pH of drinking water influences the composition of gut microbiome and type 1 diabetes incidence

Intestinal microbial community well explain larval growth than feed types

Black soldier fly larvae (BSFL) are considered a sustainable ingredient in livestock feed. However, addressing issues related to feed substrate and intestinal microbiota is essential to ensure optimal larval development. The aim of this study was to assess and elucidate the contribution of substrate nutrients and intestinal microbes to protein and fat synthesis in BSFL. The results showed that larvae that were fed high-quality feed (chicken feed) had high fat biomass, while larvae that were fed medium-quality feed (wheat bran) had high protein biomass. These results indicate that the original nutritional content of the feed cannot fully explain larval growth and nutrient utilization. However, the phenomenon could be explained by the functional metabolism of intestinal microbes. Chicken feed enhanced the fatty acid metabolism of middle intestine microorganisms in larvae within 0-7 days. This process facilitated larval fat synthesis. In contrast, wheat bran stimulated the amino acid metabolism in posterior intestine microorganisms in larvae within 4-7 days, leading to better protein synthesis. The findings of this study highlight the importance of the microbial functional potential in the intestine in regulating protein and lipid synthesis in BSFL, which is also influenced by the type of feed. In conclusion, our study suggests that both feed type and intestinal microbes play a crucial role in efficiently converting organic waste into high-quality insect protein and fat. Additionally, a mixed culture of chicken feed and wheat bran was found to be effective in promoting larval biomass while reducing feed costs. KEY POINTS: • Intestinal microbes explain BSFL growth better than feed substrates. • Chicken feed promotes fatty acid synthesis in the middle intestine • Wheat bran promotes amino acid synthesis in the posterior intestine.

Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway

The arginine dihydrolase pathway (arc operon) present in a subset of diverse human gut species enables arginine catabolism. This specialized metabolic pathway can alter environmental pH and nitrogen availability, which in turn could shape gut microbiota inter-species interactions. By exploiting synthetic control of gene expression, we investigated the role of the arc operon in probiotic Escherichia coli Nissle 1917 on human gut community assembly and health-relevant metabolite profiles in vitro and in the murine gut. By stabilizing environmental pH, the arc operon reduced variability in community composition across different initial pH perturbations. The abundance of butyrate producing bacteria were altered in response to arc operon activity and butyrate production was enhanced in a physiologically relevant pH range. While the presence of the arc operon altered community dynamics, it did not impact production of short chain fatty acids. Dynamic computational modeling of pH-mediated interactions reveals the quantitative contribution of this mechanism to community assembly. In sum, our framework to quantify the contribution of molecular pathways and mechanism modalities on microbial community dynamics and functions could be applied more broadly.

Intestinal permeability and inflammatory features of juvenile age correlate with the eventual systemic autoimmunity in lupus-prone female SWR × NZB F1 (SNF1) mice

The incidence of systemic lupus erythematosus (SLE) is about nine times higher in women than in men, and the underlying mechanisms that contribute to this gender bias are not fully understood. Previously, using lupus-prone (SWR × NZB)F1 (SNF1) mice, we have shown that the intestinal immune system could play a role in the initiation and progression of disease in SLE, and depletion of gut microbiota produces more pronounced disease protection in females than in males. Here, we show that the gut permeability features of lupus-prone female SNF1 mice at juvenile ages directly correlate with the expression levels of pro-inflammatory factors, faecal IgA abundance and nAg reactivity and the eventual systemic autoantibody levels and proteinuria onset. Furthermore, we observed that the disease protection achieved in female SNF1 mice upon depletion of gut microbiota correlates with the diminished gut inflammatory protein levels, intestinal permeability and circulating microbial DNA levels. However, faecal microbiota transplant from juvenile male and females did not result in modulation of gut inflammatory features or permeability. Overall, these observations suggest that the early onset of intestinal inflammation, systemic autoantibody production and clinical stage disease in lupus-prone females is linked to higher gut permeability in them starting at as early as juvenile age. While the higher gut permeability in juvenile lupus-prone females is dependent on the presence of gut microbes, it appears to be independent of the composition of gut microbiota.

Zamzam Water Mitigates Cardiac Toxicity Risk through Modulation of GUT Microbiota and the Renin-angiotensin System

BACKGROUND

Cardiovascular diseases (CVDs) continue to exert a substantial global influence in specific areas due to population growth, aging, microbiota, and genetic/environmental factors. Drinking water has a strong impact on the health of an individual. Further, emerging evidence has highlighted the therapeutic potential and benefits of Zamzam water (Zam).

OBJECTIVE

We investigated the influence of Zam on doxorubicin-induced cardiac toxicity, elucidating its consequential effects on GUT microbiota dysbiosis and hepatic and renal functions.

METHODS

Male rats were categorized into four groups: Group 1 as Normal control (NC), Group 2 as Zamzam control (ZC), Group 3 Disease control (DC) and Group 4 as Therapeutic control (DZ) treated with Zam against doxorubicin-induced disease at a dose of 1mg/kg boy weight) intraperitoneally (i.p).

RESULTS

Significant dysbiosis in the composition of GM was observed in the DC group along with a significant decrease (p < 0.05) in serum levels of Zinc, interleukin-10 (IL-10), IL-6 and Angiotensin II (Ang II), while C-reactive protein (CRP), fibrinogen, and CKMB increased significantly (restoration of Zinc ions (0.72 ± 0.07 mcg/mL) compared to NC. Treatment with Zamzam exhibited a marked abundance of 18-times to 72% in Romboutsia, a genus of firmicutes, along with lowering of Proteobacteria in DZ followed by significant restoration of Zinc ions (0.72 ± 0.07 mcg/mL), significant (p ˂ 0.05) reduction in CRP (7.22 ± 0.39 mg/dL), CKMB (118.8 ± 1.02 U/L) and Fibrinogen (3.18 ± 0.16 mg/dL), significant (p < 0.05) increase in IL-10 (7.22 ± 0.84 pg/mL) and IL-6 (7.18 ± 0.40 pg/ml), restoration of Ang II (18.62 ± 0.50 nmol/mL/min), marked increase in renin with normal myocyte architecture and tissue orientation of kidney, and restoration of histological architecture of hepatocyte.

CONCLUSION

Zam treatment mitigated cardiac toxicity risk through the modulation of GUT microbiota and the renin-angiotensin system and tissue histology effectively.

A Review of the Effects of Some Extrinsic Factors on Mice Used in Research

Animals have been used in research for over 2,000 y. From very crude experiments conducted by ancient scholars, animal research, as a science, was refined over hundreds of years to what we know it as today. However, the housing conditions of animals used for research did not improve significantly until less than 100 years ago when guidelines for housing research animals were first published. In addition, it was not until relatively recently that some extrinsic factors were recognized as a research variable, even when animals were housed under recommended guidelines. For example, temperature, humidity, light, noise, vibration, diet, water, caging, bedding, etc., can all potentially affect research using mice, contributing the inability of others to reproduce published findings. Consequently, these external factors should be carefully considered in the design, planning, and execution of animal experiments. In addition, as recommended by others, the housing and husbandry conditions of the animals should be described in detail in publications resulting from animal research to improve study reproducibility. Here, we briefly review some common, and less common, external factors that affect research in one of the most popular animal models, the mouse.

Global patterns in gene content of soil microbiomes emerge from microbial interactions

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.

Gut microbiota and cognitive development in infant mice: Quantity and source of potable water

Not only the water quantity consumed but also the source of drinking water has been considered for their health benefits, but there is limited evidence. We aimed to determine whether the amount and type of drinking water affect physiological and biological functions, including brain function, by confirming how it affects gut microbiota which has an important regulatory role in host physiology. Three-week-old infant mice were subjected to 1) a water restriction experiment (control group, ad libitum consumption of distilled water; dehydration group, time-limited access to distilled water [15 min/day]) and 2) different water source experiment (distilled water, purified water, spring water, and tap water groups). The gut microbiota and cognitive development were analyzed using the 16S ribosomal ribonucleic acid sequencing method and the Barnes maze, respectively. The relative abundance of Firmicutes and Bacteroidetes and the Firmicutes-to-Bacteroidetes ratio (F/B ratio) changed depending on age (juveniles vs. infants). Insufficient water intake reversed these developmental changes, showing that the relative abundances of Bacteroidetes and Firmicutes and the F/B ratio in dehydrated juvenile mice were similar to those in normal infant mice. Additionally, clustering analysis revealed no significant differences in the intestinal flora in the mice from the different drinking water sources; however, dehydration significantly altered the composition of the genera compared to the other water source groups wherein water was provided ad libitum. Moreover, cognitive development was significantly disrupted by insufficient water intake, although the type of drinking water had no significant influence. Cognitive decline, measured by relative latency, was positively associated with the relative abundance of unclassified Erysipelotrichaceae that were in significantly high relative abundance in the dehydration group. These results suggest that the water quantity consumed, rather than the mineral content of drinking water, is imperative for shaping the early gut microbiota associated with cognitive development during infancy.

The oral microbiome in autoimmune diseases: friend or foe?

The human body is colonized by abundant and diverse microorganisms, collectively known as the microbiome. The oral cavity has more than 700 species of bacteria and consists of unique microbiome niches on mucosal surfaces, on tooth hard tissue, and in saliva. The homeostatic balance between the oral microbiota and the immune system plays an indispensable role in maintaining the well-being and health status of the human host. Growing evidence has demonstrated that oral microbiota dysbiosis is actively involved in regulating the initiation and progression of an array of autoimmune diseases.Oral microbiota dysbiosis is driven by multiple factors, such as host genetic factors, dietary habits, stress, smoking, administration of antibiotics, tissue injury and infection. The dysregulation in the oral microbiome plays a crucial role in triggering and promoting autoimmune diseases via several mechanisms, including microbial translocation, molecular mimicry, autoantigen overproduction, and amplification of autoimmune responses by cytokines. Good oral hygiene behaviors, low carbohydrate diets, healthy lifestyles, usage of prebiotics, probiotics or synbiotics, oral microbiota transplantation and nanomedicine-based therapeutics are promising avenues for maintaining a balanced oral microbiome and treating oral microbiota-mediated autoimmune diseases. Thus, a comprehensive understanding of the relationship between oral microbiota dysbiosis and autoimmune diseases is critical for providing novel insights into the development of oral microbiota-based therapeutic approaches for combating these refractory diseases.

Functional Beverages in the 21st Century

Underlying the dawn of humanity was primarily the search for food and access to drinking water. Over the course of civilization, there has been a significant increase in drinking water quality. By the average of the nutritional standards, the daily water demand is 2.5 L (also including liquid products such as tea, coffee, or soup). However, it is worth noticing that the need is strictly individual for each person and depends on two major factors, namely, epidemiological (sex, age state of health, lifestyle, and diet) and environmental (humidity and air temperature). Currently, our diet is more and more often enriched with isotonic drinks, functional drinks, or drinks bearing the hallmarks of health-promoting products. As a result, manufacturing companies compete to present more interesting beverages with complex compositions. This article will discuss both the composition of functional beverages and their impact on health.

Gut microbiome in type 1 diabetes: the immunological perspective

INTRODUCTION

Type 1 diabetes (T1D) is a prevalent, and yet uncurable, autoimmune disease targeting insulin-producing pancreatic β-cells. Despite a known genetic component in T1D onset, genetics alone cannot explain the alarming worldwide rise in T1D incidence, which is attributed to a growing impact of environmental factors, including perturbations of the gut microbiome.

AREAS COVERED

Intestinal commensal bacteria plays a crucial role in host physiology in health and disease by regulating endocrine and immune functions. An aberrant gut microbiome structure and metabolic function have been documented prior and during T1D onset. In this review, we summarize and discuss the current studies depicting the taxonomic profile and role of the gut microbial communities in murine models of T1D, diabetic patients and human interventional trials.

EXPERT OPINION

Compelling evidence have shown that the intestinal microbiota is instrumental in driving differentiation and functions of immune cells. Therefore, any alterations in the intestinal microbiome composition or microbial metabolite production, particularly early in life, may impact disease susceptibility and amplify inflammatory responses and hence accelerate the course of T1D pathogenesis.

Secretome Analysis of the Plant Biostimulant Bacteria Strains Bacillus subtilis (EB2004S) and Lactobacillus helveticus (EL2006H) in Response to pH Changes

It is well-known that there is a high frequency of plant-growth-promoting strains in Bacillus subtilis and that these can be effective under both stressful and stress-free conditions. There are very few studies of this activity in the case of Lactobacillus helveticus. In this study, the effects of pH on the secretome (proteins) in the cell-free supernatants of two bacterial strains were evaluated. The bacteria were cultured at pH 5, 7 and 8, and their secretome profiles were analyzed, with pH 7 (optimal growth pH) considered as the "control". The results showed that acidity (lower pH 5) diminishes the detectable production of most of the secretome proteins, whereas alkalinity (higher pH 8) increases the detectable protein production. At pH 5, five (5) new proteins were produced by L. helveticus, including class A sortase, fucose-binding lectin II, MucBP-domain-containing protein, SLAP-domain-containing protein and hypothetical protein LHEJCM1006_11110, whereas for B. subtilis, four (4) types of proteins were uniquely produced (p ≤ 0.05), including helicase-exonuclease AddAB subunit AddB, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase, a cluster of ABC-F family ATP-binding-cassette-domain-containing proteins and a cluster of excinuclease ABC (subunit B). At pH 8, Bacillus subtilis produced 56 unique proteins. Many of the detected proteins were involved in metabolic processes, whereas the others had unknown functions. The unique and new proteins with known and unknown functions suggest potential the acclimatization of the microbes to pH stress.

Health Risk Assessment of Trace Metals in Bottled Water Purchased from Various Retail Stores in Pretoria, South Africa

Bottled water is one of the fastest growing commercial products in both developing and developed countries owing to the believe that it is safe and pure. In South Africa, over the years, there has been an increase in the sale of bottled water due to the perceived notion that water supplied by the government may not be safe for human consumption. This study investigated the concentrations of trace metals and the physicochemical properties of bottled water purchased from various supermarkets (registered and unregistered) in Pretoria with a view to determining the health risk that may be associated with the levels of trace metals resulting from the consumption of the bottled water. Twelve commonly available different brands of bottled water were purchased and analysed for trace-metal content using inductively coupled plasma mass spectrometry (ICP-MS). The water samples were also analysed for various physicochemical parameters. The health risk was assessed using the target hazard quotient (THQ). For all the bottled water, the highest concentration of all the elements was recorded for Fe. The values reported for Cr, Ni and Pb were above the limit recommended by World Health Organization. The pH values ranged from 4.67 to 7.26. Three of the samples had pH values in the acidic region below the permissible standard of 6.8-8.0 set by the International Bottled Water Association (IBWA). The target hazard quotient calculated for the water samples showed a minimum risk for Pb, Cr and Ni. The study showed the need to adhere to a strict compliance standard considering the fact that South Africa has rich natural mineral elements, which may have played a role in the high levels of trace metals reported from some of the water samples.

β-Cell Cre Expression and Reduced Ins1 Gene Dosage Protect Mice From Type 1 Diabetes

A central goal of physiological research is the understanding of cell-specific roles of disease-associated genes. Cre-mediated recombineering is the tool of choice for cell type-specific analysis of gene function in preclinical models. In the type 1 diabetes (T1D) research field, multiple lines of nonobese diabetic (NOD) mice have been engineered to express Cre recombinase in pancreatic β cells using insulin promoter fragments, but tissue promiscuity remains a concern. Constitutive Ins1tm1.1(cre)Thor (Ins1Cre) mice on the C57/bl6-J background have high β-cell specificity with no reported off-target effects. We explored whether NOD:Ins1Cre mice could be used to investigate β-cell gene deletion in T1D disease modeling. We studied wild-type (Ins1WT/WT), Ins1 heterozygous (Ins1Cre/WT or Ins1Neo/WT), and Ins1 null (Ins1Cre/Neo) littermates on a NOD background. Female Ins1Neo/WT mice exhibited significant protection from diabetes, with further near-complete protection in Ins1Cre/WT mice. The effects of combined neomycin and Cre knockin in Ins1Neo/Cre mice were not additive to the Cre knockin alone. In Ins1Neo/Cre mice, protection from diabetes was associated with reduced insulitis at age 12 weeks. Collectively, these data confirm previous reports that loss of Ins1 alleles protects NOD mice from diabetes development and demonstrates, for the first time, that Cre itself may have additional protective effects. This has important implications for the experimental design and interpretation of preclinical T1D studies using β-cell-selective Cre in NOD mice.

Acidified drinking water attenuates motor deficits and brain pathology in a mouse model of a childhood neurodegenerative disorder

We recently demonstrated that HCl-acidified drinking water, which is widely used in laboratory animal facilities, had some beneficial effects in the Cln3−/− mouse model of juvenile Batten disease, a neurodegenerative lysosomal storage disorder1. Here we tested if acidified drinking water has therapeutic effects in Cln1R151X nonsense mutant mice, a model of the infantile form of Batten disease. In Cln1R151X mice, acidified drinking water received from weaning prevented the impairment in pole climbing ability measured at 3 and 6 months of age. Histopathological analysis of the brain at 6 months showed that acidified drinking water decreased the amount of lysosomal storage material, reduced astrocytosis in the striatum and somatosensory barrelfield cortex, and attenuated microglial activation in the thalamus. Compared to wild-type mice, the gut microbiota of Cln1R151X mice was markedly different. Acidified drinking water significantly altered the gut microbiota composition of Cln1R151X mice, indicating a contribution of gut bacteria to the therapeutic effects of acidified water. Our results in Cln1R151X mice suggest that acidified drinking water may have beneficial effects for patients with infantile Batten disease. This study also verifies that acidified drinking water can modify disease phenotypes in mouse models, contributing to the inter-laboratory variations in neurological and pathological findings.

Kidney metabolism and acid-base control: back to the basics

Kidneys are central in the regulation of multiple physiological functions, such as removal of metabolic wastes and toxins, maintenance of electrolyte and fluid balance, and control of pH homeostasis. In addition, kidneys participate in systemic gluconeogenesis and in the production or activation of hormones. Acid-base conditions influence all these functions concomitantly. Healthy kidneys properly coordinate a series of physiological responses in the face of acute and chronic acid-base disorders. However, injured kidneys have a reduced capacity to adapt to such challenges. Chronic kidney disease patients are an example of individuals typically exposed to chronic and progressive metabolic acidosis. Their organisms undergo a series of alterations that brake large detrimental changes in the homeostasis of several parameters, but these alterations may also operate as further drivers of kidney damage. Acid-base disorders lead not only to changes in mechanisms involved in acid-base balance maintenance, but they also affect multiple other mechanisms tightly wired to it. In this review article, we explore the basic renal activities involved in the maintenance of acid-base balance and show how they are interconnected to cell energy metabolism and other important intracellular activities. These intertwined relationships have been investigated for more than a century, but a modern conceptual organization of these events is lacking. We propose that pH homeostasis indissociably interacts with central pathways that drive progression of chronic kidney disease, such as inflammation and metabolism, independent of etiology.

Activation of T cell checkpoint pathways during β-cell antigen presentation by engineered dendritic cells promotes protection from type 1 diabetes

Defective immune regulation has been recognized in type 1 diabetes (T1D). Immune regulatory T cell check-point receptors, which are generally upregulated on activated T cells, have been the molecules of attention as therapeutic targets for enhancing immune response in tumor therapy. Here, we show that pancreatic β-cell antigen (BcAg) presentation by engineered tolerogenic dendritic cells (tDCs) that express CTLA4 selective ligand (B7.1wa) or a combination of CTLA4, PD1 and BTLA selective ligands (B7.1wa, PD-L1, and HVEM-CRD1 respectively; multiligand-DCs) causes an increase in regulatory cytokine and T cell (Treg) responses and suppression of the effector T cell function as compared to engineered control-DCs. Non-obese diabetic (NOD) mice treated with BcAg-pulsed CTLA4-ligand-DCs and multiligand-DCs at pre-diabetic and early-hyperglycemic stages showed significantly lower degree of insulitis, higher frequencies of insulin-positive islets, profound delay in, and reversal of, hyperglycemia for a significant duration. Immune cells from the tDC treated mice not only produced lower amounts of IFNγ and higher amounts of IL10 and TGFβ1 upon BcAg challenge, but also failed to induce hyperglycemia upon adoptive transfer. While both CTLA4-ligand-DCs and multiligand-DCs were effective in inducing tolerance, multiligand-DC treatment produced an overall higher suppressive effect on effector T cell function and disease outcome. These studies show that enhanced engagement of T cell checkpoint receptors during BcAg presentation can modulate T cell function and suppress autoimmunity and progression of the disease in T1D.

Gastrin producing syngeneic mesenchymal stem cells protect non-obese diabetic mice from type 1 diabetes

Progressive destruction of pancreatic islet β-cells by immune cells is a primary feature of type 1 diabetes (T1D) and therapies that can restore the functional β-cell mass are needed to alleviate disease progression. Here, we report the use of mesenchymal stromal/stem cells (MSCs) for the production and delivery of Gastrin, a peptide hormone that is produced by intestinal cells and foetal islets and can increase β-Cell mass, to promote protection from T1D. A single injection of syngeneic MSCs that were engineered to express Gastrin (Gastrin-MSCs) caused a significant delay in hyperglycaemia in non-obese diabetic (NOD) mice compared to engineered control-MSCs. Similar treatment of early-hyperglycaemic mice caused the restoration of euglycemia for a considerable duration, and these therapeutic effects were associated with the protection of, and/or higher frequencies of, insulin-producing islets and less severe insulitis. While the overall immune cell phenotype was not affected profoundly upon treatment using Gastrin-MSCs or upon in vitro culture, pancreatic lymph node cells from Gastrin-MSC treated mice, upon ex vivo challenge with self-antigen, showed a Th2 and Th17 bias, and diminished the diabetogenic property in NOD-Rag1 deficient mice suggesting a disease protective immune modulation under Gastrin-MSC treatment associated protection from hyperglycaemia. Overall, this study shows the potential of production and delivery of Gastrin in vivo, by MSCs, in protecting insulin-producing β-cells and ameliorating the disease progression in T1D.

Impact of Prebiotic β-glucan Treatment at Juvenile Age on the Gut Microbiota Composition and the Eventual Type 1 Diabetes Onset in Non-obese Diabetic Mice

Complex dietary polysaccharides such as β-glucans are widely used for their anti-inflammatory properties. We reported before that oral administration of Yeast β-glucan (YBG) in adult mice can help delay type 1 diabetes (T1D) onset and suppress gut inflammation through modulation of the structure and function of gut microbiota. Since juvenile age is characterized by profoundly changing immature gut microbiota, we examined the impact of oral treatment with YBG in non-obese diabetic (NOD) mice at this age. Juvenile mice that received daily oral administration of YBG starting at 15 days of age for 7 or 30 days were examined for changes in gut microbiota, immune characteristics, and T1D incidence. Mice that received YBG for 30 days but not 7 days, showed considerable changes in the composition and diversity of fecal microbiota as compared to controls. Predictive functional analysis, based on 16S rDNA sequences, revealed overrepresentation of glycan biosynthesis and metabolism, energy metabolism, and fatty acid biosynthesis pathways in mice that received YBG for 30 days. Immune phenotype of the colon showed skewing toward immune regulatory and Th17 cytokines with increases in IL-10, IL-17, and IL-21 and a decrease in TNF-α, although increases in some pro-inflammatory cytokines (IL-1b, IFN-γ) were observed. Most importantly, mice that received YBG treatment for 30 days showed significantly suppressed insulitis and delayed onset of hyperglycemia compared to controls. Overall, this study suggests that oral consumption of YBG beginning at pre-diabetic juvenile ages could have positive maturational changes to gut microbiota and immune functions and could result in a delay in the disease onset in those who are pre-disposed to T1D.

Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations

BACKGROUND

The microbiome of the digestive tract exerts fundamental roles in host physiology. Extrinsic factors including lifestyle and diet are widely recognized as key drivers of gut and oral microbiome compositions. Although drinking water is among the food items consumed in the largest amount, little is known about its potential impact on the microbiome.

OBJECTIVES

We explored the associations of plain drinking water source and intake with gut and oral microbiota compositions in a population-based cohort.

METHODS

Microbiota, health, lifestyle, and food intake data were extracted from the American Gut Project public database. Associations of drinking water source (bottled, tap, filtered, or well water) and intake with global microbiota composition were evaluated using linear and logistic models adjusted for anthropometric, diet, and lifestyle factors in 3413 and 3794 individuals, respectively (fecal samples; 56% female, median [IQR] age: 48 [36-59] y; median [IQR] BMI: 23.3 [20.9-26.3] kg/m2), and in 283 and 309 individuals, respectively (oral samples).

RESULTS

Drinking water source ranked among the key contributing factors explaining the gut microbiota variation, accounting for 13% [Faith's phylogenetic diversity (Faith's PD)] and 47% (Bray-Curtis dissimilarity) of the age effect size. Drinking water source was associated with differences in gut microbiota signatures, as revealed by β diversity analyses (P < 0.05; Bray-Curtis dissimilarity, weighted UniFrac distance). Subjects drinking mostly well water had higher fecal α diversity (P < 0.05; Faith's PD, observed amplicon sequence variants), higher Dorea, and lower Bacteroides, Odoribacter, and Streptococcus than the other groups. Low water drinkers also exhibited gut microbiota differences compared with high water drinkers (P < 0.05; Bray-Curtis dissimilarity, unweighted UniFrac distance) and a higher abundance of Campylobacter. No associations were found between oral microbiota composition and drinking water consumption.

CONCLUSIONS

Our results indicate that drinking water may be an important factor in shaping the human gut microbiome and that integrating drinking water source and intake as covariates in future microbiome analyses is warranted.

The Effects of Ketamine on the Gut Microbiome on CD1 Mice

The intestinal microbiota of an organism can significantly alter outcome data in otherwise identical experiments. Occasionally, animals may require sedation or anesthesia for scientific or health-related purposes, and certain anesthetics, such as ketamine, can profoundly affect the gastrointestinal system. While many factors can alter the gut microbiome (GM), the effects of anesthetics on the composition or diversity of the GM have not been established. The goal of the current study was to determine whether daily administration of ketamine would significantly alter the microbiome of CD1 mice. To achieve this goal, female CD1 mice received daily injections of ketamine HCl (100 mg/kg) or the equivalent volume of 0.9% saline for 10 consecutive days. Fecal samples were collected before the first administration and 24 h after the final dose of either ketamine or saline. Samples were analyzed by 16S rRNA sequencing to identify changes between groups in diversity or composition of GM. The study found no significant changes to the GM after serial ketamine administration when treated mice were housed with controls. Therefore, ketamine administration is unlikely to alter the GM of a CD1 mouse and should not serve be a confounding factor in reproducibility of research.

Gut microbiota in pancreatic diseases: possible new therapeutic strategies

Pancreatic diseases such as pancreatitis, type 1 diabetes and pancreatic cancer impose substantial health-care costs and contribute to marked morbidity and mortality. Recent studies have suggested a link between gut microbiota dysbiosis and pancreatic diseases; however, the potential roles and mechanisms of action of gut microbiota in pancreatic diseases remain to be fully elucidated. In this review, we summarize the evidence that supports relationship between alterations of gut microbiota and development of pancreatic diseases, and discuss the potential molecular mechanisms of gut microbiota dysbiosis in the pathogenesis of pancreatic diseases. We also propose current strategies toward gut microbiota to advance a developing research field that has clinical potential to reduce the cost of pancreatic diseases.

Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium

Animal models play a critical role in establishing causal relationships between gut microbiota and disease. The laboratory mouse is widely used to study the role of microbes in various disorders; however, differences between mouse vendors, genetic lineages and husbandry protocols have been shown to contribute to variation in phenotypes and to non-reproducibility of experimental results. We sought to understand how gut microbiome profiles of mice vary by vendor, vendor production facility and health status upon receipt into an academic facility and how they change over 12 weeks in the new environment. C57BL/6 mice were sourced from two different production sites for each of three different vendors. Mice were shipped to an academic research vivarium, and fresh-catch stool samples were collected from mice immediately from the shipping box upon receipt, and again after 2, 6 and 12 weeks in the new facility. Substantial variation in bacterial proportional abundance was observed among mice from each vendor at the time of receipt, but shared microbes accounted for most sequence reads. Vendor-specific microbes were generally of low abundance. Microbial profiles of mice from all vendors exhibited shifts over time, highlighting the importance of environmental conditions on microbial dynamics. Our results emphasize the need for continued efforts to account for sources of variation in animal models and understand how they contribute to experimental reproducibility.

Acute Radiation Syndrome and the Microbiome: Impact and Review

Study of the human microbiota has been a centuries-long endeavor, but since the inception of the National Institutes of Health (NIH) Human Microbiome Project in 2007, research has greatly expanded, including the space involving radiation injury. As acute radiation syndrome (ARS) is multisystemic, the microbiome niches across all areas of the body may be affected. This review highlights advances in radiation research examining the effect of irradiation on the microbiome and its potential use as a target for medical countermeasures or biodosimetry approaches, or as a medical countermeasure itself. The authors also address animal model considerations for designing studies, and the potential to use the microbiome as a biomarker to assess radiation exposure and predict outcome. Recent research has shown that the microbiome holds enormous potential for mitigation of radiation injury, in the context of both radiotherapy and radiological/nuclear public health emergencies. Gaps still exist, but the field is moving forward with much promise.

A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD

Graft-versus-host disease (GVHD) is a pathological process caused by an exaggerated donor lymphocyte response to host antigens after allogeneic hematopoietic cell transplantation (allo-HCT). Donor T cells undergo extensive clonal expansion and differentiation, which culminate in damage to recipient target organs. Damage to the gastrointestinal tract is a main contributor to morbidity and mortality. The loss of diversity among intestinal bacteria caused by pretransplant conditioning regimens leads to an outgrowth of opportunistic pathogens and exacerbated GVHD after allo-HCT. Using murine models of allo-HCT, we found that an increase of Bacteroides in the intestinal microbiota of the recipients was associated with reduced GVHD in mice given fecal microbial transplantation. Administration of Bacteroides fragilis through oral gavage increased gut microbiota diversity and beneficial commensal bacteria and significantly ameliorated acute and chronic GVHD development. Preservation of gut integrity following B. fragilis exposure was likely attributed to increased short chain fatty acids, IL-22, and regulatory T cells, which in turn improved gut tight junction integrity and reduced inflammatory cytokine production of pathogenic T cells. The current study provides a proof of concept that a single strain of commensal bacteria can be a safe and effective means to protect gut integrity and ameliorate GVHD after allo-HCT.

The acidified drinking water-induced changes in the behavior and gut microbiota of wild-type mice depend on the acidification mode

Acidification of drinking water to a pH between 2.5 and 3.0 is widely used to prevent the spread of bacterial diseases in animal colonies. Besides hydrochloric acid (HCl), sulfuric acid (H₂SO₄) is also used to acidify drinking water. Here we examined the effects of H₂SO₄-acidified drinking water (pH = 2.8) received from weaning (postnatal day 21) on the behavior and gut microflora of 129S6/SvEv mice, a mouse strain commonly used in transgenic studies. In contrast to HCl-acidified water, H₂SO₄-acidified water only temporarily impaired the pole-descending ability of mice (at 3 months of age), and did not change the performance in an accelerating rotarod test. As compared to 129S6/SvEv mice receiving non-acidified or HCl-acidified drinking water, the gut microbiota of 129S6/SvEv mice on H₂SO₄-acidified water displayed significant alterations at every taxonomic level especially at 6 months of age. Our results demonstrate that the effects of acidified drinking water on the behavior and gut microbiota of 129S6/SvEv mice depends on the acid used for acidification. To shed some light on how acidified drinking water affects the physiology of 129S6/SvEv mice, we analyzed the serum and fecal metabolomes and found remarkable, acidified water-induced alterations.

NF-κB activity during pancreas development regulates adult β-cell mass by modulating neonatal β-cell proliferation and apoptosis

NF-κB is a well-characterized transcription factor, widely known for its roles in inflammation and immune responses, as well as in control of cell division and apoptosis. However, its function in β-cells is still being debated, as it appears to depend on the timing and kinetics of its activation. To elucidate the temporal role of NF-κB in vivo, we have generated two transgenic mouse models, the ToIβ and NOD/ToIβ mice, in which NF-κB activation is specifically and conditionally inhibited in β-cells. In this study, we present a novel function of the canonical NF-κB pathway during murine islet β-cell development. Interestingly, inhibiting the NF-κB pathway in β-cells during embryogenesis, but not after birth, in both ToIβ and NOD/ToIβ mice, increased β-cell turnover, ultimately resulting in a reduced β-cell mass. On the NOD background, this was associated with a marked increase in insulitis and diabetes incidence. While a robust nuclear immunoreactivity of the NF-κB p65-subunit was found in neonatal β-cells, significant activation was not detected in β-cells of either adult NOD/ToIβ mice or in the pancreata of recently diagnosed adult T1D patients. Moreover, in NOD/ToIβ mice, inhibiting NF-κB post-weaning had no effect on the development of diabetes or β-cell dysfunction. In conclusion, our data point to NF-κB as an important component of the physiological regulatory circuit that controls the balance of β-cell proliferation and apoptosis in the early developmental stages of insulin-producing cells, thus modulating β-cell mass and the development of diabetes in the mouse model of T1D.

The gut microbiome of laboratory mice: considerations and best practices for translational research

Just as the gut microbiota (GM) is now recognized as an integral mediator of environmental influences on human physiology, susceptibility to disease, and response to pharmacological intervention, so too does the GM of laboratory mice affect the phenotype of research using mouse models. Multiple experimental factors have been shown to affect the composition of the GM in research mice, as well as the model phenotype, suggesting that the GM represents a major component in experimental reproducibility. Moreover, several recent studies suggest that manipulation of the GM of laboratory mice can substantially improve the predictive power or translatability of data generated in mouse models to the human conditions under investigation. This review provides readers with information related to these various factors and practices, and recommendations regarding methods by which issues with poor reproducibility or translatability can be transformed into discoveries.

Water quality and management in the Australian pig industry

Context Water is the first nutrient and an essential component of all agricultural production systems. Despite its importance there has been limited research on water, and in particular, the impact of its availability, management and quality on production systems. Aims This research sought to describe the management and quality of water used within the Australian pig industry. Specifically, the water sources utilised, how water was managed and to evaluate water quality at both the source and the point of delivery to the pig. Methods Fifty-seven commercial piggeries across Australia participated in this study by completing a written survey on water management. In addition, survey participants undertook physical farm parameter measurements including collecting water samples. Each water sample was tested for standard quality parameters including pH, hardness, heavy metals and microbiological status. Key results Responses were received from 57 farms, estimated to represent at least 22% of ‘large’ pig herds. Bore water was the most common water source being utilised within the farms surveyed. Management practices and infrastructure delivering water from the source to the point of consumption were found to differ across the farms surveyed. Furthermore, water was regularly used as a delivery mechanism for soluble additives such as antibiotics. The quality of water at the source and point of consumption was found to be highly variable with many parameters, particularly pH, hardness, salinity, iron, manganese and microbiological levels, exceeding the acceptable standard. Conclusions In general, water quality did not appear to be routinely monitored or managed. As a result, farm managers had poor visibility of the potential negative impacts that inferior water quality or management may be having on pig production and in turn the economics of their business. Indeed, inferior water quality may impact the delivery of antibiotics and in turn undermine the industry’s antimicrobial stewardship efforts. Implications The study findings suggest that water quality represents a significant challenge to the Australian pig industry. Access to drinking water of an acceptable quality is essential for optimal pig performance, health and welfare but also to ensure farm to fork supply chain integrity, traceability and food safety.

The emerging roles of the gut microbiome in allogeneic hematopoietic stem cell transplantation

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is used for the treatment of hematologic cancers and disorders. However, graft-versus-host disease (GVHD) in which the donor immune cells attack the genetically-disparate recipient is a significant cause of morbidity. Acute GVHD is an inflammatory condition and the gastrointestinal system is a major organ affected but is also tied to beneficial graft-versus-tumor (GVT) effects. There is increasing interest on the role of the microbiome on immune function as well as on cancer progression and immunotherapy outcomes. However, there are still significant unanswered questions on the role the microbiome plays in GVHD progression or how to exploit the microbiome in GVHD prevention or treatment. In this review, concepts of HSCT with the focus on GVHD pathogenesis as well as issues in preclinical models used to study GVHD will be discussed with an emphasis on the impact of the microbiome. Factors affecting the microbiome and GVHD outcome such as obesity are also examined. The bridging of preclinical models and clinical outcomes in relation to the role of the microbiome will also be discussed along with possibilities for therapeutic exploitation.

Associations between UK tap water and gut microbiota composition suggest the gut microbiome as a potential mediator of health differences linked to water quality

Tap water composition has been widely linked to differences in human health, however the biological pathways underlying this association are less clearly defined. We provide the first investigation of the potential for the gut microbiota to mediate this association. Tap water samples and drinking habits from 85 Mono-zygotic twins with existing faecal microbiota profiles from around the UK were used to assess associations of water composition with the gut microbiome. Water composition was captured using the first 3 principle components (PCs) from multiple factor analysis of ion concentrations, additionally estimating average daily dose (ADD) of the primary three solutes contributing to its variance: chloride, sulphate and sodium. Geographic differences in water composition were assessed. We used measures of faecal microbial diversity, between-individual differences in composition and differences in taxa abundance estimated from 16S rRNA sequencing data. Differences between twin pairs were also considered. We observed significant associations of sodium ADD with microbiota diversity (Chao1), chloride, sodium and sulphate ADD with dissimilarity between samples, and significant associations for all PCs and ADD-adjusted solutes with abundances of individual microbial taxa. These results support the hypothesis that the gut microbiota could mediate the effects of tap water composition on host health, warranting further investigation into tap-water as an influencer of microbiota composition.

Study logistics that can impact medical countermeasure efficacy testing in mouse models of radiation injury

PURPOSE

To address confounding issues that have been noted in planning and conducting studies to identify biomarkers of radiation injury, develop animal models to simulate these injuries, and test potential medical countermeasures to mitigate/treat damage caused by radiation exposure.

METHODS

The authors completed an intensive literature search to address several key areas that should be considered before embarking on studies to assess efficacy of medical countermeasure approaches in mouse models of radiation injury. These considerations include: (1) study variables; (2) animal selection criteria; (3) animal husbandry; (4) medical management; and (5) radiation attributes.

RESULTS

It is important to select mouse strains that are capable of responding to the selected radiation exposure (e.g. genetic predispositions might influence radiation sensitivity and proclivity to certain phenotypes of radiation injury), and that also react in a manner similar to humans. Gender, vendor, age, weight, and even seasonal variations are all important factors to consider. In addition, the housing and husbandry of the animals (i.e. feed, environment, handling, time of day of irradiation and animal restraint), as well as the medical management provided (e.g. use of acidified water, antibiotics, routes of administration of drugs, consideration of animal numbers, and euthanasia criteria) should all be addressed. Finally, the radiation exposure itself should be tightly controlled, by ensuring a full understanding and reporting of the radiation source, dose and dose rate, shielding and geometry of exposure, while also providing accurate dosimetry. It is important to understand how all the above factors contribute to the development of radiation dose response curves for a given animal facility with a well-defined murine model.

CONCLUSIONS

Many potential confounders that could impact the outcomes of studies to assess efficacy of a medical countermeasure for radiation-induced injuries are addressed, and recommendations are made to assist investigators in carrying out research that is robust, reproducible, and accurate.

PCR and RT-PCR in the Diagnosis of Laboratory Animal Infections and in Health Monitoring

Molecular diagnostics (PCR and RT-PCR) have become commonplace in laboratory animal research and diagnostics, augmenting or replacing serological and microbiologic methods. This overview will discuss the uses of molecular diagnostics in the diagnosis of pathogenic infections of laboratory animals and in monitoring the microbial status of laboratory animals and their environment. The article will focus primarily on laboratory rodents, although PCR can be used on samples from any laboratory animal species.

Metagenomic insights into the effects of nanobubble water on the composition of gut microbiota in mice

The particular physicochemical and biological properties of nanobubbles (NBs) have prompted many researchers to conduct an in-depth study on their potential application in various fields. This study aims to investigate the effects of nanobubble water (NBW) on the community structure of the gut microbiota in mice. In this study, supplementation with nitrogen NBW (SD-N₂ group), hydrogen NBW (SD-H₂ group) and deionized water (SD-C group) to a standard diet of mice was performed for five weeks. The composition of fecal microbiota was analyzed by using 16S rRNA gene sequencing. Compared with the SD-C group, the species diversity of the fecal microbiota in mice in NBW groups was significantly increased. At the genus level, supplementation with nitrogen NBW to mice significantly increased the relative abundance of two beneficial genera Clostridium and Coprococcus (mean growth 6.3 times and 9.7 times, respectively), while supplementation with hydrogen NBW significantly decreased the relative abundance of two pathogenic genera Mucispirillum and Helicobacter (mean reduction rate 86% and 60%, respectively). These results demonstrate that supplementation with NBW might optimize the composition of gut microbiota in mice.

The Influence of Feed and Drinking Water on Terrestrial Animal Research and Study Replicability

For more than 50 years, the research community has made strides to better determine the nutrient requirements for many common laboratory animal species. This work has resulted in high-quality animal feeds that can optimize growth, maintenance, and reproduction in most species. We have a much better understanding of the role that individual nutrients play in physiological responses. Today, diet is often considered as an independent variable in experimental design, and specialized diet formulations for experimental purposes are widely used. In contrast, drinking water provided to laboratory animals has rarely been a consideration in experimental design except in studies of specific water-borne microbial or chemical contaminants. As we advance in the precision of scientific measurements, we are constantly discovering previously unrecognized sources of experimental variability. This is the nature of science. However, science is suffering from a lack of experimental reproducibility or replicability that undermines public trust. The issue of reproducibility/replicability is especially sensitive when laboratory animals are involved since we have the ethical responsibility to assure that laboratory animals are used wisely. One way to reduce problems with reproducibility/replicability is to have a strong understanding of potential sources of inherent variability in the system under study and to provide "…a clear, specific, and complete description of how the reported results were reached [1]." A primary intent of this review is to provide the reader with a high-level overview of some basic elements of laboratory animal nutrition, methods used in the manufacturing of feeds, sources of drinking water, and general methods of water purification. The goal is to provide background on contemporary issues regarding how diet and drinking water might serve as a source of extrinsic variability that can impact animal health, study design, and experimental outcomes and provide suggestions on how to mitigate these effects.

Dental erosion in mice with impaired salivary gland function

Objective: Salivary flow rate exerts an essential impact on the development and progression of dental erosion. In this work, the experimental dental erosion in non-obese diabetic (NOD) mice with reduced salivary flow rate was induced, and the erosive effect of acidic drinks on their dentition was studied.Material and methods: Three acidic drinks (sports drink, cola light drink and sugar containing cola drink) were given to adult NOD mice (groups: N = 11) as the only drink for 6 weeks. Two control groups were included; wild type and NOD control (groups: N = 9). Experimental and control (water) teeth were dissected out and observed by scanning electron microscopy (SEM). Mandibular first molars were subsequently embedded in Epon, ground transversely, observed again by SEM, and the enamel thickness and tooth height were measured.Results: Mandibular molars were considerably more eroded than maxillary molars. The erosive process started at the top of the cusps and subsequently extended in the cervical, mesio-distal, and pulpal direction. Erosive lesions were evident in increased succession from sports drink, cola light to cola drink exposed mandibular molars, with the lingual tooth height being approximately 23%, 26%, and 37% lower, respectively, compared to the control. The lingual enamel was approximately 48% thinner in sports drink molars and 62% thinner in cola light molars. In cola drink molars, the lingual enamel was totally eroded, and significant erosion of dentine was evident.Conclusion: Reduced salivary flow, together with a high consumption of acidic drinks, results in severe erosion of NOD mice molars.

Pretreatment with Yeast-Derived Complex Dietary Polysaccharides Suppresses Gut Inflammation, Alters the Microbiota Composition, and Increases Immune Regulatory Short-Chain Fatty Acid Production in C57BL/6 Mice

BACKGROUND

β-Glucans (BGs), a group of complex dietary polysaccharides (CDPs), are available as dietary supplements. However, the effects of orally administered highly purified BGs on gut inflammation are largely unknown.

OBJECTIVES

The aim of this study was to investigate the impact of orally administering highly purified, yeast-derived BG (YBG; β-1,3/1,6-d-glucan) on susceptibility to colitis.

METHODS

Eight-week-old C57BL/6 (B6) mice were used in a series of experiments. Experiment (Expt) 1: male and female mice were treated every day, for 40 d, with saline (control) or 250 μg YBG, followed by 2.5% (wt:vol) dextran sulfate sodium (DSS) in drinking water during days 30-35; and colitis severity and intestinal immune phenotype were determined. Expt 2: female B6 mice were treated with saline or YBG for 30 d and intestinal immune phenotype, gut microbiota composition, and fecal SCFA concentrations were determined. Expt 3: female B6 mice were treated as in Expt 2, given drinking water with or without antibiotics [Abx; ampicillin (1 g/L), vancomycin (0.5 g/L), neomycin (1 g/L), and metronidazole (1 g/L)] during days 16-30, and gut immune phenotype and fecal SCFA concentrations were determined. Expt 4: female B6 Foxp3-green fluorescent protein (-GFP) reporter mice were treated as in Expt 3, and intestinal T-regulatory cell (Treg) frequencies and immune phenotypes were determined. Expt 5: female mice were treated as in Expt 1, given drinking water with or without antibiotics during days 16-40, and colitis severity and intestinal cytokine production were determined.

RESULTS

Compared with controls, the YBG group in Expt 1 exhibited suppressive effects on features of colitis, such as loss of body weight (by 47%; P < 0.001), shortening of colon (by 24%; P = 0.016), and histopathology severity score (by 45%; P = 0.01). The YBG group of Expt 2 showed a shift in the abundance of gut microbiota towards Bacteroides (by 16%; P = 0.049) and Verrucomicrobia (mean ± SD: control = 7.8 ± 0.44 vs. YBG = 21.0 ± 9.6%) and a reduction in Firmicutes (by 66%; P < 0.001). The YBG group also showed significantly higher concentrations of fecal SCFAs such as acetic (by 37%; P = 0.016), propionic (by 47%; P = 0.026), and butyric (by 57%; P = 0.013) acids. Compared with controls, the YBG group of Expt 2 showed higher frequencies of Tregs (by 32%; P = 0.043) in the gut mucosa. Depletion of gut microbiota in the YBG group of mice caused diminished fecal SCFA concentrations (Expt 3) and intestinal Treg frequencies (Expt 4). Compared with the YBG group, the YBG-(Abx) group of Expt 5 showed aggravated colitis features including loss of body weight (by >100%; P < 0.01) and colonic inflammation score (by 42%; P = 0.04).

CONCLUSIONS

Studies using B6 mice show that dietary BGs are beneficial for promoting intestinal health when the gut microbiota is intact. However, these CDPs may produce adverse effects if gut microbiota is compromised.

Beginning to offer drinking water at birth increases the species richness and the abundance of Faecalibacterium and Bifidobacterium in the gut of preweaned dairy calves

We previously demonstrated that dairy calves having access to drinking water since birth (W0) achieved greater body weight, fiber digestibility, and feed efficiency than those that first received drinking water at 17 d of age (W17). Since gut microbiota composition could be linked to growth and development of animals, the objective of this study was to examine the effect of offering drinking water to newborn calves on composition of bacteria in the gut using a fecal microbiota analysis. Fresh feces were collected directly from the rectum of calves in W0 (n = 14) and W17 (n = 15) at 2, 6, and 10 wk of age. All of the calves were fed pasteurized waste milk, weaned at 7 wk of age, and offered tap water according to the treatment. The DNA was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq system (Illumina Inc., San Diego, CA). The sequences were clustered into operational taxonomic units (OTU) with a 99% similarity threshold. Treatment effects on α-diversity indices and relative abundance of the 10 most abundant genera were analyzed using GLIMMIX procedure of SAS (SAS Institute Inc., Cary, NC). Statistical significance (q-value) of treatment effects on the 50 most abundant OTU was determined with a false discovery rate analysis. At 2 wk of age, W0 had a greater number of observed OTU (5,908 vs. 4,698) and species richness (Chao 1 index) than W17. The number of OTU and richness indices increased from wk 2 to 6, but the increment of W17 was greater than that of W0. The Shannon and inverse-Simpson indices increased linearly with age, but no difference was observed between W0 and W17 at any time point. The Firmicutes to Bacteroidetes ratios were also similar at every time point but decreased markedly when calves were weaned. The relative abundance of genera Faecalibacterium and Bacteroides was greater in W0 than W17 at 2 wk of age. The genus Faecalibacterium continued to be more abundant in W0 than W17 at 6 wk of age but had similar abundance 3 wk after weaning (10 wk of age). The abundance of Faecalibacterium at wk 6 was positively correlated with apparent total-tract digestibility of acid detergent fiber at 10 wk of age. Calves receiving water since birth had greater abundance of OTU related to Faecalibacterium prausnitzii, and Bifidobacterium breve at 6 wk of age (q < 0.085). These species are known to improve growth in preweaned calves. The abundance of none of the genera and OTU was different between W0 at W17 at 10 wk of age (q > 0.100). Overall, beginning to offer drinking water at birth has a potential to modulate gut microbiota composition and thereby positively affect performance of young dairy heifer calves (≤10 wk of age).

Gut microbiota differently contributes to intestinal immune phenotype and systemic autoimmune progression in female and male lupus-prone mice

The risk of developing systemic lupus erythematosus (SLE) is about 9 times higher in women as compared to men. Our recent report, which used (SWRxNZB) F1 (SNF1) mouse model of spontaneous lupus, showed a potential link between immune response initiated in the gut mucosa at juvenile age (sex hormone independent) and SLE susceptibility. Here, using this mouse model, we show that gut microbiota contributes differently to pro-inflammatory immune response in the intestine and autoimmune progression in lupus-prone males and females. We found that gut microbiota composition in male and female littermates are significantly different only at adult ages. However, depletion of gut microbes causes suppression of autoimmune progression only in females. In agreement, microbiota depletion suppressed the pro-inflammatory cytokine response of gut mucosa in juvenile and adult females. Nevertheless, microbiota from females and males showed, upon cross-transfer, contrasting abilities to modulate disease progression. Furthermore, orchidectomy (castration) not only caused changes in the composition of gut microbiota, but also a modest acceleration of autoimmune progression. Overall, our work shows that microbiota-dependent pro-inflammatory immune response in the gut mucosa of females initiated at juvenile ages and androgen-dependent protection of males contribute to gender differences in the intestinal immune phenotype and systemic autoimmune progression.

Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities

The Oligo-Mouse-Microbiota (OMM¹²) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM¹² model has been established in several germ-free mouse facilities world-wide and is employed to address a growing variety of research questions related to infection biology, mucosal immunology, microbial ecology and host-microbiome metabolic cross-talk. The OMM¹² consists of 12 sequenced and publically available strains isolated from mice, representing five bacterial phyla that are naturally abundant in the murine gastrointestinal tract (Lagkouvardos et al., 2016). Under germ-free conditions, the OMM¹² colonizes mice stably over multiple generations. Here, we investigated whether stably colonized OMM¹² mouse lines could be reproducibly established in different animal facilities. Germ-free C57Bl/6J mice were inoculated with a frozen mixture of the OMM¹² strains. Within 2 weeks after application, the OMM¹² community reached the same stable composition in all facilities, as determined by fecal microbiome analysis. We show that a second application of the OMM¹² strains after 72 h leads to a more stable community composition than a single application. The availability of such protocols for reliable de novo generation of gnotobiotic rodents will certainly contribute to increasing experimental reproducibility in biomedical research.

Long-Term Potable Effects of Alkalescent Mineral Water on Intestinal Microbiota Shift and Physical Conditioning

Background

An alkalescent (pH 8.3) mineral water (AMW) of Hita basin, located in the northwestern part of Kyushu island in Japan, has been recognized for the unique quality of ingredients including highly concentrated silicic acid, sodium, potassium, and hydrogen carbonate. The biological effects of AMW intake were evaluated with a particular focus on its “antiobesity” properties through its modulation of the gut microbiota population.

Methods

Two groups of C57BL6/J mice (8-week-old male) were maintained with a standard diet and tap water (control: TWC group) or AMW (AMW group) for 6 months and the following outputs were quantitated: (1) food and water intake, (2) body weight (weekly), (3) body fat measurements by CT scan (monthly), (4) sera biochemical values (TG, ALT, AST, and ALP), and (5) UCP-1 mRNA in fat tissues (terminal point). Two groups of ICR mice (7-week-old male) were maintained with the same method and their feces were collected at the 0, 1st, 3rd, and 6th month at which time the population rates of gut microbiota were quantitated using metagenomic sequencing analysis of 16S-rRNA.

Results

Among all antiobesity testing items, even though a weekly dietary consumption was increased (p=0.012), both ratios of weight gain (p=1.21E − 10) and visceral fat accumulation (p=0.029) were significantly reduced in the AMW group. Other criteria including water intake (p=0.727), the amounts of total (p=0.1602), and subcutaneous fat accumulation (p=0.052) were within the margin of error and UCP-1 gene expression level (p=0.171) in the AMW group was 3.89-fold higher than that of TWC. Among 8 major gut bacteria families, Lactobacillaceae (increased, p=0.029) and Clostridiaceae (decreased, p=0.029) showed significant shift in the whole population.

Conclusion

We observed significantly reduced (1) weight gaining ratio (average −1.86%, up to −3.3%), (2) visceral fat accumulation ratio (average −4.30%, up to −9.1%), and (3) changes in gut microbiota population. All these consequences could support the “health benefit” functionality of AMW.

Gut Microbiota Influences Experimental Outcomes in Mouse Models of Colorectal Cancer

Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Mouse models are a valuable resource for use throughout the development and testing of new therapeutic strategies for CRC. Tumorigenesis and response to therapy in humans and mouse models alike are influenced by the microbial communities that colonize the gut. Differences in the composition of the gut microbiota can confound experimental findings and reduce the replicability and translatability of the resulting data. Despite this, the contribution of resident microbiota to preclinical tumor models is often underappreciated. This review does the following: (1) summarizes evidence that the gut microbiota influence CRC disease phenotypes; (2) outlines factors that can influence the composition of the gut microbiota; and (3) provides strategies that can be incorporated into the experimental design, to account for the influence of the microbiota on intestinal phenotypes in mouse models of CRC. Through careful experimental design and documentation, mouse models can continue to rapidly advance efforts to prevent and treat colon cancer.

Changes in motor behavior, neuropathology, and gut microbiota of a Batten disease mouse model following administration of acidified drinking water

CLN3 mutations cause the fatal neurodegenerative disorder, CLN3 Batten disease. The Cln3^−/− mouse model displays characteristic features of the human disease including motor deficits. When mice received acidified drinking water (pH 2.5–2.9) instead of normal tap water (pH 8.4) for several generations, the motor skills of Cln3^−/− mice normalized to control levels, indicating a disease-modifying effect of acidified water. Here we investigated if acidified water administered from postnatal day 21 has therapeutic benefits in Cln3^−/− mice. Indeed, acidified water temporarily attenuated the motor deficits, had beneficial effects on behavioral parameters and prevented microglial activation in the brain of Cln3^−/− mice. Interestingly, in control mice, acidified drinking water caused brain region-specific glial activation and significant changes in motor performance. Since the gut microbiota can influence neurological functions, we examined it in our disease model and found that the gut microbiota of Cln3^−/− mice was markedly different from control mice, and acidified water differentially changed the gut microbiota composition in these mice. These results indicate that acidified water may provide therapeutic benefit to CLN3 Batten disease patients, and that the pH of drinking water is a major environmental factor that strongly influences the results of murine behavioral and pathological studies.

Polysaccharide A-Dependent Opposing Effects of Mucosal and Systemic Exposures to Human Gut Commensal Bacteroides fragilis in Type 1 Diabetes

Bacteroides fragilis (BF) is an integral component of the human colonic commensal microbiota. BF is also the most commonly isolated organism from clinical cases of intra-abdominal abscesses, suggesting its potential to induce proinflammatory responses upon accessing the systemic compartment. Hence, we examined the impact of mucosal and systemic exposures to BF on type 1 diabetes (T1D) incidence in NOD mice. The impact of intestinal exposure to BF under a chemically induced enhanced gut permeability condition, which permits microbial translocation, in T1D was also examined. While oral administration of heat-killed (HK) BF to prediabetic mice caused enhanced immune regulation and suppression of autoimmunity, resulting in delayed hyperglycemia, mice that received HK BF by intravenous injection showed rapid disease progression. Importantly, polysaccharide A-deficient BF failed to produce these opposing effects upon oral and systemic deliveries. Furthermore, BF-induced modulation of disease progression was observed in wild-type, but not TLR2-deficient, NOD mice. Interestingly, oral administration of BF under enhanced gut permeability conditions resulted in accelerated disease progression and rapid onset of hyperglycemia in NOD mice. Overall, these observations suggest that BF-like gut commensals can cause proinflammatory responses upon gaining access to the systemic compartment and contribute to T1D in at-risk subjects.

Engineered Dendritic Cell-Directed Concurrent Activation of Multiple T cell Inhibitory Pathways Induces Robust Immune Tolerance

Inhibitory/repressor-receptors are upregulated significantly on activated T cells, and have been the molecules of attention as targets for inducing immune tolerance. Induction of effective antigen specific tolerance depends on concurrent engagement of the TCR and one or more of these inhibitory receptors. Here, we show, for the first time that dendritic cells (DCs) can be efficiently engineered to express multiple T cell inhibitory ligands, and enhanced engagement of T cell inhibitory receptors, upon antigen presentation, by these DCs can induce effective CD4+ T cell tolerance and suppress autoimmunity. Compared to control DCs, antigen presentation by DCs that ectopically express CTLA4, PD1 and BTLA selective ligands (B7.1wa, PD-L1, and HVEM-CRD1 respectively) individually (mono-ligand DCs) or in combination (multi-ligand DCs) causes an inhibition of CD4+ T cell proliferation and pro-inflammatory cytokine response, as well as increase in Foxp3+ Treg frequency and immune regulatory cytokine production. Administration of self-antigen (mouse thyroglobulin; mTg) loaded multi-ligand DCs caused hyporesponsiveness to mTg challenge, suppression of autoantibody production, and amelioration of experimental autoimmune thyroiditis. Overall, this study shows that engineered DC-directed enhanced concurrent activation of multiple T cell coinhibitory pathways is an effective way to induce self-antigen specific T cell tolerance to suppress ongoing autoimmunity.

High Thymic Output of Effector CD4+ Cells May Lead to a Treg : T Effector Imbalance in the Periphery in NOD Mice

Regulatory T cells (Tregs) play a critical role in controlling autoreactive T cells, and quantitative and/or qualitative deficiencies in Tregs are associated with autoimmune diseases, including type 1 diabetes (T1D), in both humans and mice. Both the incidence of T1D and percentages of peripheral Tregs in NOD mice vary considerably between animal facilities. In our animal facility, the incidence of T1D in NOD mice is high at 90-100% and the percentages of peripheral CD4⁺Foxp3⁺ cells in ~9-10-week-old female NOD mice are decreased compared to control (B6) mice shortly before high glucose is first detected (~12 weeks). These data suggest that there is an imbalance between Tregs and potentially pathogenic effector T cells at this age that could have significant impact on disease progression to overt diabetes. The goal of the current study was to investigate mechanisms that play a role in peripheral Treg : T effector cell balance in NOD mice, including differences in persistence/survival, peripheral homeostatic proliferation, and thymic production and output of CD4⁺ T cells. We found no differences in persistence/survival or homeostatic proliferation of either Tregs or effector T cells between NOD and B6 mice. Furthermore, although the percentages and absolute numbers of CD4⁺Foxp3⁺ cells in thymus were not decreased in NOD compared to B6 mice, the percentage of CD4⁺ recent thymic emigrants (RTE) that were Foxp3⁺ was significantly lower in 9-week-old NOD mice. Interestingly, the thymic output of CD4⁺Foxp3⁺ cells was not lower in NOD mice, whereas the thymic output of CD4⁺Foxp3⁻ cells was significantly higher in NOD mice at that age compared to B6 mice. These data suggest that the higher thymic output of CD4⁺Foxp3⁻ T cells contributes, at least in part, to the lower percentages of peripheral CD4⁺Foxp3⁺ Tregs in NOD mice and an imbalance between Tregs and T effector cells that may contribute to the development of full-blown diabetes.

Complex dietary polysaccharide modulates gut immune function and microbiota, and promotes protection from autoimmune diabetes

The dietary supplement and prebiotic values of β-glucan-rich products have been widely recognized and dietary approaches for modulating autoimmunity have been increasingly explored, we assess the impact of oral administration of high-purity yeast β-glucan (YBG) on gut immune function, microbiota and type 1 diabetes (T1D) using mouse models. Oral administration of this non-digestible complex polysaccharide caused a dectin-1-dependent immune response involving increased expression of interleukin-10 (IL-10), retinaldehyde dehydrogenase (Raldh) and pro-inflammatory cytokines in the gut mucosa. YBG-exposed intestinal dendritic cells induced/expanded primarily Foxp3⁺ , IL-10⁺ and IL-17⁺ T cells, ex vivo. Importantly, prolonged oral administration of low-dose YBG at pre-diabetic stage suppressed insulitis and significantly delayed the appearance of T1D in non-obese diabetic (NOD) mice. Further, prolonged treatment with YBG showed increased Foxp3⁺ T-cell frequencies, and a significant change in the gut microbiota, particularly an increase in the abundance of Bacteroidetes and a decrease in the Firmicute members. Oral administration of YBG, together with Raldh-substrate and β-cell antigen, resulted in better protection of NOD mice from T1D. These observations suggest that YBG not only has a prebiotic property, but also an oral tolerogenic-adjuvant-like effect, and these features could be exploited for modulating autoimmunity in T1D.

Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity

The role of microorganism in human diseases cannot be ignored. These microorganisms have evolved together with humans and worked together with body's mechanism to maintain immune and metabolic function. Emerging evidence shows that gut microbe and their metabolites open up new doors for the study of human response mechanism. The complexity and interdependence of these microbe-metabolite-host interactions are rapidly being elucidated. There are various changes of microbial levels in models or in patients of various autoimmune diseases (AIDs). In addition, the relevant metabolites involved in mechanism mainly include short-chain fatty acids (SCFAs), bile acids (BAs), and polysaccharide A (PSA). Meanwhile, the interaction between microbes and host genes is also a factor that must be considered. It has been demonstrated that human microbes are involved in the development of a variety of AIDs, including organ-specific AIDs and systemic AIDs. At the same time, microbes or related products can be used to remodel body's response to alleviate or cure diseases. This review summarizes the latest research of microbes and their related metabolites in AIDs. More importantly, it highlights novel and potential therapeutics, including fecal microbial transplantation, probiotics, prebiotics, and synbiotics. Nonetheless, exact mechanisms still remain elusive, and future research will focus on finding a specific strain that can act as a biomarker of an autoimmune disease.

Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers

Background: Association between oral bacteria and increased risk of lung cancer have been reported in several previous studies, however, the potential association between salivary microbiome and lung cancer in non-smoking women have not been evaluated. There is also no report on the relationship between immunocytochemistry markers and salivary microbiota.

Method: In this study, we assessed the salivary microbiome of 75 non-smoking female lung cancer patients and 172 matched healthy individuals using 16S rRNA gene amplicon sequencing. We also calculated the Spearman's rank correlation coefficient between salivary microbiota and three immunohistochemical markers (TTF-1, Napsin A and CK7).

Result: We analyzed the salivary microbiota of 247 subjects and found that non-smoking female lung cancer patients exhibited oral microbial dysbiosis. There was significantly lower microbial diversity and richness in lung cancer patients when compared to the control group (Shannon index, P < 0.01; Ace index, P < 0.0001). Based on the analysis of similarities, the composition of the microbiota in lung cancer patients also differed from that of the control group (r = 0.454, P < 0.001, unweighted UniFrac; r = 0.113, P < 0.01, weighted UniFrac). The bacterial genera Sphingomonas (P < 0.05) and Blastomonas (P < 0.0001) were relatively higher in non-smoking female lung cancer patients, whereas Acinetobacter (P < 0.001) and Streptococcus (P < 0.01) were higher in controls. Based on Spearman's correlation analysis, a significantly positive correlation can be observed between CK7 and Enterobacteriaceae (r = 0.223, P < 0.05). At the same time, Napsin A was positively associated with genera Blastomonas (r = 0.251, P < 0.05). TTF-1 exhibited a significantly positive correlation with Enterobacteriaceae (r = 0.262, P < 0.05). Functional analysis from inferred metagenomes indicated that oral microbiome in non-smoking female lung cancer patients were related to cancer pathways, p53 signaling pathway, apoptosis and tuberculosis.

Conclusions: The study identified distinct salivary microbiome profiles in non-smoking female lung cancer patients, revealed potential correlations between salivary microbiome and immunocytochemistry markers used in clinical diagnostics, and provided proof that salivary microbiota can be an informative source for discovering non-invasive lung cancer biomarkers.

H2Oh No! The importance of reporting your water source in your in vivo microbiome studies

Water is a fundamental part of any in vivo microbiome experiment however, it is also one of the most overlooked and underreported variables within the literature. Currently there is no established standard for drinking water quality set by the Canadian Council on Animal Care. Most water treatment methods focus on inhibiting bacterial growth within the water while prolonging the shelf-life of bottles once poured. When reviewing the literature, it is clear that some water treatment methods, such as water acidification, alter the gut microbiome of experimental animals resulting in dramatic differences in disease phenotype progression. Furthermore, The Jackson Lab, one of the world's leading animal vendors, provides acidified water to their in-house animals and is often cited in the literature as having a dramatically different gut microbiome than animals acquired from either Charles River or Taconic. While we recognize that it is impossible to standardize water across all animal facilities currently conducting microbiome research, we hope that by drawing attention to the issue in this commentary, researchers will consider water source as an experimental variable and report their own water sources to facilitate experimental reproducibility. Moreover, researchers should be cognisant of potential phenotypic differences observed between commercial animal vendors due to changes in the gut microbiome as a result of various sources of water used.

The effect of drinking water pH on the human gut microbiota and glucose regulation: results of a randomized controlled cross-over intervention

Studies in rodent models have shown that alterations in drinking water pH affect both the composition of the gut microbiota and host glucose regulation. To explore a potential impact of electrochemically reduced alkaline (pH ≈ 9) versus neutral (pH ≈ 7) drinking water (2 L/day) on human intestinal microbiota and host glucose metabolism we conducted a randomized, non-blinded, cross-over study (two 2-week intervention periods, separated by a 3-week wash-out) in 29 healthy, non-smoking Danish men, aged 18 to 35 years, with a body mass index between 20.0 to 27.0 kg m-2. Volunteers were ineligible if they had previously had abdominal surgery, had not been weight stabile for at least two months, had received antibiotic treatment within 2 months, or had a habitual consumption of caloric or artificially sweetened beverages in excess of 1 L/week or an average intake of alcohol in excess of 7 units/week. Microbial DNA was extracted from faecal samples collected at four time points, before and after each intervention, and subjected to 16S rRNA gene amplicon sequencing (Illumina MiSeq, V4 region). Glycaemic regulation was evaluated by means of an oral glucose tolerance test.No differential effect of alkaline versus neutral drinking water was observed for the primary outcome, overall gut microbiota diversity as represented by Shannon's index. Similarly, neither a differential effect on microbiota richness or community structure was observed. Nor did we observe a differential effect on the abundance of individual operational taxonomic units (OTUs) or genera. However, analyses of within period effects revealed a significant (false discovery rate ≤5%) increase in the relative abundance of 9 OTUs assigned to order Clostridiales, family Ruminococcaceae, genus Bacteroides, and species Prevotella copri, indicating a potential effect of quantitative or qualitative changes in habitual drinking habits. An increase in the concentration of plasma glucose at 30 minutes and the incremental area under the curve of plasma glucose from 0 30 and 0 120 minutes, respectively, was observed when comparing the alkaline to the neutral intervention. However, results did not withstand correction for multiplicity. In contrast to what has been reported in rodents, a change in drinking water pH had no impact on the composition of the gut microbiota or glucose regulation in young male adults. The study is registered at www.clinicaltrials.gov (NCT02917616).