, IFN-γ, IL-12p70, IL-33) and monocyte chemoattractant protein-1 (MCP-1) were significantly higher in the plasma of the osteoporotic group compared to the osteopenic and/or healthy groups. Meanwhile CRP levels were significantly lower in women with osteoporosis (P = 0.040) than the osteopenic and healthy groups. Hip BMD values were significantly lower in women with high/detectable values of IL-1β (P = 0.020) and IL-6 (P = 0.030) compared to women where these were not detected. Similarly, women with high/detectable values of IL-1β had significantly lower spine BMD than those where IL-1β was not detected (P = 0.030). Participants’ CRP levels were significantly positively correlated with BMI, fat mass and fat percentage (P

Autophagy may play a critical role in colon cancer stem cells (CCSCs)-related cancer development. Here, we investigate whether accumulation of infection/injury-induced CCSCs due to impaired autophagy influences colon cancer development and progression. When Apc++ mice were infected with Citrobacter rodentium (CR; 109CFUs), we discovered presence of autophagosomes with increases in Beclin-1, LC3B and p62 staining during crypt hyperplasia. Apc1638N/+ mice when infected with CR or subjected to CR+AOM treatment, exhibited increased colon tumorigenesis with elevated levels of Ki-67, β-catenin, EZH2 and CCSC marker Dclk1, respectively. AOM/DSS treatment of Apc1638N/+ mice phenocopied CR+AOM treatment as colonic tumors exhibited pronounced changes in Ki-67, EZH2 and Dclk1 accompanied by infiltration of F4/80+ macrophages, CD3+ lymphocytes and CD3/β-catenin co-localization. Intestinal and colonic tumors also stained positive for migrating CSC markers CD110 and CDCP1 wherein, colonic tumors additionally exhibited stromal positivity. In tumors from CR-infected, CR+AOM or AOM/DSS-treated Apc1638N/+ mice and surgically-resected colon tumor/metastatic liver samples, significant accumulation of p62 and it's co-localization with LC3B and Dclk1 was evident. ApcMin/+ mice when infected with CR and BLT1−/−;ApcMin/+ mice, exhibited similar co-localization of p62 with LC3B and Dclk1 within the tumors. Studies in HCT116 and SW480 cells further confirmed p62/Dclk1 co-localization and Chloroquin/LPS-induced increases in Dclk1 promoter activity. Thus, co-localization of p62 with Dclk1 may hamper Dclk1's elimination to impact colon cancer development and progression.

Hydrogen plays a key role in many microbial metabolic pathways in the human gastrointestinal tract (GIT) that have an impact on human nutrition, health and wellbeing. Hydrogen is produced by many members of the GIT microbiota, and may be subsequently utilized by cross-feeding microbes for growth and in the production of larger molecules. Hydrogenotrophic microbes fall into three functional groups: sulfate-reducing bacteria, methanogenic archaea and acetogenic bacteria, which can convert hydrogen into hydrogen sulfide, methane and acetate, respectively. Despite different energy yields per molecule of hydrogen used between the functional groups, all three can coexist in the human GIT. The factors affecting the numerical balance of hydrogenotrophs in the GIT remain unconfirmed. There is increasing evidence linking both hydrogen sulfide and methane to GIT diseases such as irritable bowel syndrome, and strategies for the mitigation of such health problems through targeting of hydrogenotrophs constitute an important field for further investigation.

The spatial distribution of benthic foraminiferal morpho-groups has been documented from the Kongsfjorden-Krossfjorden, to assess its environmental significance. Benthic foraminiferal abundance increases from the inner-most fjord towards the mouth in Kongsfjorden. The calcareous forms dominate the benthic foraminiferal population in Kongsfjorden as compared to Krossfjorden. The agglutinated benthic foraminifera are relatively more abundant in Krossfjorden. The rounded symmetrical benthic foraminifera are the dominant morpho-group, due to the high energy conditions and generally well-oxygenated waters. A significant positive correlation between the relative abundance of rounded symmetrical benthic foraminifera and water depth, however, suggests the influence of factors other than turbulence. A more significant positive correlation is observed between the relative abundance of agglutinated rounded symmetrical benthic foraminifera and water depth. The relative abundance of calcareous angular asymmetrical benthic foraminifera is significantly negatively correlated with water depth. The significant correlation between foraminiferal parameters and water depth, suggests that melt-water and glacial calving, as well as associated changes in the sedimentation rate, grain size, pH and organic carbon, affect benthic foraminifera in high latitudinal fjords. The difference in the surface distribution of calcareous and agglutinated benthic foraminiferal morpho-groups implies their differential response to ambient conditions.

Purpose Hides are the by product of slaughter houses which are mostly used for leather production. In Canada, the hides are either disposed of with other slaughter waste or sold at a very low price. Dehairing of hides is a prerequisite for either leather or gelatin production from it. Therefore, the effect of hide dehairing method on subsequent gelatin extraction and quality was investigated.Methods Bovine hides (BH) were dehaired using either 5% acetic acid (AA), 10% calcium hydroxide (CH), 0.02% keratinase (KTN), 2.5% papain (PP), or not at all (control; CT), with control BH subsequently treated with 5% AA (CTAA).Results Mean bovine hide gelatin (BHG) yields (dry basis) were 11.37%, 54.25%, 45.07%, 18.88% and 55.02% for CT, AA, CTAA, CH, and KTN, respectively. Gel strength was highest in AA followed by the CTAA, CT and CH and KTN treatments. The molecular weight (MW) distribution pattern showed that dehairing of BH with enzymes degraded the collagen extensively, increased proportions of low MW peptides that translated into low gel strength.Conclusions Acetic acid, which is extensively using in food industry, can be used to dehair BH as pre-treatment to extracting high quality gelatin.

Osteoporosis and its precursor osteopenia are common metabolic bone diseases in postmenopausal women. A growing body of evidence suggests that the gut microbiota is involved in the regulation of bone metabolism; however, there are few studies examining how gut microbiomes in osteoporosis and osteopenia may differ from those in healthy individuals. The aim of this study was to characterize the diversity, composition, and functional gene potential of the gut microbiota of healthy, osteopenic, and osteoporotic women. Body composition, bone density, and fecal metagenomes were analyzed in 86 postmenopausal women. The women were classified as healthy, osteopenic, or osteoporotic based on T‐scores. The taxonomic and functional gene compositions of the microbiome were analyzed using shotgun metagenomic sequencing. Both osteoporotic and osteopenic taxonomic compositions were found to be significantly different from healthy participants. Linear discriminant‐analysis effect‐size analyses identified that healthy participants had more unclassified Clostridia and methanogenic archaea (Methanobacteriaceae) than in both osteoporotic and osteopenic participants. Bacteroides was found to be more abundant in osteoporosis and osteopenia groups. Some KEGG pathways, including carbohydrate metabolism, biosynthesis of secondary metabolites, and cyanoamino acid metabolism, were found to be more abundant in both osteoporosis and osteopenia. These results show that osteoporosis and osteopenia alter the gut microbiome of postmenopausal women and identify potential microbial taxonomic and functional pathways that may be involved in this disease. © 2020 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.

Segmented filamentous bacteria (SFB) are thought to play a role in small intestine immunological maturation. Studies in weanling mice have shown a positive correlation between ileal SFB abundance and plasma and faecal interleukin 17 (IL-17) and immunoglobulin A (IgA) concentrations. Although the first observation of SFB presence was reported in rats, most studies use mice. The size of the mouse ileum is a limitation whereas the rat could be a suitable alternative for sufficient samples. Changes in SFB abundance over time in rats were hypothesized to follow the pattern reported in mice and infants. We characterized the profile of SFB colonization in the ileum tissue and contents and its correlation with two immune markers of gastrointestinal tract (GIT) maturation. We also compared two published ileum collection techniques to determine which yields data on SFB abundance with least variability. Whole ileal tissue and ileal mucosal scrapings were collected from 20- to 32-day-old Sprague-Dawley rats. SFB abundance was quantified from proximal, middle and distal ileal tissues, contents and faeces by quantitative PCR using SFB-specific primers. Antibody-specific ELISAs were used to determine IL-17 and IgA concentrations. Significant differences in SFB abundance were observed from whole and scraped tissues peaking at day 22. Variability in whole ileum data was less, favouring it as a better collection technique. A similar pattern of SFB abundance was observed in ileum contents and faeces peaking at day 24, suggesting faeces can be a proxy for ileal SFB abundance. SFB abundance at day 26 was higher in females than males across all samples. There were significant differences in IgA concentration between days 20, 30 and 32 and none in IL-17 concentration, which was different from reports in mice and infants.

Faecal proteomics targeting biomarkers of immunity and inflammation have demonstrated clinical application for the identification of changes in gastrointestinal function. However, there are limited comprehensive analyses of the host faecal proteome and how it may be influenced by dietary factors. To examine this, the Homo sapiens post-diet proteome of older males was analysed at the completion of a 10-week dietary intervention, either meeting the minimum dietary protein recommendations (RDA; n = 9) or twice the recommended dietary allowance (2RDA, n = 10). The host faecal proteome differed markedly between individuals, with only a small subset of proteins present in ≥ 60% of subjects (14 and 44 proteins, RDA and 2RDA, respectively, with only 7 common to both groups). No differences were observed between the diet groups on the profiles of host faecal proteins. Faecal proteins were detected from a wide range of protein classes, with high inter-individual variation and absence of obvious impact in response to diets with markedly different protein intake. This suggests that well-matched whole food diets with two-fold variation in protein intake maintained for 10 weeks have minimal impact on human faecal host proteins.

Lactobacillus fermentum is found in food products and is generally considered safe. L. fermentum AGR1485 promotes barrier integrity in Caco-2 cells and has genetic similarities to other known probiotic L. fermentum strains. L. fermentum AGR1485 has potential as a probiotic and was sequenced to explore these probiotic properties. The genome is a 2.2-Mbp circular chromosome with no plasmids and a GC content of 51., Lactobacillus fermentum is found in food products and is generally considered safe. L. fermentum AGR1485 promotes barrier integrity in Caco-2 cells and has genetic similarities to other known probiotic L. fermentum strains. L. fermentum AGR1485 has potential as a probiotic and was sequenced to explore these probiotic properties. The genome is a 2.2-Mbp circular chromosome with no plasmids and a GC content of 51.15%.

Background Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing. Results An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version. Conclusions Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.

Understanding the metabolic dynamics of the human gastrointestinal tract (GIT) microbiota is of growing importance as research continues to link the microbiome to host health status. Microbial strains that metabolize hydrogen have been associated with a variety of both positive and negative host nutritional and health outcomes, but limited data exists for their competition in the GIT. To enable greater insight into the behaviour of these microbes, a mathematical model was developed for the metabolism and growth of the three major hydrogenotrophic groups: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens. In batch culture simulations with abundant sulphate and hydrogen, the SRB outcompeted the methanogen for hydrogen due to having a half-saturation constant 106 times lower than that of the methanogen. The acetogen, with a high model threshold for hydrogen uptake of around 70 mM, was the least competitive. Under high lactate and zero sulphate conditions, hydrogen exchange between the SRB and the methanogen was the dominant interaction. The methanogen grew at 70% the rate of the SRB, with negligible acetogen growth. In continuous culture simulations, both the SRB and the methanogen were washed out at dilution rates above 0.15 h−1 regardless of substrate availability, whereas the acetogen could survive under abundant hydrogen conditions. Specific combinations of conditions were required for survival of more than one hydrogenotroph in continuous culture, and survival of all three was not possible. The stringency of these requirements and the inability of the model to simulate survival of all three hydrogenotrophs in continuous culture demonstrates that factors outside of those modelled are vital to allow hydrogenotroph coexistence in the GIT.

Objective Reprocessing reusable medical devices is crucial in the healthcare industry. To ensure patient safety, strict standards are dictated to validate thermal disinfection in automated washer-disinfectors. The United States Food and Drug Administration (FDA) has specific recommendations on the vegetative bacterial challenge but comparatively vague guidance on the use of a thermophilic Mycobacterium strain for thermal disinfection studies. This study aims to compare thermal resistance of Mycobacterium hassiacum and Mycobacterium terrae and determine which strain is suitable for medical device thermal disinfection validation testing in automated washer-disinfectors. Results Thermal resistance was demonstrated in vitro by calculating D-values for each strain at different exposure temperatures, and correlated with actual in situ processing conditions. M. terrae was completely killed (> 7 log reduction) at temperatures above 68 °C, with D-values between 46.6 and 27.8 s at temperatures between 59.5 and 67.2 °C. M. hassiacum was completely killed (> 8 log reduction) at temperatures above 75 °C, with D-values between 82.1 and 21.7 s at temperatures ranging between 69.2 and 73.6 °C. In vitro results were correlated in a washer-disinfector performance validation setup.

Consumption of caprine milk oligosaccharides (CMO) by dams during gestation and lactation, compared to a control diet or a diet supplemented with galacto-oligosaccharides (GOS), was associated with decreased maternal liver weight, increased offspring body weight and length at weaning, and increased offspring visceral fat and serum leptin concentration 30 days after weaning. These changes suggest that dietary CMO alters lipid metabolism, both in dams and offspring. We hypothesized that perinatal CMO intake affected expression of maternal genes in the liver involved in energy metabolism, and programmed pups’ metabolic function leading to increased post-weaning visceral adiposity. To characterise the effects of perinatal consumption of CMOs on maternal and offspring liver gene expression, C57BL/6 mice were fed either a control, CMO, or GOS diet from mating to weaning. From weaning, half of the pups from each maternal group were fed the control diet for 30 days. Microarray analysis was conducted on liver samples from dams and offspring. Differences in the expression of genes involved in lipid metabolism were observed in dams and changes in expression of hepatic genes involved in energy balance and steroid metabolism were observed in pups at weaning. Increased visceral fat was observed in pups 30 days. Perinatal consumption of CMO diet affected infant lipid metabolism, which may be related to altered expression of genes in the liver involved in energy balance and lipid metabolism in dams.

Diet has a major influence on the composition and metabolic output of the gut microbiome. Higher-protein diets are often recommended for older consumers; however, the effect of high-protein diets on the gut microbiota and faecal volatile organic compounds (VOC) of elderly participants is unknown. The purpose of the study was to establish if the faecal microbiota composition and VOC in older men are different after a diet containing the recommended dietary intake (RDA) of protein compared with a diet containing twice the RDA (2RDA). Healthy males (74⋅2 (sd 3⋅6) years; n 28) were randomised to consume the RDA of protein (0⋅8 g protein/kg body weight per d) or 2RDA, for 10 weeks. Dietary protein was provided via whole foods rather than supplementation or fortification. The diets were matched for dietary fibre from fruit and vegetables. Faecal samples were collected pre- and post-intervention for microbiota profiling by 16S ribosomal RNA amplicon sequencing and VOC analysis by head space/solid-phase microextraction/GC-MS. After correcting for multiple comparisons, no significant differences in the abundance of faecal microbiota or VOC associated with protein fermentation were evident between the RDA and 2RDA diets. Therefore, in the present study, a twofold difference in dietary protein intake did not alter gut microbiota or VOC indicative of altered protein fermentation.

Histone proteins are crucial in the study of chromatin dynamics owing to their wide-ranging implications in the regulation of gene expression. Modifications of histones are integral to these regulatory processes in concert with associated proteins, such as transcription factors and coactivators. One of the biochemical techniques available to enhance analysis of histone proteins is chemical derivatization using propionic anhydride. In this protocol, we describe the use of propionylation to efficiently derivatize acid-extracted histones from rice. We also synthesize H3 and H4 tryptic peptides, thus mimicking the nature of derivatized extracted peptides to aid in identification and quantification using targeted-mass spectrometry. Here we make available the masses of the precursor ions and the retention times (RT) of each synthesized peptide. These provide useful information to facilitate histone data analysis. Lastly, we note that we will distribute these synthetic peptides in nanomolar (nM) concentrations to those who wish to utilize them for assays and further experimental studies.

The simultaneous effects of microwave processing variables affecting the microbial quality and preservation of milk bioactive proteins were evaluated. Response surface methodology was used to investigate the individual and combined effects of ramp time (2.9–5.5 min), holding time (6.6–23.4 s), and final temperature (60–80°C) on the inactivation of two surrogates (Staphylococcus aureus and Escherichia coli) added to the milk and on the preservation of the main antimicrobial proteins present in milk (lysozyme, lactoferrin, lactoperoxidase, xanthine oxidase, and immunoglobulin G). Experimental conditions resulting in 5 log reduction of E.coli and S. aureus (75°C, ramp time of 4.10 min, and holding time of 20 s) were replicated in quintuplicate for validation of the observed effects. At this experimental condition, more than 95% of the naturally present antimicrobial proteins were inactivated. The inactivation of antimicrobial proteins observed in this study was similar to the ones observed for ultra‐high temperature milk. PRACTICAL APPLICATIONS: The current study demonstrates that microwave heating conditions leading to microbial safety (5 log reduction of surrogates) result in significant inactivation of bovine milk antimicrobial proteins (>95%), being similar to the ones observed for ultra‐high temperature milk.

The hypothesis that genetic relationships exist between loin muscle collagen characteristics and sub-primal and meat quality traits was tested. Data from 500 pigs from crosses between Duroc sires and hybrid Large White ✕ Landrace sows with pedigree back to about eight generations were used. Significant fixed effects (slaughter group and company) and a random additive effect were fitted in bivariate animal models to estimate phenotypic and genetic correlations using ASReml 4.1. Moderate heritabilities were obtained for sub-primal traits ranging from 0.21 for bone weight to 0.44 for loin muscle weight with a low estimate of 0.10 being obtained for loin weight. Meat quality traits were low to moderately heritable with the highest estimate being found for intramuscular fat (0.42). The heritability estimates for percentages of heat soluble and insoluble collagen were 0.12 and 0.15, respectively, while 0.33 was found for total collagen. Moderate to relatively high heritabilities imply the possibility of improving these traits through selective breeding. In general, moderate to high phenotypic and genetic correlations were obtained for sub-primal traits, whilst meat quality traits had moderate phenotypic and moderate to high genetic correlations. Strong negative genetic correlations between moisture traits and fat traits and a further negative correlation between fat and muscling traits were estimated confirming that selecting for improved muscling over time can negatively affect fat traits and indirectly decrease meat eating quality. The strong genetic correlation between pH and L* (-0.95) suggested possible pleiotropic gene effects on these traits. Warner-Braztler shear force (WBSF) had moderate genetic correlations with insoluble collagen (0.42) and soluble collagen (-0.38) suggesting a potential relationship between some of the genes impacting these traits. Genetic correlations between WBSF and collagen characteristics indicate that despite the relative youthfulness of pigs at slaughter, genetic selection for collagen solubility may decrease pork toughness.

Linseed is an industrial crop cultivated for its seeds, fibres and oil purpose. Linseed crop can met their requirement i.e. moisture and nutritional demand from stored soil moisture and residual fertility status in "utera‟ or "paira‟ system of cropping. On the basis of this fact an experiment was conducted on “Seed yield of linseed varieties grown as paira crop as influenced by dates of sowing” in red and laterite zone of West Bengal during rabi season of 2012-13 and 2013-14 at Rice Research Station, Bankura, West Bengal, India. Poor in organic matter content, available phosphate and bases, hard structure of iron and aluminium patterned as honeycomb are present in the subsurface regions of the profiles and kaolinite is the predominant clay minerals of red and lateritic zone (western part) of West Bengal. This experiment was laid out in a split-plot design with three replications and compared two factors (dates of sowing and linseed varieties). Objective was identifying the optimum date of sowing and suitable linseed varieties grown as „paira‟ crop under changed climate in red and laterite zone of West Bengal. The experimental results revealed that the highest seed yield (534 kg ha-1 as pooled value) was recorded from the treatment D1 i.e. linseed sown on 15th November. The lowest seed yield (489.2 kg ha-1 as pooled value) was obtained with treatment D3 i.e. linseed sown on 29th November. Among linseed varieties, T-397 has yielded highest seed yield (573.4 kg ha-1 as pooled value). Lowest seed yield (409. 3 kg ha-1 as pooled data) was recorded from Neela variety. From the present study it may be concluded that linseed sown on 15th November is the best time and T-397 is the suitable linseed variety grown as "paira‟ crop under changed climate in red and laterite zone of West Bengal.

Carcass attributes of steers were examined for influences of selection for residual feed intake (RFI), and exposure to different levels of prenatal nutrition. Heifers characterized for RFI corrected for backfat were mated to bulls with genetic potential for either High-RFI or Low-RFI, such that the progeny were expected to be H/H or L/L RFI (sire/dam). Pregnant heifers were assigned to a low diet (Ldiet; 0.40 kg/d ADG), or moderate diet (Mdiet; 0.57 kg/d ADG), from 30 to 150 days of gestation, after which all heifers were managed similarly. Steer offspring (n = 23) were also managed similarly until slaughter. Dressing percentage of steers from H-RFI dams/sires exposed to Ldiet during gestation was lower than all other groups (P = 0.02). Marbling was greater for steers from H-RFI parents, as was fat content of longissimus thoracis et lumborum and triceps brachii (P ≤ 0.02). Results suggest that parental selection for RFI and prenatal maternal diet can influence carcass characteristics of progeny.

The objective of this study was to investigate the effects of initial heat extraction time and enzyme concentration during subsequent pepsin digestion on gelatin quality from bovine heart (BH) connective tissue (CT). BH gelatin was extracted from isolated BH CT at 80 °C for 4 or 6 h. Gelatin remaining in the CT residue was extracted with pepsin at either 100 or 200 mg pepsin/g CT to examine the yield and properties of enzyme-extracted gelatin. BH gelatins extracted at 80 °C showed very good gel strength (241–269 g) compared to that subsequently extracted with pepsin (54–96 g) and gelatin yield increased with the length of heat extraction (3%) although gel strength was reduced. Heat-extracted BH gelatin regardless of duration of heat extraction contained α1 and α2 chain as main components with some degradation peptides. The frequency sweep test of BH gelatins showed independency in a wide range of frequency (1–196 Hz) regardless of whether extracted by heat or pepsin. Heat-extracted BH gelatins exhibited the highest storage modulus values (1165–1245 pa). BH gelatins extracted with the lowest concentration of pepsin showed a higher mean storage modulus value than gelatin extracted with the highest pepsin concentration. The present study is the first to demonstrate that gelatin extracted from BH collagen using heat and pepsin has characteristics comparable to other sources of gelatin, making it suitable for many applications, and confirms that the use of pepsin increases BH gelatin yield with a concomitant reduction in gelatin quality.

Background There is strong evidence suggesting that prebiotics and probiotics regulate gut microbiota, reducing inflammation and thereby potentially improving bone health status. Similarly, mechanistic evidence suggests that either low-impact or high-impact weight-bearing exercises improve body composition and consequently increase bone mineral density in individuals with osteoporosis and osteoarthritis. Objective This study aims to investigate the effects of a synbiotic (probiotic+prebiotic) supplementation, an exercise intervention, or a combination of both on gut microbiota, inflammation, and bone biomarkers in postmenopausal women. Methods A total of 160 postmenopausal women from New Zealand will be recruited and randomized to one of four interventions or treatments for 12 weeks: control, synbiotic supplementation, exercise intervention, or synbiotic supplementation and exercise. The primary outcome measure is the bone and joint biomarkers at baseline and week 12, whereas the gut microbiota profile and inflammatory cytokine measurements will serve as the secondary outcome measures at baseline and week 12. Baseline data and exercise history will be used to assess, allocate, and stratify participants into treatment measures. Results Recruitment of participants will begin in September 2021, and the anticipated completion date is June 2022. Conclusions To the best of our knowledge, this will be the first randomized controlled trial to analyze the effects of both a synbiotic supplement and an exercise intervention in postmenopausal women. On the basis of the results obtained, a combination of synbiotic supplements and exercise might serve as a noninvasive approach to manage and/or improve body composition and bone health in postmenopausal women. Trial Registration Australian New Zealand Clinical Trials Registry ACTRN12620000998943p; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=380336&isClinicalTrial=False

Low molecular weight (LMW) collagen peptides show skin and bone health benefits for human. However, the production of LMW collagen peptides from land vertebrate sources remains challenging due to the presence of advanced glycation end products (AGEs) cross-links. In this study, the effect of α-amylase pre-treatment on proteolytic production of LMW collagen peptides by papain was investigated; spent hen, bovine, porcine, and tilapia skin collagens (HSC, BSC, PSC, and TSC, respectively) were chosen. Results showed that pre-treatment with α-amylase considerably improved the production of LMW peptides (2 kDa) from HSC (33.79-67.66%), PSC (86.03-90.85%), BSC (6.60-28.78%), and TSC (89.92-90.27%). The HSC presented the highest carbohydrate content and was increased the most in LMW peptides after amylase pretreatment. These results suggested that α-amylase could cleave glycosidic bonds of AGEs between collagen and thus enhance the production of LMW collagen peptides.

The benefits of various functional foods are often negated by stomach digestion and poor targeting to the lower gastrointestinal tract. Layer-by-Layer assembled protein-tannic acid (TA) films are suggested as a prospective material for microencapsulation of food-derived bioactive compounds. Bovine serum albumin (BSA)-TA and pepsin-TA films demonstrate linear growth of 2.8 ± 0.1 and 4.2 ± 0.1 nm per bi-layer, correspondingly, as shown by ellipsometry. Both multilayer films are stable in simulated gastric fluid but degrade in simulated intestinal fluid. Their corresponding degradation constants are 0.026 ± 0.006 and 0.347 ± 0.005 nm−1 min−1. Milk proteins possessing enhanced adhesion to human intestinal surface, Immunoglobulin G (IgG) and β-Lactoglobulin (BLG), are explored to tailor targeting function to BSA-TA multilayer film. BLG does not adsorb onto the multilayer while IgG is successfully incorporated. Microcapsules prepared from the multilayer demonstrate 2.7 and 6.3 times higher adhesion to Caco-2 cells when IgG is introduced as an intermediate and the terminal layer, correspondingly. This developed material has a great potential for oral delivery of numerous active food-derived ingredients.

The low-molecular-weight (LMW) peptides derived from collagen have shown a potential for various nutritional and pharmaceutical applications. However, production of LMW peptides from vertebrate collagen remains a challenge. Herein, we report a new method to produce LMW collagen peptides using pepsin pretreatment that removed cross-linked telopeptides in collagen molecules. After the pretreatment, the proportion of LMW collagen peptides (1.4 kDa) that were obtained from pepsin-soluble collagen increased to 32.59% compared to heat-soluble collagen peptides (16.10%). Fourier transform infrared spectroscopy results indicated that telopeptide cleavage retained the triple-helical conformation of collagen. Liquid chromatography-tandem mass spectrometry analysis suggested that Gly-X-Y (X is often proline, while Y is either hydroxyproline or hydroxylysine) repeats were not the main factors that hindered the enzymatic hydrolysis of collagen molecules. However, cross-link quantification demonstrated that trivalent cross-links that included pyridinolines and pyrroles were the primary obstacles to producing small peptides from collagen of spent hens. This study demonstrated for the first time that removing cross-linked telopeptides could enhance the production of LMW peptides from spent hen collagen, which is also of interest to manufacturers who produce LMW collagen peptides from other vertebrate animals, such as bovids and porcids.

Se is an essential micronutrient for human health, and fluctuations in Se levels and the potential cellular dysfunction associated with it may increase the risk for disease. Although Se has been shown to influence several biological pathways important in health, little is known about the effect of Se on the expression of microRNA (miRNA) molecules regulating these pathways. To explore the potential role of Se-sensitive miRNA in regulating pathways linked with colon cancer, we profiled the expression of 800 miRNA in the CaCo-2 human adenocarcinoma cell line in response to a low-Se (72 h at m) environment using nCounter direct quantification. These data were then examined using a range ofin silicodatabases to identify experimentally validated miRNA–mRNA interactions and the biological pathways involved. We identified ten Se-sensitive miRNA (hsa-miR-93-5p, hsa-miR-106a-5p, hsa-miR-205-5p, hsa-miR-200c-3p, hsa-miR-99b-5p, hsa-miR-302d-3p, hsa-miR-373-3p, hsa-miR-483-3p, hsa-miR-512-5p and hsa-miR-4454), which regulate 3588 mRNA in key pathways such as the cell cycle, the cellular response to stress, and the canonical Wnt/β-catenin, p53 and ERK/MAPK signalling pathways. Our data show that the effects of low Se on biological pathways may, in part, be due to these ten Se-sensitive miRNA. Dysregulation of the cell cycle and of the stress response pathways due to low Se may influence key genes involved in carcinogenesis.

The middle Andaman Island populations of Momordica cochinchinensis are quite distinct from true M. cochinchinensis in some floral characters. Such deviating specimens are described here as a new subspecies. A full technical description, a morphological comparison between the two subspecies, ecology, phenology, confirmation of genomic distinctiveness through DNA barcoding of matK and rbcL chloroplast loci and viability under cultivation are discussed. An epitype is also designated for Momordica cochinchinensis subsp. cochinchinensis.

This study reveals that the stress-prone Wistar-Kyoto rat strain has a baseline physiology of gastroparesis and rapid small intestine transit, together with metabolic changes consistent with lipid metabolism-associated dysbiosis, compared with nonstress-prone rats. This suggests that the Wistar-Kyoto rat strain may be an appropriate animal model for gastroparesis., Altered gastric accommodation and intestinal morphology suggest impaired gastrointestinal (GI) transit may occur in the Wistar-Kyoto (WKY) rat strain, as common in stress-associated functional GI disorders. Because changes in GI transit can alter microbiota composition, we investigated whether these are altered in WKY rats compared with the resilient Sprague-Dawley (SD) rats under basal conditions and characterized plasma lipid and metabolite differences. Bead transit was tracked by X-ray imaging to monitor gastric emptying (4 h), small intestine (SI) transit (9 h), and large intestine transit (12 h). Plasma extracts were analyzed by lipid and hydrophilic interaction liquid chromatography (HILIC) and liquid chromatography-mass spectrometry (LC-MS). Cecal microbial composition was determined by Illumina MiSeq 16S rRNA amplicon sequencing and analysis using the QIIME pipeline. Stomach retention of beads was 77% for WKY compared with 35% for SD rats. GI transit was decreased by 34% (9 h) and 21% (12 h) in WKY compared with SD rats. Excluding stomach retention, transiting beads moved 29% further along the SI over 4–9 h for WKY compared with SD rats. Cecal Ruminococcus, Roseburia, and unclassified Lachnospiraceae genera were less abundant in WKY rats, whereas the minor taxa Dorea, Turicibacter, and Lactobacillus were higher. Diglycerides, triglycerides, phosphatidyl-ethanolamines, and phosphatidylserine were lower in WKY rats, whereas cholesterol esters and taurocholic acids were higher. The unexpected WKY rat phenotype of delayed gastric emptying, yet rapid SI transit, was associated with altered lipid and metabolite profiles. The delayed gastric emptying of the WKY phenotype suggests this rat strain may be useful as a model for gastroparesis. NEW & NOTEWORTHY This study reveals that the stress-prone Wistar-Kyoto rat strain has a baseline physiology of gastroparesis and rapid small intestine transit, together with metabolic changes consistent with lipid metabolism-associated dysbiosis, compared with nonstress-prone rats. This suggests that the Wistar-Kyoto rat strain may be an appropriate animal model for gastroparesis. View this article's corresponding video summary at https://youtu.be/BeI39Jh2BLk.

Bovine lactoferrin is an important milk protein with many health-promoting properties, including improving intestinal barrier integrity. Dysfunction of this barrier, commonly referred to as "leaky gut," has been linked to inflammatory and autoimmune diseases. With some processing techniques, lactoferrin isolated from milk collected at the start of the milking season (early lactation) may have lower purity than that isolated from milk collected during the rest of the milking season (mid-lactation) and could result in differences in bioactivity based on the stage of lactation. We compared reversed-phase HPLC chromatographs of early-lactation and mid-lactation preparations and found that both had large chromatograph peaks at the time predicted for lactoferrin. The notable difference between the 2 chromatographs was a much larger peak in the early-lactation lactoferrin sample that was determined to be angiogenin. Angiogenin was first identified due to its ability to induce new blood vessel formation, but is now known to be involved in numerous physiological processes. Then, we compared the effects of early-lactation and mid-lactation lactoferrin preparations in 2 bioassays: trans-epithelial electrical resistance (TEER), a measure of intestinal barrier integrity, and peripheral blood mononuclear cell cytokine secretion, a measure of immune-stimulatory properties. We found that early-lactation lactoferrin increased TEER across Caco-2 cell layers compared with control from 10 to 48 h, mid-lactation lactoferrin did not alter TEER. We also found that early-lactation lactoferrin reduced the amount of IL-8 produced by peripheral blood mononuclear cells (compared with those treated with control medium) to a greater extent than mid-lactation lactoferrin. A pro-inflammatory chemokine, IL-8 is also known to decrease barrier function. These results suggest that the decrease in IL-8 production in the presence of early-lactation lactoferrin may be the mechanism by which it increases TEER. The anti-inflammatory effect of early-lactation lactoferrin may be related to the presence of angiogenin, which is known to suppress inflammatory responses. This work indicates that products rich in angiogenin may have intestinal health benefits, and further work to investigate this is warranted.

The amount and ratio of organic acids from carbohydrate fermentation by the gut microbiota is dependent upon both the ability of members of the microbiota to exploit undigested dietary carbohydrate and the type of organic acids they have the capability to generate. Additionally, some bacteria feed upon carbohydrate degradation products, as well as organic acids produced by other bacteria, further affecting the overall organic acid profile. Experimentally unentangling these complex trophic food webs is challenging. Here we demonstrate a mathematical model that calculates the organic acid profile resulting from an in vitro human faecal microbial fermentation of kiwifruit cell wall polysaccharides, parameterised with organic acid and microbial abundance data. The model was based on our hypothesis that in conditions of carbohydrate excess, changes in the abundance of members of the microbiota will be reflected in an equivalent change in those organic acids they have the capability to produce. We used microbial abundance data to calculate changes in organic acids over time, and the resulting data was shown to recapitulate the measured organic acid profiles. We also demonstrate here the successful mathematical simulation of the metabolic cross-feeding which occurs upon simulated digestion and fermentation of a fresh whole fruit carbohydrate. We assign the relative propensity of various members of a complex microbial community to generate selected acids within the organic acid profiles. We anticipate this case study to be a starting point for more sophisticated research and clinical tools to investigate and predict the interactions with food, the microbiota and the host.

Stress negatively impacts gut and brain health. Individual differences in response to stress have been linked to genetic and environmental factors and more recently, a role for the gut microbiota in the regulation of stress-related changes has been demonstrated. However, the mechanisms by which these factors influence each other are poorly understood, and there are currently no established robust biomarkers of stress susceptibility. To determine the metabolic and microbial signatures underpinning physiological stress responses, we compared stress-sensitive Wistar Kyoto (WKY) rats to the normo-anxious Sprague Dawley (SD) strain. Here we report that acute stress-induced strain-specific changes in brain lipid metabolites were a prominent feature in WKY rats. The relative abundance of Lactococcus correlated with the relative proportions of many brain lipids. In contrast, plasma lipids were significantly elevated in response to stress in SD rats, but not in WKY rats. Supporting these findings, we found that the greatest difference between the SD and WKY microbiomes were the predicted relative abundance of microbial genes involved in lipid and energy metabolism. Our results provide potential insights for developing novel biomarkers of stress vulnerability, some of which appear genotype specific.

Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.

Glycans are present exogenously in the diet, expressed and secreted endogenously by host cells, and produced by microbes. All of these processes result in them being available to the gut microbiome, firmly placing glycans at the interface of diet–microbe–host interactions. The most dramatic shift in dietary sources of glycans occurs during the transition from the milk-based neonatal diet to the diverse omnivorous adult diet, and this has profound effects on the composition of the gut microbiome, gene expression by microbes and host cells, mucin composition, and immune development from innate towards adaptive responses. Understanding the glycan-mediated interactions occurring during this transitional window may inform dietary recommendations to support gut and immune development during a vulnerable age. This review aims to summarise the current state of knowledge on dietary glycan mediated changes that may occur in the infant gut microbiome and immune system during weaning.

Drug-resistance of tumor-initiating cells, impaired NK cell immune-response, PP2A loss-of-function and aberrant miRNA expression are cancer features resulting from microenvironmental- and tumor-specific signals. Here we report that genomic-imprintedMIR300is a cell context-independent dual function tumor suppressor which is upregulated in quiescent leukemic stem (LSC) and NK cells by microenvironmental signals to induce quiescence and impair immune-response, respectively, but inhibited in CML and AML proliferating blasts to prevent PP2A-induced apoptosis.MIR300anti-proliferative and PP2A-activating functions are differentially activated through dose-dependent CCND2/CDK6 and SET inhibition, respectively. LSCs escape PP2A-mediated apoptosis through TUG1 lncRNA that uncouples and limitsMIR300functions to cytostasis by regulating unbound-MIR300levels. HaltingMIR300homeostasis restores NK cell activity and suppresses leukemic but not normal hematopoiesis by eradicating nearly all LSCs. Thus,MIR300tumor suppressor activity is essential and therapeutically important for LSC-driven leukemias.

OBJECTIVES: Metabolomic profiling of plasma provides a biochemical fingerprint of the circulating metabolites from the host and microbiome, and may assist with understanding mechanisms underlying functional gastrointestinal (GI) disorders such as Irritable Bowel Syndrome (IBS). In a case-control study, we aimed to identify microbial and host factors in plasma to provide mechanistic insights into functional GI disorders and increase the predictability of phenotypes for use in nutrition intervention studies. METHODS: Plasma samples from 246 individuals with functional GI disorders (cases) or asymptomatic (controls), consisting of 93 healthy controls, 54 with functional constipation (C) or IBS-C, 60 with functional diarrhoea (D) or IBS-D, and 39 diagnosed as IBS-mixed or awaiting diagnosis. Plasma was subjected to biphasic extraction and global metabolite profiling was performed using three separate untargeted liquid chromatography high resolution mass spectrometry analysis (LC-MS) methods (polar, semi-polar and non-polar chromatography). RESULTS: Plasma metabolomic profiles differed considerably between the IBS phenotypes and those of the control subjects. Multivariate partial least squares discriminant analysis of 428 annotated lipid species highlighted significant differences (P

OBJECTIVES: Nutrition modulates the interactions between the host and the gut microbiota. Changes in metabolites resulting from this interaction in a healthy compared to a perturbed gut is a critical approach to identify putative biomarkers that can be used to assess how diet effects gut function. Bile acids (BAs) are metabolites produced from cholesterol and the microbial-conversion of BAs play an important role in digestion and metabolism. Modification of BA metabolism has been reported in participants with Irritable Bowel Syndrome (IBS), which is characterised by abdominal bloating, pain, dysfunction, and a perturbed gut microbiota. One aim of the clinical nutrition study was to characterise BA profiles of healthy control and IBS participants. This work is part of a wider study investigating gut health and how food can be used to alleviate symptoms. METHODS: Healthy control and IBS participants were recruited and IBS subtypes determined (n = 337) (Rome Criteria IV). Biological samples and dietary questionnaire information were collected. 97 plasma samples (n = 42 healthy control, n = 25 IBS-diarrhoea, n = 17 IBS-constipation, n = 13 IBS-mixed) were quantitatively analysed for 13 BAs using a SCIEX 6500 + QTrap liquid chromatography-mass spectrometer in multiple reaction monitoring mode. Partial least squares discriminant analysis (SIMCA 14.1) and analysis of variance (Metaboanalyst 4.0) were used to perform multivariate and univariate analyses respectively. Ethical approval was obtained from the University of Otago Human Ethics Committee (Health) (Reference H16/094). RESULTS: Univariate analysis of the 13 BAs showed no significant difference within or between IBS subtypes or healthy controls (P > 0.05). However, multivariate analysis of 13 BAs showed separation of the data between IBS subtypes and healthy controls indicating that while individual BA concentrations did not vary significantly, differences in profiles existed in IBS participants. CONCLUSIONS: Data from a subset of an IBS cohort shows BA metabolism is likely perturbed in IBS. Further analysis of faecal samples will provide additional information that could confirm the relationships to IBS subtypes, and provide putative biomarkers for food interventions targeting improvement of gut comfort and function. FUNDING SOURCES: High-Value Nutrition National Science Challenge, New Zealand.

Bacterial feeding has evolved towards specific evolutionary niches and the sources of energy differ between species and strains. Although bacteria fundamentally compete for nutrients, the excreted products from one strain may be the preferred energy source or a source of essential nutrients for another strain. The large variability in feeding preferences between bacterial strains often provides for complex cross-feeding relationships between bacteria, particularly in complex environments such as the human lower gut, which impacts on the host’s digestion and nutrition. Although a large amount of information is available on cross-feeding between bacterial strains, it is important to consider the evolution of cross-feeding. Adaptation to environmental stimuli is a continuous process, thus understanding the evolution of microbial cross-feeding interactions allows us to determine the resilience of microbial populations to changes to this environment, such as changes in nutrient supply, and how new interactions might emerge in the future. In this review, we provide a framework of terminology dividing bacterial cross-feeding into four forms that can be used for the classification and analysis of cross-feeding dynamics. Under the proposed framework, we discuss the evolutionary origins for the four forms of cross-feeding and factors such as spatial structure that influence their emergence and subsequent persistence. This review draws from both the theoretical and experimental evolutionary literature to provide a cross-disciplinary perspective on the evolution of different types of cross-feeding.