The microbiome of two strategies for ammonia removal with the sequencing batch moving bed biofilm reactor treating cheese production wastewater.

IMPORTANCE: Cheese production facilities must abide by sewage discharge bylaws that prevent overloading municipal water resource recovery facilities, eutrophication, and toxicity to aquatic life. Compact treatment systems can permit on-site treatment of cheese production wastewater; however, competition between heterotrophs and nitrifiers impedes the implementation of the sequencing batch moving bed biofilm reactor (SB-MBBR) for nitrification from high-carbon wastewaters. This study demonstrates that a single SB-MBBR is not feasible for nitrification when operated with anerobic and aerobic cycling for carbon and phosphorous removal from cheese production wastewater, as nitrification does not occur in a single reactor. Thus, two reactors in series are recommended to achieve nitrification from cheese production wastewater in SB-MBBRs. These findings can be applied to pilot and full-scale SB-MBBR operations. By demonstrating the potential to implement partial nitrification in the SB-MBBR system, this study presents the possibility of implementing partial nitrification in the SB-MBBR, resulting in the potential for more sustainable treatment of nitrogen from cheese production wastewater.

Effects of pair-housing pubertal and adult male and female mice on LPS-induced age-dependent immune responses: A potential role for the gut microbiota.

Puberty is a critical period of development that is marked by the maturation of the stress and immune systems. There are marked age and sex differences in peripheral and central inflammatory responses to an immune challenge between pubertal and adult mice. Given the strong link between the gut microbiome and immune system, it is possible that the age and sex differences in immune responses are mediated by age and sex differences in gut microbial composition. The current study investigated whether cohousing adult and pubertal CD1 mice through three weeks of pair-housing, with the potential for microbiome exchange via coprophagy and other close contact, could mitigate age-dependent immune responses. Cytokine concentrations in the blood and cytokine mRNA expression in the brain were assessed following exposure to the immune challenge lipopolysaccharide (LPS). The results show that all mice displayed increased cytokine concentrations in serum and central cytokine mRNA expression in the hippocampus, hypothalamus and prefrontal cortex (PFC) at eight hours following LPS treatment. Pubertal male and female mice, that were pair-housed with a pubertal counterpart, displayed lower cytokine concentrations in serum and lower cytokine mRNA expression in the brain compared to adult mice that were pair-housed with an adult counterpart. However, when adult and pubertal mice were pair-housed, the age differences in both peripheral cytokine concentrations and central cytokine mRNA expression were mitigated. We also found that pair-housing adult and pubertal mice eliminated the age difference in gut bacterial diversity. These results suggest that microbial composition could be involved in modulating these age-associated immune responses and thus may represent a potential therapeutic target.

Pubertal consumption of R. badensis subspecies acadiensis modulates LPS-induced immune responses and gut microbiome dysbiosis in a sex-specific manner.

Puberty is a critical period of development characterized by significant brain remodeling and increased vulnerability to immune challenges. Exposure to an immune challenge such as LPS during puberty can result in inflammation and gut dysbiosis which may lead to altered brain functioning and psychiatric illnesses later in life. However, treatment with probiotics during puberty has been found to mitigate LPS-induced peripheral and central inflammation, prevent LPS-induced changes to the gut microbiota and protect against enduring behavioural disorders in a sex-specific manner. Recent findings from our laboratory revealed that pubertal R. badensis subspecies acadiensis (R. badensis subsp. acadiensis) treatment prevents LPS-induced depression-like behavior and alterations in 5HT1A receptor expression in a sex-specific manner. However, the underlying mechanism remains unclear. Thus, the aim of this study was to gain mechanistic insights and to investigate the ability of R. badensis subsp. acadiensis consumption during puberty to mitigate the effects of LPS treatment on the immune system and the gut microbiome. Our results revealed that pubertal treatment with R. badensis subsp. acadiensis reduced sickness behaviors in females more than males in a time-specific manner. It also mitigated LPS-induced increases in pro-inflammatory cytokines in the blood and in TNFα mRNA expression in the prefrontal cortex and the hippocampus of female mice. There were sex-dependent differences in microbiome composition that persisted after LPS injection or R. badensis subsp. acadiensis consumption. R. badensis subsp. acadiensis had greater impact on the microbiota of male mice but female microbiota's were more responsive to LPS treatment. This suggested that female mice microbiota's may be more prone to modulation by this probiotic. These findings emphasize the sex-specific effects of probiotic use during puberty on the structure of the gut microbiome and the immune system and highlight the critical role of gut colonization with probiotics during adolescence on immunomodulation and prevention of the enduring effects of infections.

Maternal Diet and Infant Feeding Practices Are Associated with Variation in the Human Milk Microbiota at 3 Months Postpartum in a Cohort of Women with High Rates of Gestational Glucose Intolerance.

BACKGROUND: Human milk contains a diverse community of bacteria believed to play a role in breast health and inoculation of the infant's gastrointestinal tract. The role of maternal nutrition and infant feeding practices on the human milk microbiota remains poorly understood. OBJECTIVE: Our aim was to explore the associations between maternal diet (delivery to 3 mo postpartum), infant feeding practices, and the microbial composition and predicted function in milk from women with varied metabolic status. METHODS: This was an exploratory analysis of a previously completed prospective cohort study of women with varying degrees of gestational glucose intolerance (NCT01405547). Milk samples (n = 93 mothers) were collected at 3 mo postpartum. Maternal dietary information (validated food-frequency questionnaire) and infant feeding practices (human milk exclusivity, frequency of direct breastfeeding per day) were collected. V4-16S ribosomal RNA gene sequencing (Illumina MiSeq) was conducted to determine microbiota composition. RESULTS: Intake of polyunsaturated fat [ß estimate (SE): 0.036 (0.018), P = 0.047] and fiber from grains [0.027 (0.013), P = 0.048] were positively associated with ɑ-diversity (Shannon index) of human milk. Overall microbial composition of human milk clustered based on human milk exclusivity (weighted UniFrac R2 = 0.034, P = 0.015; Bray-Curtis R2 = 0.041, P = 0.007), frequency of direct breastfeeding per day (Bray-Curtis R2 = 0.057, P = 0.026), and maternal fiber intake from grains (Bray-Curtis R2 = 0.055, P = 0.040). Total fiber, fiber from grains, dietary fat, and infant feeding practices were also associated with a number of differentially abundant taxa. The overall composition of predicted microbial functions was associated with total fiber consumption (Bray-Curtis R2 = 0.067, P = 0.036) and human milk exclusivity (Bray-Curtis R2 = 0.041, P = 0.013). CONCLUSIONS: Maternal consumption of fiber and fat, as well as mother's infant feeding practices, are important determinants of the human milk microbiota. Understanding whether these microbial changes impact an infant's overall health and development requires future study.

Oligosaccharides and Microbiota in Human Milk Are Interrelated at 3 Months Postpartum in a Cohort of Women with a High Prevalence of Gestational Impaired Glucose Tolerance.

BACKGROUND: Human milk is a rich source of human milk oligosaccharides (HMOs) and bacteria. It is unclear how these components interact within the breast microenvironment. OBJECTIVES: The objectives were first, to investigate the association between maternal characteristics and HMOs, and second, to assess the association between HMOs and microbial community composition and predicted function in milk from women with high rates of gestational glucose intolerance. METHODS: This was an exploratory analysis of a previously completed prospective cohort study (NCT01405547) where milk samples (n = 107) were collected at 3 mo postpartum. Milk microbiota composition was analyzed by V4-16S ribosomal RNA gene sequencing and HMOs by rapid high-throughput HPLC. Data were stratified and analyzed by maternal secretor status phenotype and associations between HMOs and microbiota were determined using linear regression models (ɑ-diversity), Adonis (B-diversity), Poisson regression models (differential abundance), and general linear models (predicted microbial function). RESULTS: Prepregnancy BMI, race, and frequency of direct breastfeeding, but not gestational glucose intolerance, were found to be significantly associated with a number of HMOs among secretors and non-secretors. Fucosyllacto-N-hexaose was negatively associated with microbial richness (Chao1) among secretors [B-estimate (SE): -9.3 × 102 (3.4 × 102); P = 0.0082] and difucosyllacto-N-hexaose was negatively associated with microbiota diversity (Shannon index) [-1.7 (0.78); P = 0.029] among secretors. Lacto-N-neotetraose (LNnT) was associated with both microbial B-diversity (weighted UniFrac R2 = 0.040, P = 0.036) and KEGG ortholog B-diversity (Bray-Curtis R2 = 0.039, P = 0.043) in secretors. Additionally, difucosyllactose in secretors and disialyllacto-N-hexaose and LNnT in non-secretors were associated with enrichment of predicted microbial genes encoding for metabolism- and infection-related pathways (P-false discovery rate < 0.1). CONCLUSIONS: HMOs are associated with the microbial composition and predicted microbial functions in human milk at 3 mo postpartum. Further research is needed to investigate the role these relations play in maternal and infant health.

Examining the relationship between maternal body size, gestational glucose tolerance status, mode of delivery and ethnicity on human milk microbiota at three months post-partum.

BACKGROUND: Few studies have examined how maternal body mass index (BMI), mode of delivery and ethnicity affect the microbial composition of human milk and none have examined associations with maternal metabolic status. Given the high prevalence of maternal adiposity and impaired glucose metabolism, we systematically investigated the associations between these maternal factors in women ≥20 years and milk microbial composition and predicted functionality by V4-16S ribosomal RNA gene sequencing (NCT01405547;  https://clinicaltrials.gov/ct2/show/NCT01405547 ). Demographic data, weight, height, and a 3-h oral glucose tolerance test were gathered at 30 (95% CI: 25-33) weeks gestation, and milk samples were collected at 3 months post-partum (n = 113). RESULTS: Multivariable linear regression analyses demonstrated no significant associations between maternal characteristics (maternal BMI [pre-pregnancy, 3 months post-partum], glucose tolerance, mode of delivery and ethnicity) and milk microbiota alpha-diversity; however, pre-pregnancy BMI was associated with human milk microbiota beta-diversity (Bray-Curtis R2 = 0.037). Women with a pre-pregnancy BMI > 30 kg/m2 (obese) had a greater incidence of Bacteroidetes (incidence rate ratio [IRR]: 3.70 [95% CI: 1.61-8.48]) and a reduced incidence of Proteobacteria (0.62 [0.43-0.90]) in their milk, compared to women with an overweight BMI (25.0-29.9 kg/m2) as assessed by multivariable Poisson regression. An increased incidence of Gemella was observed among mothers with gestational diabetes who had an overweight BMI versus healthy range BMI (5.96 [1.85-19.21]). An increased incidence of Gemella was also observed among mothers with impaired glucose tolerance with an obese BMI versus mothers with a healthy range BMI (4.04 [1.63-10.01]). An increased incidence of Brevundimonas (16.70 [5.99-46.57]) was found in the milk of women who underwent an unscheduled C-section versus vaginal delivery. Lastly, functional gene inference demonstrated that pre-pregnancy obesity was associated with an increased abundance of genes encoding for the biosynthesis of secondary metabolites pathway in milk (coefficient = 0.0024, PFDR < 0.1). CONCLUSIONS: Human milk has a diverse microbiota of which its diversity and differential abundance appear associated with maternal BMI, glucose tolerance status, mode of delivery, and ethnicity. Further research is warranted to determine whether this variability in the milk microbiota impacts colonization of the infant gut.

Bovine Lactoferrin Supplementation Does Not Disrupt Microbiota Development in Preterm Infants Receiving Probiotics.

OBJECTIVE: The aim of the study was to assess whether bovine lactoferrin (bLf) supplementation disrupts intestinal microbiota development in preterm infants less than 31 weeks gestational age receiving prophylactic probiotic administration. METHODS: Subjects were recruited from the LACUNA trial (ISRCTN66482337), designed to assess bLf safety. These subjects were randomized to daily receive either probiotic supplements or probiotics supplemented with 100 mg bLf mixed with their feeds (human milk or formula). Stools were collected weekly from enrolled infants for 1 month and the microbiota characterized using V6-16S rRNA gene amplicon profiling. RESULTS: Infants' microbiomes did not increase in alpha diversity over time in both feeding interventions. Infants receiving bLf supplementation had overall higher species richness as compared with those not receiving these supplements and lactoferrin supplementation had differing effects on infant microbiota species richness depending on the infant's gestational age. Principal co-ordinate analysis revealed that the infant microbiotas did not separate by intervention group, gestational age bracket at birth or sampling time and the main factor dictating sample clustering was infant identity. There were very few detectable differences in taxa relative abundance or functional gene content between the microbiotas in the 2 study groups. CONCLUSIONS: Bovine lactoferrin supplementation has minimal impact on microbiota composition/function in preterm infants receiving probiotics, and therefore, is unlikely to disrupt microbiota development.

The mucosal-luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography.

BACKGROUND: Alterations in gastrointestinal microbial communities have been linked to human disease. Most studies use fecal samples as a proxy for the intestinal microbiota; however, the fecal microbiome is not fully representative of the mucosa-associated microbiota at the site of disease. While mucosal biopsies can be used instead, they often contain a high proportion of host DNA that can confound 16S ribosomal RNA (rRNA) gene sequencing studies. METHODS: To overcome these limitations, we sampled the mucosal-luminal interface (MLI) to study the mucosa-associated microbiota. We also employed a simple bioinformatics workflow to remove contaminants from 16S rRNA gene profiling results. RESULTS: Our results indicate that the microbial differences between individuals are greater than those between different microenvironments within the same individual. Moreover, biopsy samples frequently contained contaminants that could significantly impact biopsy profiling results. CONCLUSIONS: Our findings highlight the utility of collecting MLI aspirates to complement biopsies and stools for characterizing human microbial communities.

The impact of probiotics and lactoferrin supplementation on piglet gastrointestinal microbial communities.

Probiotics and lactoferrin are currently being used in neonatal intensive care units in the hopes of reducing rates of sepsis and necrotizing enterocolitis (NEC). While studies have shown that these measures can be clinically beneficial to premature babies, and there are ongoing trials to measure their impact on NEC and sepsis rates, little is known about how they may impact microbiota development. We thus employed a newborn piglet model to assess the impact of feeding probiotics or a combination of probiotics and lactoferrin on development of the gastrointestinal microbiota. Healthy full-term piglets were fed either probiotics alone or probiotics and a bovine lactoferrin supplement over the first weeks of life, and their microbiota profiles were compared with unsupplemented controls. We found that both probiotic and probiotic plus lactoferrin treatments impacted the microbial composition within the gastrointestinal tract, with differing impacts on various regions within the gut. In addition, the impact of probiotics was often reversed by the presence of lactoferrin and both feeding interventions altered the microbiota's genetic propensity to use ferric versus ferrous ions. These results suggest that iron availability may be a key factor to consider when designing feeding interventions that target the microbiome.

Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach.

In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.

Independent of Birth Mode or Gestational Age, Very-Low-Birth-Weight Infants Fed Their Mothers' Milk Rapidly Develop Personalized Microbiotas Low in Bifidobacterium.

Background: Very-low-birth-weight (VLBW; born weighing <1500 g) infant feeding with mother's own milk (mother's milk) is associated with numerous beneficial health outcomes. Several interventions, including the prophylactic use of probiotics, are being adopted to promote a gastrointestinal microbiota favorable to the gut health of VLBW infants. An improved understanding of the microbiota that results from mother's milk feeding would therefore facilitate progress in this field. Objective: A preplanned primary objective of this research was to characterize the development of the gut microbiota in exclusively mother's milk-fed VLBW infants and describe the reference taxonomic profile that results from mother's milk feeding. Methods: In this prospective longitudinal cohort study, we collected weekly stool samples from exclusively mother's milk-fed VLBW infants admitted to Mount Sinai Hospital and profiled their gastrointestinal microbiota development from birth (primary outcome of stool collection). In total, we profiled 231 stools from 54 exclusively mother's milk-fed VLBW infants with the use of V6-16S ribosomal RNA gene sequencing. Results: Bacterial evenness, but not bacterial richness, increased over time in VLBW infants (P < 0.001). Bifidobacterium relative abundances were consistently low in all microbiotas at all time points (<0.5% in 97% of samples). VLBW infant microbiotas did not cluster by birth mode, gestational age, or weeks after birth and instead clustered as a function of patient identity (R2 = 0.51, P < 0.001). Conclusions: Exclusively mother's milk-fed VLBW infants rapidly develop personalized gut microbiotas that show increasing evenness and are seemingly unaffected by birth mode or gestational age at birth. The benefits from mother's milk feeding are likely modulated through microbes or pathways that are not dependent on Bifidobacterium because these microbes are present at low levels in VLBW infants. These results help define a reference VLBW infant microbiota profile derived from mother's milk, the optimal source of nutrition for these infants. This trial was registered at ISRCTN (http://www.isrctn.com/) as ISRCTN35317141.

Variation on a theme: investigating the structural repertoires used by ferric uptake regulators to control gene expression.

In every living organism, the control of metal homoeostasis is a tightly regulated process coordinated by several intertwined biological pathways. In many bacteria, the ferric uptake regulator (Fur) family of transcriptional factors (TFs) are key factors in controlling the expression of genes involved in metal homeostasis and can also regulate the expression of genes involved in responses to oxidative stresses. Since the crystallization of Escherichia coli Fur DNA binding domain, the crystal structure of several metalloregulators have been reported. While the Fur family of proteins adopt similar structures, each contains unique structural features relating to their specific biological functions. Moreover, recent groundbreaking studies have provided additional insights into the mechanisms underlying the binding of DNA by these metalloregulators. In this review, we present a comprehensive overview of the crystal structure of Fur family metalloregulators with a specific focus on the new structures of these TFs bound to DNA.

In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics.

Intestinal microbiota is emerging as one of the key environmental factors influencing or causing the development of numerous human diseases. Metaproteomics can provide invaluable information on the functional activities of intestinal microbiota and on host-microbe interactions as well. However, the application of metaproteomics in human microbiota studies is still largely limited, in part due to the lack of accurate quantitative intestinal metaproteomic methods. Most current metaproteomic microbiota studies are based on label-free quantification, which may suffer from variability during the separate sample processing and mass spectrometry runs. In this study, we describe a quantitative metaproteomic strategy, using in vitro stable isotopically ((15)N) labeled microbiota as a spike-in reference, to study the intestinal metaproteomes. We showed that the human microbiota were efficiently labeled (>95% (15)N enrichment) within 3 days under in vitro conditions, and accurate light-to-heavy protein/peptide ratio measurements were obtained using a high-resolution mass spectrometer and the quantitative proteomic software tool Census. We subsequently employed our approach to study the in vitro modulating effects of fructo-oligosaccharide and five different monosaccharides on the microbiota. Our methodology improves the accuracy of quantitative intestinal metaproteomics, which would promote the application of proteomics for functional studies of intestinal microbiota.

Refined analysis of the Campylobacter jejuni iron-dependent/independent Fur- and PerR-transcriptomes.

BACKGROUND: The genome of Campylobacter jejuni contains two iron activated Fur-family transcriptional regulators, CjFur and CjPerR, which are primarily responsible for regulating iron homeostasis and oxidative stress respectively. Both transcriptional regulators have been previously implicated in regulating diverse functions beyond their primary roles in C. jejuni. To further characterize their regulatory networks, RNA-seq was used to define the transcriptional profiles of C. jejuni NCTC11168 wild type, Δfur, ΔperR and ΔfurΔperR isogenic deletion mutants under both iron-replete and iron-limited conditions. RESULTS: It was found that 202 genes were differentially expressed in at least one mutant under iron-replete conditions and 331 genes were differentially expressed in at least one mutant under iron-limited conditions. The CjFur and CjPerR transcriptomes characterized in this study were compared to those previously identified using microarray profiling and found to be more extensive than previously understood. Interestingly, our results indicate that CjFur/CjPerR appear to co-regulate the expression of flagellar biogenesis genes in an opposing and iron-independent fashion. Moreover the ΔfurΔperR isogenic deletion mutant revealed that CjFur and CjPerR can compensate for each other in certain cases, suggesting that both regulators may compete for binding to specific promoters. CONCLUSIONS: The CjFur and CjPerR transcriptomes are larger than previously reported. In particular, deletion of perR results in the differential expression of a large group of genes in the absence of iron, suggesting that CjPerR may also regulate genes in an iron-independent manner, similar to what has already been demonstrated with CjFur. Moreover, subsets of genes were found which are only differentially expressed when both CjFur and CjPerR are deleted and includes genes that appear to be simultaneously activated by CjFur and repressed by CjPerR. In particular the iron-independent co-regulation of flagellar biogenesis by CjFur/CjPerR represents a potentially novel regulatory function for these proteins. These findings represent additional modes of co-regulation by these two transcriptional regulators in C. jejuni.

Structure and regulon of Campylobacter jejuni ferric uptake regulator Fur define apo-Fur regulation.

The full regulatory potential of the ferric uptake regulator (Fur) family of proteins remains undefined despite over 20 years of study. We report herein an integrated approach that combines both genome-wide technologies and structural studies to define the role of Fur in Campylobacter jejuni (Cj). CjFur ChIP-chip assays identified 95 genomic loci bound by CjFur associated with functions as diverse as iron acquisition, flagellar biogenesis, and non-iron ion transport. Comparative analysis with transcriptomic data revealed that CjFur regulation extends beyond solely repression and also includes both gene activation and iron-independent regulation. Computational analysis revealed the presence of an elongated holo-Fur repression motif along with a divergent holo-Fur activation motif. This diversity of CjFur DNA-binding elements is supported by the crystal structure of CjFur, which revealed a unique conformation of its DNA-binding domain and the absence of metal in the regulatory site. Strikingly, our results indicate that the apo-CjFur structure retains the canonical V-shaped dimer reminiscent of previously characterized holo-Fur proteins enabling DNA interaction. This conformation stems from a structurally unique hinge domain that is poised to further contribute to CjFur's regulatory functions by modulating the orientation of the DNA-binding domain upon binding of iron. The unique features of the CjFur crystal structure rationalize the binding sequence diversity that was uncovered during ChIP-chip analysis and defines apo-Fur regulation.

Phenotypic screening of a targeted mutant library reveals Campylobacter jejuni defenses against oxidative stress.

During host colonization, Campylobacter jejuni is exposed to harmful reactive oxygen species (ROS) produced from the host immune system and from the gut microbiota. Consequently, identification and characterization of oxidative stress defenses are important for understanding how C. jejuni survives ROS stress during colonization of the gastrointestinal tract. Previous transcriptomic studies have defined the genes belonging to oxidant stimulons within C. jejuni. We have constructed isogenic deletion mutants of these identified genes to assess their role in oxidative stress survival. Phenotypic screening of 109 isogenic deletion mutants identified 22 genes which were either hypersensitive or hyposensitive to oxidants, demonstrating important roles for these genes in oxidant defense. The significance of these genes in host colonization was also assessed in an in vivo chick model of C. jejuni colonization. Overall, our findings identify an indirect role for motility in resistance to oxidative stress. We found that a nonmotile flagellum mutant, the ΔmotAB mutant, displayed increased sensitivity to oxidants. Restoration of sensitivity to superoxide in the ΔmotAB mutant was achieved by fumarate supplementation or tandem deletion of motAB with ccoQ, suggesting that disruption of the proton gradient across the inner membrane resulted in increased superoxide production in this strain. Furthermore, we have identified genes involved in cation transport and binding, detoxification, and energy metabolism that are also important factors in oxidant defense. This report describes the first isogenic deletion mutant library construction for screening of relevant oxidative stress defense genes within C. jejuni, thus providing a comprehensive analysis of the total set of oxidative stress defenses.

Glycomacropeptide as an Efficient Agent to Fight Pathophysiological Mechanisms of Metabolic Syndrome.

There is currently a growing interest in the use of nutraceuticals as a means of preventing the development of complex diseases. Given the considerable health potential of milk-derived peptides, the aim of this study was to investigate the protective effects of glycomacropeptide (GMP) on metabolic syndrome. Particular emphasis was placed on the potential mechanisms mitigating cardiometabolic disorders in high-fat, high-fructose diet-fed mice in the presence of GMP or Bipro, an isocaloric control. The administration of GMP for 12 weeks reduced obesity, hyperglycemia and hyperinsulinemia caused by a high-fat, high-fructose diet, resulting in a decline in insulin resistance. GMP also lessened systemic inflammation, as indicated by decreased circulating inflammatory cytokines. In the intestinal and hepatic tissues, GMP improved homeostasis by increasing insulin sensitivity and attenuating high-fat, high-fructose-induced inflammation, oxidative stress and endoplasmic reticulum stress. Biochemical and histological analyses revealed improved hepatic steatosis and fatty acid composition in the livers of high-fat, high-fructose diet-fed mice treated with GMP compared to Bipro. A trend toward a decrease in bile acids without any marked changes in intestinal microbiota composition characterized GMP-treated animals compared to those administered Bipro. GMP offers considerable potential for fighting metabolic syndrome-related components and complications given its beneficial effects on risk factors such as inflammation, oxidative stress and endoplasmic reticulum stress without involving the intestinal microbiota.

Multiomic spatial analysis reveals a distinct mucosa-associated virome.

The human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage-host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.