99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: darwinian medicine and the 'hygiene' or 'old friends' hypothesis

Association of the live microbe intake from foods with all-cause and cardiovascular disease-specific mortality: a prospective cohort study

BACKGROUND

Live dietary microbes have been hypothesized to promoting human health. However, there has been lacking perceptions to crystallize nexus between consumption of foods with live microbes and mortality.

OBJECTIVE

To investigate the association of consumption of foods with medium to high amounts of live microbes with all-cause, cancer-specific, and cardiovascular disease (CVD)-specific mortality.

METHODS

The data were obtained from the National Health and Nutrition Examination Survey 1999-2018 at baseline linked to the 2019 National Death Index records. Based on consumption of foods that were categorized as either having medium or high microbial content (MedHi foods), participants were classified into three groups. Kaplan-Meier survival curves and multivariable Cox regression models were used to estimate the association of consumption of MedHi foods with mortality. Population-attributable fractions (PAFs) of consumption of MedHi foods in relation to mortality risk were also estimated.

RESULTS

A total of 35,299 adults aged ≥ 20 years were included in this study. During a median follow-up of 9.67 years, compared with adults in G1, those in G3 had 16% (hazard ratio [HR], 0.84; 95% confidence interval [CI], 0.77-0.90) reduced risk of all-cause mortality, and 23% (HR, 0.77; 95% CI, 0.67-0.89) reduced risk of CVD-specific mortality. The PAF of high (G3) vs. intermediate or low consumption of MedHi foods (G1 + G2) with all-cause and CVD-specific mortality was 3.4% and 4.3%, respectively.

CONCLUSIONS

Consumption of foods with higher microbial concentrations is associated with a reduced risk of all-cause and CVD-specific mortality in US adults.

The Early Appearance of Asthma and Its Relationship with Gut Microbiota: A Narrative Review

Asthma is, worldwide, the most frequent non-communicable disease affecting both children and adults, with high morbidity and relatively low mortality, compared to other chronic diseases. In recent decades, the prevalence of asthma has increased in the pediatric population, and, in general, the risk of developing asthma and asthma-like symptoms is higher in children during the first years of life. The "gut-lung axis" concept explains how the gut microbiota influences lung immune function, acting both directly, by stimulating the innate immune system, and indirectly, through the metabolites it generates. Thus, the process of intestinal microbial colonization of the newborn is crucial for his/her future health, and the alterations that might generate dysbiosis during the first 100 days of life are most influential in promoting hypersensitivity diseases. That is why this period is termed the "critical window". This paper reviews the published evidence on the numerous factors that can act by modifying the profile of the intestinal microbiota of the infant, thereby promoting or inhibiting the risk of asthma later in life. The following factors are specifically addressed in depth here: diet during pregnancy, maternal adherence to a Mediterranean diet, mode of delivery, exposure to antibiotics, and type of infant feeding during the first three months of life.

Lifestyle Changes and Industrialization in the Development of Allergic Diseases

PURPOSE OF REVIEW

Modernization and Westernization in industrialized and developing nations is associated with a substantial increase in chronic noncommunicable diseases. This transformation has far-reaching effects on lifestyles, impacting areas such as economics, politics, social life, and culture, all of which, in turn, have diverse influences on public health. Loss of contact with nature, alternations in the microbiota, processed food consumption, exposure to environmental pollutants including chemicals, increased stress and decreased physical activity jointly result in increases in the frequency of inflammatory disorders including allergies and many autoimmune and neuropsychiatric diseases. This review aims to investigate the relationship between Western lifestyle and inflammatory disorders.

RECENT FINDINGS

Several hypotheses have been put forth trying to explain the observed increases in these diseases, such as 'Hygiene Hypothesis', 'Old Friends', and 'Biodiversity and Dysbiosis'. The recently introduced 'Epithelial Barrier Theory' incorporates these former hypotheses and suggests that toxic substances in cleaning agents, laundry and dishwasher detergents, shampoos, toothpastes, as well as microplastic, packaged food and air pollution damage the epithelium of our skin, lungs and gastrointestinal system. Epithelial barrier disruption leads to decreased biodiversity of the microbiome and the development of opportunistic pathogen colonization, which upon interaction with the immune system, initiates local and systemic inflammation. Gaining a deeper comprehension of the interplay between the environment, microbiome and the immune system provides the data to assist with legally regulating the usage of toxic substances, to enable nontoxic alternatives and to mitigate these environmental challenges essential for fostering a harmonious and healthy global environment.

Association of dietary live microbe intake with diabetic kidney disease in patients with type 2 diabetes mellitus in US adults: a cross-sectional study of NHANES 1999-2018

AIMS

Several studies have reported dietary microorganisms' beneficial effects on human health. We aimed to detect the potential association between dietary live microbe intake and diabetic kidney disease (DKD) in patients with type 2 diabetes mellitus (T2DM) through a cross-sectional analysis of the National Health and Nutrition Examination Survey from 1999 to 2018.

METHODS

According to the Sanders classification system of dietary live microbes, the study participants were divided into three groups: low, medium, and high live microbe groups. In patients with T2DM, DKD was assessed by glomerular filtration rate (< 60 mL/min/1.73 m2 using the Chronic Kidney Disease Epidemiology Collaboration algorithm), proteinuria (urinary albumin to creatinine ratio ≥ 30 mg/g), or both. Weighted univariate and multivariate logistic regression and subgroup analyses were conducted to investigate the independent association between dietary live microbe and DKD.

RESULTS

The study included 3836 participants, of whom 1467 (38.24%) had DKD for the diagnosis. Our study demonstrated that participants in the high dietary live microbe group were more likely to be older, female, non-Hispanic White, have higher education levels, have a lower prevalence of smoking, have a high poverty-income ratio, have higher energy intake, lower haemoglobin (HbA1c) and serum creatinine levels, and lower risk of progression. After adjustment for covariates, patients in the high dietary live microbe group had a low prevalence of DKD, whereas no significant association with DKD was found between the medium and low dietary live microbe groups. No statistically significant interaction was observed in all subgroup analyses except for HbA1c (p for interaction < 0.05).

CONCLUSIONS

Our results indicate that high dietary live microbe intake was associated with a low DKD prevalence.

Integrating microbiome science and evolutionary medicine into animal health and conservation

Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.

How tapeworms interact with cancers: a mini-review

Cancer is one of the leading causes of death, with an estimated 19.3 million new cases and 10 million deaths worldwide in 2020 alone. Approximately 2.2 million cancer cases are attributed to infectious diseases, according to the World Health Organization (WHO). Despite the apparent involvement of some parasitic helminths (especially trematodes) in cancer induction, there are also records of the potential suppressive effects of helminth infections on cancer. Tapeworms such as Echinococcus granulosus, Taenia crassiceps, and more seem to have the potential to suppress malignant cell development, although in a few cases the evidence might be contradictory. Our review aims to summarize known epidemiological data on the cancer-helminth co-occurrence in the human population and the interactions of tapeworms with cancers, i.e., proven or hypothetical effects of tapeworms and their products on cancer cells in vivo (i.e., in experimental animals) or in vitro. The prospect of bioactive tapeworm molecules helping reduce the growth and metastasis of cancer is within the realm of future possibility, although extensive research is yet required due to certain concerns.

Association Between Live Microbe Intake and NAFLD: Evidence From NHANES 2003-2018

OBJECTIVE

This study aimed to shed light on the potential relationship between live microbe intake and nonalcoholic fatty liver disease (NAFLD).

METHOD

By using a cross-sectional study design, the researchers were able to investigate the possible causal association between the two variables in a rigorous and systematic manner.

RESULTS

Our study investigated the correlation between the intake of live microbe-containing foods and NAFLD in a representative sample of adults. The study found that the intake of live microbe-containing foods was associated with lower blood pressure, plasma glucose, NAFLD, body mass index, glycated hemoglobin, alanine aminotransferase, aspartate aminotransferase, gamma-glutamyl transpeptidase, and low-density lipoprotein cholesterol, as well as higher high-density lipoprotein cholesterol levels (p < 0.05). In univariate logistic regression, high dietary live microbe intake was associated with lower NAFLD prevalence than low intake (OR = 0.830; 95% CI, 0.759 to 0.908; p < 0.001). After adjusting for multiple variables, the same conclusion was supported (p < 0.05). In subgroup analyses, there was a significant difference in the race and smoking groups, with p for interaction of 0.01 and 0.02, respectively. This study's findings serve to augment the existing body of evidence linking live microbes with favorable health outcomes.

CONCLUSIONS

Our study revealed a robust correlation between dietary intake of live microbes and the prevalence of NAFLD in a cross-sectional analysis. Our findings offer a novel perspective on NAFLD research, highlighting the potential of targeted modulation of specific bacterial taxa, including the promotion of beneficial bacteria and suppression of harmful ones, as a promising strategy for preventing and treating NAFLD.

Association between dietary live microbe intake and Life's Essential 8 in US adults: a cross-sectional study of NHANES 2005-2018

Background

Assessing the impact of dietary live microbe intake on health outcomes has gained increasing interest. This study aimed to elucidate the relationship between dietary live microbe intake and Life's Essential 8 (LE8) scores, a metric for cardiovascular health (CVH), in the U.S. adult population.

Methods

We analyzed data from 10,531 adult participants of the National Health and Nutrition Examination Survey (NHANES) spanning 2005-2018. Participants were stratified into low, medium, and high intake groups of dietary live microbe based on Marco's classification system. We employed weighted logistic and linear regression analyses, along with subgroup, interaction effect, and sensitivity analyses. Additionally, Restricted Cubic Splines (RCS) were used to explore the dose-response relationship between food intake and CVH in different groups.

Results

Compared to the low live microbe intake group, the medium and high live microbe intake groups had significantly higher LE8, with β coefficients of 2.75 (95% CI: 3.89-5.65) and 3.89 (95% CI: 6.05-8.11) respectively. Additionally, moderate and high groups significantly reduced the risk of high cardiovascular health risk, defined as an LE8 score below 50, with odds ratios (OR) of 0.73 and 0.65 respectively. Subgroup analysis and sensitivity analysis proved the stability of the results. In the low intake group, food intake shows a linear negative correlation with LE8, whereas in the high intake group, it exhibits a linear positive correlation. In contrast, in the moderate live microbe intake group, the relationship between food intake and LE8 presents a distinct inverted "U" shape.

Conclusion

This study highlights the potential benefits of medium to high dietary intake of live microbe in improving LE8 scores and CVH in adults. These findings advocate for the inclusion of live microbes in dietary recommendations, suggesting their key role in CVH enhancement.

Exploratory analysis on the relationship between dietary live microbe intake and arthritis: a national population based cross-sectional study

Objective

The pathogenesis of arthritis such as rheumatoid arthritis (RA) and osteoarthritis (OA) remains unclear. This study aims to investigate whether the intake of live dietary microbes can be used as an auxiliary means for the treatment of arthritis.

Methods

Data used in the present research were originated from the US National Health and Nutrition Examination Survey (NHANES) from 2003-2018. Participants involved in the present study were categorized into three groups based on the dietary live microbe classification system, namely low, medium, and high dietary live microbe groups. The analyses utilized weighted univariate and multivariate logistic regression. The restricted cubic spline plot was used to explore the relationship between the high dietary live microbe group and the odds of arthritis.

Results

12,844 participants were included in the present study. The intake of high live dietary microbes in RA group was lower than that in healthy control group and OA group. The proportion of RA patients in the high live dietary microbe group was lower than that in the low and medium live dietary microbe group. Following the comprehensive adjustment for covariates, it was observed that participants in both the high and medium dietary live microbe groups exhibited lower odds of RA compared to those in the low dietary live microbe group (High OR: 0.71, 95% CI: 0.53-0.96; Medium OR: 0.77, 95% CI: 0.59-1.00, p = 0.02). A restricted cubic spline plot indicates a negative correlation between the quantity of dietary live microbes and the occurrence of RA within the high dietary live microbe group.

Conclusion

The results of our study revealed a significant difference in dietary live microbe intake between healthy and RA patients. Higher dietary intake was correlated with a decreased odds of RA. However, no significant association was found between the occurrence of OA and the quantity of dietary live microbes.

Opioid trail: Tracking contributions to opioid use disorder from host genetics to the gut microbiome

Opioid use disorder (OUD) is a worldwide public health crisis with few effective treatment options. Traditional genetics and neuroscience approaches have provided knowledge about biological mechanisms that contribute to OUD-related phenotypes, but the complexity and magnitude of effects in the brain and body remain poorly understood. The gut-brain axis has emerged as a promising target for future therapeutics for several psychiatric conditions, so characterizing the relationship between host genetics and the gut microbiome in the context of OUD will be essential for development of novel treatments. In this review, we describe evidence that interactions between host genetics, the gut microbiome, and immune signaling likely play a key role in mediating opioid-related phenotypes. Studies in humans and model organisms consistently demonstrated that genetic background is a major determinant of gut microbiome composition. Furthermore, the gut microbiome is susceptible to environmental influences such as opioid exposure. Additional work focused on gene by microbiome interactions will be necessary to gain improved understanding of their effects on OUD-related behaviors.

Revisiting geophagy: An evolved sickness behavior to microbiome-mediated gastrointestinal inflammation

Geophagy, the consumption of clay or similar substances, is known as an evolved behavior that protects vulnerable populations, such as pregnant women and children, against gastrointestinal injury. However, perplexing questions remain, like the presence of geophagy in the absence of overt gastrointestinal infection and the potential causal relationship between geophagy and iron deficiency anemia. In this review, we hypothesize that geophagy is an inflammation-mediated sickness behavior regulated via the vagus nerve. We further hypothesize that the gut microbiome plays a critical role in mediating the relationship between inflammation and geophagy. By including inflammation and the microbiome within the existing protection hypothesis, we can explain how subclinical gastrointestinal states induce geophagy. Furthermore, we can explain how gastrointestinal inflammation is responsible for both geophagy and iron-deficiency anemia, explaining why the two phenomena frequently co-occur. Ultimately, defining geophagy as a sickness behavior allows us to integrate the gut-brain axis into geophagy research.

Applying an evolutionary mismatch framework to understand disease susceptibility

Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.

Immunologic, genetic, and ecological interplay of factors involved in allergic diseases

An allergic or type I hypersensitivity reaction involves a misdirected immune overreaction to innocuous environmental and dietary antigens called allergens. The genetic predisposition to allergic disease, referred to as atopy, can be expressed as a variety of manifestations-e.g., allergic rhinitis, allergic conjunctivitis, atopic dermatitis, allergic asthma, anaphylaxis. Globally, allergic diseases are one the most common types of chronic conditions. Several factors have been identified to contribute to the pathogenesis and progression of the disease, leading to distinctively variable clinical symptoms. The factors which can attenuate or exacerbate allergic reactions can range from genetic heterozygosity, the prominence of various comorbid infections, and other factors such as pollution, climate, and interactions with other organisms and organism-derived products, and the surrounding environment. As a result, the effective prevention and control of allergies remains to be one of the most prominent public health problems. Therefore, to contextualize the current knowledge about allergic reactions, this review paper attempts to synthesize different aspects of an allergic response to describe its significance in the global health scheme. Specifically, the review shall characterize the biomolecular mechanisms of the pathophysiology of the disease based on underlying disease theories and current findings on ecologic interactions and describe prevention and control strategies being utilized. An integrated perspective that considers the underlying genetic, immunologic, and ecologic aspects of the disease would enable the development of more effective and targeted diagnostic tools and therapeutic strategies for the management and control of allergic diseases.

How do parasitic worms prevent diabetes? An exploration of their influence on macrophage and β-cell crosstalk

Diabetes is the fastest growing chronic disease globally, with prevalence increasing at a faster rate than heart disease and cancer. While the disease presents clinically as chronic hyperglycaemia, two distinct subtypes have been recognised. Type 1 diabetes (T1D) is characterised as an autoimmune disease in which the insulin-producing pancreatic β-cells are destroyed, and type 2 diabetes (T2D) arises due to metabolic insufficiency, in which inadequate amounts of insulin are produced, and/or the actions of insulin are diminished. It is now apparent that pro-inflammatory responses cause a loss of functional β-cell mass, and this is the common underlying mechanism of both T1D and T2D. Macrophages are the central immune cells in the pathogenesis of both diseases and play a major role in the initiation and perpetuation of the proinflammatory responses that compromise β-cell function. Furthermore, it is the crosstalk between macrophages and β-cells that orchestrates the inflammatory response and ensuing β-cell dysfunction/destruction. Conversely, this crosstalk can induce immune tolerance and preservation of β-cell mass and function. Thus, specifically targeting the intercellular communication between macrophages and β-cells offers a unique strategy to prevent/halt the islet inflammatory events underpinning T1D and T2D. Due to their potent ability to regulate mammalian immune responses, parasitic worms (helminths), and their excretory/secretory products, have been examined for their potential as therapeutic agents for both T1D and T2D. This research has yielded positive results in disease prevention, both clinically and in animal models. However, the focus of research has been on the modulation of immune cells and their effectors. This approach has ignored the direct effects of helminths and their products on β-cells, and the modulation of signal exchange between macrophages and β-cells. This review explores how the alterations to macrophages induced by helminths, and their products, influence the crosstalk with β-cells to promote their function and survival. In addition, the evidence that parasite-derived products interact directly with endocrine cells to influence their communication with macrophages to prevent β-cell death and enhance function is discussed. This new paradigm of two-way metabolic conversations between endocrine cells and macrophages opens new avenues for the treatment of immune-mediated metabolic disease.

The Role of the Microbiome in the Pathogenesis and Treatment of Asthma

The role of the microbiome in the pathogenesis and treatment of asthma is significant. The purpose of this article is to show the interplay between asthma and the microbiome, and main areas that require further research are also highlighted. The literature search was conducted using the PubMed database. After a screening process of studies published before May 2023, a total of 128 articles were selected in our paper. The pre-treatment bronchial microbiome in asthmatic patients plays a role in their responsiveness to treatment. Gut microbiota and its dysbiosis can contribute to immune system modulation and the development of asthma. The association between the microbiome and asthma is complex. Further research is necessary to clarify which factors might moderate that relationship. An appropriate gut microbiome and its intestinal metabolites are a protective factor for asthma development. Prebiotics and certain dietary strategies may have a prophylactic or therapeutic effect, but more research is needed to establish final conclusions. Although the evidence regarding probiotics is ambiguous, and most meta-analyses do not support the use of probiotic intake to reduce asthma, several of the most recent studies have provided promising effects. Further studies should focus on the investigation of specific strains and the examination of their mechanistic and genetic aspects.

Fermented Vegetables as a Potential Treatment for Irritable Bowel Syndrome

Foods and supplements containing microorganisms with expected beneficial effects are increasingly investigated and utilized in the treatment of human illness, including irritable bowel syndrome (IBS). Research points to a prominent role of gut dysbiosis in the multiple aberrations in gastrointestinal function, immune balance, and mental health seen in IBS. The proposition of the current Perspective is that fermented vegetable foods, in combination with a healthy and stable diet, may be particularly useful for addressing these disturbances. This is based on the recognition that plants and their associated microorganisms have contributed to shaping human microbiota and adaptation over evolutionary time. In particular, lactic acid bacteria with immunomodulatory, antipathogenic, and digestive properties are prevalent in products such as sauerkraut and kimchi. Additionally, by adjusting the salt content and fermentation time, products with a microbial and therapeutic potential beyond that of regular ferments could potentially be produced. Although more clinical data are required to make firm assertions, the low-risk profile, combined with biological considerations and reasoning and considerable circumstantial and anecdotal evidence, indicate that fermented vegetables are worthy of consideration by health professionals and patients dealing with IBS-related issues. To maximize microbial diversity and limit the risk of adverse effects, small doses of multiple products, containing different combinations of traditionally fermented vegetables and/or fruits, is suggested for experimental research and care.

Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu, Philippines

OBJECTIVES

The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members.

MATERIALS AND METHODS

As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition.

RESULTS

Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables.

CONCLUSIONS

Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.

Allergic sensitization to foods in India and other Low-Middle-income countries

Food allergy is an important cause of morbidity, significantly affecting the quality of life of the sufferer. Most food allergy research has been undertaken in high-income countries. Here, we summarize literature regarding food allergy in India and other low-middle-income countries (LMIC). We provide summaries of self-reported adverse food reactions and food sensitization in these regions by reviewing published community-based studies of prevalence, burden, and risk factors. We identified 2 community-based studies of food allergy prevalence in Karnataka, India, which estimate that food allergy affects just 0.14% of children and 1.2% of adults. The overall prevalence of allergic sensitization to 'any' food was 26.5% in adults and 19.1% in children by serum-specific IgE; but only 4.48% in children by skin prick test. We identified a further 28 studies in other LMICs, mainly from China but also Turkey, South Africa, Ghana, Mexico, Brazil, Thailand, Philippines, and Korea. The overall prevalence of allergic sensitization to 'any' food ranged from 0.11% to 16.8% in children using serum-specific IgE and 0.14% to 9.6% in children by skin prick test. The questionnaires and skin prick testing materials used and number of allergens tested varied significantly between studies. Other than Karnataka, there is no information on prevalence of food sensitization and probable food allergy in the community in India. Similar lack of information is noted among the majority of the 136 LMICs. Where community-based studies have been undertaken, there is wide variation in the prevalence and patterns of food sensitization across different LMICs, at least partly due to variations in study methodology. International collaboration is required in order to formally assess food allergy prevalence and burden across representative samples from multiple LMICs.

Evolutionary mismatch and the role of GxE interactions in human disease

Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases that were rare throughout human history but are now common. A key idea from anthropology and evolutionary biology-the evolutionary mismatch hypothesis-seeks to explain this phenomenon. It posits that humans evolved in environments that radically differ from the ones experienced by most people today, and thus traits that were advantageous in past environments may now be "mismatched" and disease-causing. This hypothesis is, at its core, a genetic one: it predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions and have differential health effects in ancestral versus modern environments. Here, we discuss how this concept could be leveraged to uncover the genetic architecture of NCDs in a principled way. Specifically, we advocate for partnering with small-scale, subsistence-level groups that are currently transitioning from environments that are arguably more "matched" with their recent evolutionary history to those that are more "mismatched". These populations provide diverse genetic backgrounds as well as the needed levels and types of environmental variation necessary for mapping GxE interactions in an explicit mismatch framework. Such work would make important contributions to our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and sociocultural contexts.

Explanatory integration and integrated explanations in Darwinian medicine and evolutionary medicine

Recently, two research traditions that bring together evolutionary biology and medicine, that is to say, Darwinian medicine and evolutionary medicine, have been identified. In this paper, I analyse these two research traditions with respect to explanatory and interdisciplinary integration. My analysis shows that Darwinian medicine does not integrate medicine and evolutionary biology in any strong sense but does incorporate evolutionary concepts into medicine. I also show that backward-looking explanations in Darwinian medicine are not integrated proximate-and-ultimate explanations but functional explanations that include reference to evolutionary concepts. Nevertheless, explanations in Darwinian medicine have heuristic roles as they potentially contribute to conceptual change and tie pieces of knowledge from different fields of medical research together. I argue that Darwinian medicine is an "interfield" that fosters cross-disciplinary exchange between evolutionary biologists and medical researchers and practitioners based on division of labour and separation, rather than unity. Research in evolutionary medicine, on the other hand, happens at the intersection of evolutionary biology and medicine where the two disciplines are already integrated and is designed to produce entangled proximate-evolutionary explanations. My analysis thus adds another important aspect to the philosophical discussion on the distinction between Darwinian medicine and evolutionary medicine.

The helminth derived peptide FhHDM-1 redirects macrophage metabolism towards glutaminolysis to regulate the pro-inflammatory response

We have previously identified an immune modulating peptide, termed FhHDM-1, within the secretions of the liver fluke, Fasciola hepatica, which is sufficiently potent to prevent the progression of type 1 diabetes and multiple sclerosis in murine models of disease. Here, we have determined that the FhHDM-1 peptide regulates inflammation by reprogramming macrophage metabolism. Specifically, FhHDM-1 switched macrophage metabolism to a dependence on oxidative phosphorylation fuelled by fatty acids and supported by the induction of glutaminolysis. The catabolism of glutamine also resulted in an accumulation of alpha ketoglutarate (α-KG). These changes in metabolic activity were associated with a concomitant reduction in glycolytic flux, and the subsequent decrease in TNF and IL-6 production at the protein level. Interestingly, FhHDM-1 treated macrophages did not express the characteristic genes of an M2 phenotype, thereby indicating the specific regulation of inflammation, as opposed to the induction of an anti-inflammatory phenotype per se. Use of an inactive derivative of FhHDM-1, which did not modulate macrophage responses, revealed that the regulation of immune responses was dependent on the ability of FhHDM-1 to modulate lysosomal pH. These results identify a novel functional association between the lysosome and mitochondrial metabolism in macrophages, and further highlight the significant therapeutic potential of FhHDM-1 to prevent inflammation.

Asthma, obesity, and microbiota: A complex immunological interaction

Obesity and allergic asthma are inflammatory chronic diseases mediated by distinct immunological features, obesity presents a Th1/Th17 profile, asthma is commonly associated with Th2 response. However, when combined, they result in more severe asthma symptoms, greater frequency of exacerbation episodes, and lower therapy responsiveness. These features lead to decreased life quality, associated with higher morbidity/mortality rates.  In addition, obesity prompts specific asthma phenotypes, which can be dependent on atopic status, age, and gender. In adults, obesity is associated with neutrophilic/Th17 profile, while in children, the outcome is diverse, in some cases children with obesity present aggravation of atopy, and Th2 inflammation, and in others an association with a Th1 profile, with reduced IgE levels and eosinophilia. These alterations occur due to a complex group of factors among which the microbiome has been recently explored. Particularly, evidence shows its important role in susceptibility or resistance to asthma development, via gut-lung-axis, and demonstrates its relevance to the immune pathogenesis of the syndrome. Few studies address the relevance of the lung microbiome in shaping the immune response, locally. However, specific bacteria, like Moraxella catarrhalis, Haemophilus influenza, and Streptococcus pneumoniae, correlate with important features of the obese-asthmatic phenotype. Although maternal obesity is known to increase asthma risk in offspring, the impact on lung colonization is unknown. This review details the main key immune mechanisms involved in obesity-aggravated asthma, featuring the effect of maternal obesity in the establishment of gut and lung microbiota of the offspring, acting as potential childhood asthma inducer.

The hygiene hypothesis for allergy - conception and evolution

In 1989, a short paper entitled "Hay fever, hygiene and household size" observed that British children from larger families were less likely to develop hay fever and suggested that this could be because early exposure to infection prevents allergy. This sibship size association for hay fever, since replicated many times in Britain and other affluent countries and confirmed by objective measures of atopy, prompted what has come to be known as the "hygiene hypothesis for allergy", although that term was not specifically used in the 1989 paper. The present paper reviews the historical roots of the "hygiene hypothesis" and charts its development over more than 30 years. Initial scepticism among immunologists turned to enthusiasm in the mid-1990s as the Th1/Th2 paradigm for allergic sensitisation emerged from animal experiments and the concept of "immunological old friends" became popular from the early 2000s. From the late 1990s, observations of reduced allergy risk among children of anthroposophic families and those brought up on farms suggested that the sibship size effects formed part of a broader range of "hygiene-related" determinants of allergy. Children from large families with farming exposure have approximately sixfold reduction in prevalence of hay fever, indicating the potential strength and epidemiological importance of these environmental determinants. During the 21st century, a wide range of specific microbial, environmental and lifestyle factors have been investigated as possible underlying mechanisms, but sadly none have emerged as robust explanations for the family size and farming effects. Thus, while the "hygiene hypothesis" led to a fundamental reappraisal of our relationship with our microbial environment and to the concept that early exposure, rather than avoidance, is beneficial for developing a healthy immune system, the underlying mechanism for variations in allergy prevalence with family size remains, in Churchillian terms, "a riddle wrapped in a mystery inside an enigma".

Association of Dietary Live Microbe Intake with Cardiovascular Disease in US Adults: A Cross-Sectional Study of NHANES 2007-2018

Objective: To detect the potential association between dietary live microbe and cardiovascular diseases (CVD). Methods: Data of 10,875 participants aged 18 years or older in this study were collected from the National Health and Nutrition Examination Survey (NHANES). Participants in this study were divided into three groups according to the Sanders dietary live microbe classification system: low, medium, and high dietary live microbe groups. CVD was defined by a combination of self-reported physician diagnoses and standardized medical status questionnaires. The analyses utilized weighted logistic regression models. Results: After the full adjustment for confounders, patients in the medium dietary live microbe group had a low prevalence of CVD in contrast to those in the low dietary live microbe group (OR: 0.78, 95% CI: 0.52−0.99, and p < 0.05), but no significant association with CVD was detected between the high and low dietary live microbe groups. Higher dietary live microbe groups were negatively associated with the prevalence of stroke (p for trend = 0.01) and heart attack (p for trend = 0.01). People who were male were more likely to suffer stroke due to low dietary live microbe (p for interaction = 0.03). Conclusion: A high dietary live microbe intake was associated with a low prevalence of CVD, and the significant association was detected when the analysis was limited to stroke and heart attack.

BCG Vaccine-The Road Not Taken

The Bacillus Calmette-Guérin (BCG) vaccine has been used for over one hundred years to protect against the most lethal infectious agent in human history, tuberculosis. Over four billion BCG doses have been given and, worldwide, most newborns receive BCG. A few countries, including the United States, did not adopt the WHO recommendation for routine use of BCG. Moreover, within the past several decades, most of Western Europe and Australia, having originally employed routine BCG, have discontinued its use. This review article articulates the impacts of those decisions. The suggested consequences include increased tuberculosis, increased infections caused by non-tuberculous mycobacteria (NTM), increased autoimmune disease (autoimmune diabetes and multiple sclerosis) and increased neurodegenerative disease (Parkinson's disease and Alzheimer's disease). This review also offers an emerged zoonotic pathogen, Mycobacteriumavium ss. paratuberculosis (MAP), as a mostly unrecognized NTM that may have a causal role in some, if not all, of these diseases. Current clinical trials with BCG for varied infectious, autoimmune and neurodegenerative diseases have brought this century-old vaccine to the fore due to its presumed immuno-modulating capacity. With its historic success and strong safety profile, the new and novel applications for BCG may lead to its universal use-putting the Western World back onto the road not taken.

A Classification System for Defining and Estimating Dietary Intake of Live Microbes in US Adults and Children

BACKGROUND

Consuming live microbes in foods may benefit human health. Live microbe estimates have not previously been associated with individual foods in dietary databases.

OBJECTIVES

We aimed to estimate intake of live microbes in US children (aged 2-18 y) and adults (≥19 y) (n = 74,466; 51.2% female).

METHODS

Using cross-sectional data from the NHANES (2001-2018), experts assigned foods an estimated level of live microbes per gram [low (Lo), <104 CFU/g; medium (Med), 104-107 CFU/g; or high (Hi), >107 CFU/g]. Probiotic dietary supplements were also assessed. The mean intake of each live microbe category and the percentages of subjects who ate from each live microbe category were determined. Nutrients from foods with live microbes were also determined using the population ratio method. Because the Hi category comprised primarily fermented dairy foods, we also looked at aggregated data for Med or Hi (MedHi), which included an expanded range of live microbe-containing foods, including fruits and vegetables.

RESULTS

Our analysis showed that 52%, 20%, and 59% of children/adolescents, and 61%, 26%, and 67% of adults, consumed Med, Hi, or MedHi foods, respectively. Per capita intake of Med, Hi, and MedHi foods was 69, 16, and 85 g/d for children/adolescents, and 106, 21, and 127 g/d for adults, respectively. The proportion of subjects who consumed live microbes and overall per capita intake increased significantly over the 9 cycles/18-y study period (0.9-3.1 g/d per cycle in children across categories and 1.4 g/d per cycle in adults for the Med category).

CONCLUSIONS

This study indicated that children, adolescents, and adults in the United States steadily increased their consumption of foods with live microbes between the earliest (2001-2002) and latest (2017-2018) survey cycles. Additional research is needed to determine the relations between exposure to live microbes in foods and specific health outcomes or biomarkers.

Bacillus Calmette-Guérin in Immuno-Regulation of Alzheimer's Disease

Bacillus Calmette-Guérin is frequently the treatment of choice of superficial bladder cancer. Exposing the urinary bladder of elderly patients with bladder cancer to the BCG vaccine reduced the risk of Alzheimer's disease (AD) substantially. Vaccines against other infectious microorganisms by other vaccination methods showed a similar but a lesser effect. This suggests that immune effects on AD are antigenically non-specific, likely being a metabolic result of immune system activation, similar to that shown for Juvenile diabetes. In this mini review we point to the benefit of BCG vaccine. We then briefly highlight the pathological involvement of the immune system in the AD both, in the peripheral and the central (brain) compartments. Given the uncertain prophylactic mechanism of the BCG effect against AD we propose to take advantage of the therapeutically planned bladder exposure to BCG. Based on pathological aggregation of wrongly cleaved amyloid precursor protein (APP) resistant to the unfolded protein response (UPR) which results in amyloid beta plaques we predict that BCG may impact the UPR signaling cascade. In addition pathways of innate immunity training concerned with energy metabolism, predict capability of activated immune cells to substitute deranged astrocytes that fail to support neuronal energy metabolism. This mini review points to ways through which immune cells can mediate between BCG vaccination and AD to support the wellness of the central nervous system.

Perspective: Darwinian Applications to Nutrition-The Value of Evolutionary Insights to Teachers and Students

Evolutionary biology informs us that the living world is a product of evolution, guided by the Darwinian mechanism of natural selection. This recognition has been fruitfully employed in a number of issues in health and nutrition sciences; however, it has not been incorporated into education. Nutrition and dietetics students generally learn very little or nothing on the subject of evolution, despite the fact that evolution is the process by which our genetically determined physiological traits and needs were shaped. In the present Perspective article, 3 examples of topics (inflammatory diseases, nutrition transition, and food intolerance) that can benefit from evolutionary information and reasoning are given, with relevant lines of research and inquiry provided throughout. It is argued that the application of evolutionary science to these and other areas of nutrition education can facilitate a deeper and more coherent teaching and learning experience. By recognizing and reframing nutrition as an aspect and discipline of biology, grounded in the fundamental principle of adaptation, revelatory light is shed on physiological states and responses, contentious and unresolved issues, genomic, epigenomic, and microbiomic features, and optimal nutrient status and intakes.

Epigenetic Differences in Long Non-coding RNA Expression in Finnish and Russian Karelia Teenagers With Contrasting Risk of Allergy and Asthma

Background

Previously, we investigated skin microbiota and blood cell gene expression in Finnish and Russian teenagers with contrasting incidence of allergic conditions. The microbiota and transcriptomic signatures were distinctly different, with high Acinetobacter abundance and suppression of genes regulating innate immune response in healthy subjects.

Objective

Here, we investigated long non-coding RNA (lncRNA) expression profiles of blood mononuclear cells (PBMC) from healthy and allergic subjects, to identify lncRNAs that act at the interphase of microbiome-mediated immune homeostasis in allergy/asthma.

Methods

Genome-wide co-expression network analyses of blood cell lncRNA/mRNA expression was integrated with skin microbiota profiles of Finnish (69) and Russian (75) subjects. Selected lncRNAs were validated by stimulation of cohort-derived PBMCs and a macrophage cell model with birch pollen allergen (Betv1) or lipopolysaccharide, respectively.

Results

Finnish and Russian PBMCs were differentiated by 3,818 lncRNA transcripts. In the Finnish subjects with high prevalence of allergy and asthma, a subset of 37 downregulated lncRNAs (including, FAM155A-IT1 and LOC400958) were identified. They were part of a co-expression network with 20 genes known to be related to asthma and allergic rhinitis (R > 0.95). Incidentally, all these 20 genes were also components of pathways corresponding to cellular response to bacterium. The Finnish and Russian samples were also differentiated by the abundance of 176 bacterial OTU (operational taxonomic units). The subset of 37 lncRNAs, associated with allergy, was most correlated with the abundance of Acinetobacter (R > +0.5), Jeotgalicoccus (R > +0.5), Corynebacterium (R < −0.5) and Micrococcus (R < −0.5).

Conclusion

In Finnish and Russian teenagers with contrasting allergy and asthma prevalence, epigenetic differences in lncRNA expression appear to be important components of the underlying microbiota-immune interactions. Unraveling the functions of the 37 differing lncRNAs may be the key to understanding microbiome-immune crosstalk, and to develop clinically relevant biomarkers.

Fecal and soil microbiota composition of gardening and non-gardening families

Historically, humans have interacted with soils, which contain a rich source of microorganisms. Fruit and vegetable gardening is the primary interaction humans have with soil today. Animal research reveals that soil microorganisms can be transferred to the rodent intestine. However, studies on fecal and soil microbial changes associated with gardening in humans are lacking. The current case-controlled cohort study aimed to characterize the fecal and soil microbiota of gardening families (n = 10) and non-gardening (control) families (n = 9). Families included two adults and one child (5-18 years) for a total of 56 participants. All participants provided a fecal sample, soil sample, and diet history questionnaires before the gardening season (April) and during the peak of the gardening season (August). Healthy Eating Index (HEI-2015) scores and nutrient analysis were performed. Fecal and soil DNA were extracted and amplified. Sequence data were then processed and analyzed. Peak season gardening families tended to have greater fecal operational features, a greater Faith's Phylogenetic Diversity score, greater fiber intake, and higher abundances of fiber fermenting bacteria than peak control families. Soil endemic microbes were also shared with gardening participant's fecal samples. This study revealed that the fecal microbiota of gardening families differs from non-gardening families, and that there are detectable changes in the fecal microbial community of gardeners and their family members over the course of the gardening season. Additional research is necessary to determine if changes induced by gardening on the gut microbiota contribute to human health.

Helminth Glycans at the Host-Parasite Interface and Their Potential for Developing Novel Therapeutics

Helminths are parasitic worms that have successfully co-evolved with their host immune system to sustain long-term infections. Their successful parasitism is mainly facilitated by modulation of the host immune system via the release of excretory-secretory (ES) products covered with glycan motifs such as Lewis X, fucosylated LDN, phosphorylcholine and tyvelose. Evidence is accumulating that these glycans play key roles in different aspects of helminth infection including interactions with immune cells for recognition and evasion of host defences. Moreover, antigenic properties of glycans can be exploited for improving the efficacy of anti-helminthic vaccines. Here, we illustrate that glycans have the potential to open new avenues for the development of novel biopharmaceuticals and effective vaccines based on helminth glycoproteins.

Early life, life course and gender influences on levels of C-reactive protein among migrant Bangladeshis in the UK

Background and objectives

Humans co-evolved with pathogens, especially helminths, that educate the immune system during development and lower inflammatory responses. The absence of such stimuli in industrialized countries is associated with higher baseline levels of C-reactive protein (CRP) among adults who appear at greater risk for inflammatory disorders. This cross-sectional study examined effects of early life development on salivary CRP levels in 452 British-Bangladeshis who spent varying periods growing up in Bangladesh or UK. We also analyzed how gender and central obesity modulate effects on CRP. We hypothesized that: (i) first-generation Bangladeshis with higher childhood exposure to pathogens would have chronically lower CRP levels than second-generation British-Bangladeshis; (ii) effects would be greater with early childhoods in Bangladesh; (iii) effects by gender would differ; and (iv) increasing obesity would mitigate early life effects.

Methodology

Saliva samples were assayed for CRP using ELISAs, and anthropometric data collected. Participants completed questionnaires about demographic, socioeconomic, lifestyle and health histories. Data were analyzed using multiple linear regression.

Results

First-generation migrants who spent early childhoods in mostly rural, unhygienic areas, and moved to UK after age 8, had lower salivary CRP compared to the second-generation. Effects differed by gender, while waist circumference predicted higher CRP levels. CRP increased with years in UK, alongside growing obesity.

Conclusions and implications

Our study supports the hypothesis that pathogen exposure in early life lowers inflammatory responses in adults. However, protective effects differed by gender and can be eroded by growing obesity across the life course which elevates risks for other inflammatory disorders.

Lay Summary: Migrants to the UK who spent early childhoods in less hygienic environments in Bangladesh that help to educate their immune systems had lower levels of the inflammatory marker, C-reactive protein (CRP) compared to migrants who grew up in UK. Both gender and increasing obesity were associated with increased levels of CRP.

Rapidly Growing Mycobacterium Species: The Long and Winding Road from Tuberculosis Vaccines to Potent Stress-Resilience Agents

Inflammatory diseases and stressor-related psychiatric disorders, for which inflammation is a risk factor, are increasing in modern Western societies. Recent studies suggest that immunoregulatory approaches are a promising tool in reducing the risk of suffering from such disorders. Specifically, the environmental saprophyte Mycobacterium vaccae National Collection of Type Cultures (NCTC) 11659 has recently gained attention for the prevention and treatment of stress-related psychiatric disorders. However, effective use requires a sophisticated understanding of the effects of M. vaccae NCTC 11659 and related rapidly growing mycobacteria (RGMs) on microbiome–gut–immune–brain interactions. This historical narrative review is intended as a first step in exploring these mechanisms and provides an overview of preclinical and clinical studies on M. vaccae NCTC 11659 and related RGMs. The overall objective of this review article is to increase the comprehension of, and interest in, the mechanisms through which M. vaccae NCTC 11659 and related RGMs promote stress resilience, with the intention of fostering novel clinical strategies for the prevention and treatment of stressor-related disorders.

Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts

BACKGROUND

Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases.

RESULTS

Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups.

CONCLUSIONS

Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.

Infection-exposure in infancy is associated with reduced allergy-related disease in later childhood in a Ugandan cohort

Background

Lack of early infection-exposure has been associated with increased allergy-related disease (ARD) susceptibility. In tropical Africa, little is known about which infections contribute to development of ARDs, and at which time.

Methods

We used latent class analysis to characterise the early infection-exposure of participants in a Ugandan birth cohort and assessed ARDs in later childhood.

Results

Of 2345 live births, 2115 children (90%) had data on infections within the first year of life while 1179 (50%) had outcome data at 9 years. We identified two latent classes of children based on first-year infection-exposure. Class 1 (32% membership), characterised by higher probabilities for malaria (80%), diarrhoea (76%), and lower respiratory tract infections (LRTI) (22%), was associated with lower prevalence of wheeze, eczema, rhinitis, and Dermatophagoides skin prick test (SPT) positivity at 9 years. Based on 5-year cumulative infection experience, class 1 (31% membership), characterised by higher probabilities for helminths (92%), malaria (79%), and LRTI (45%), was associated with lower probabilities of SPT positivity at 9 years.

Conclusions

In this Ugandan birth cohort, early childhood infection-exposure, notably to malaria, helminths, LRTI, and diarrhoea, is associated with lower prevalence of atopy and ARDs in later childhood.

Funding

This work was supported by several funding sources. The Entebbe Mother and Baby Study (EMaBS) was supported by the Wellcome Trust, UK, senior fellowships for AME (grant numbers 064693, 079110, 95778) with additional support from the UK Medical Research Council. LL is supported by a PhD fellowship through the DELTAS Africa Initiative SSACAB (grant number 107754). ELW received funding from MRC Grant Reference MR/K012126/1. SAL was supported by the PANDORA-ID-NET Consortium (EDCTP Reg/Grant RIA2016E-1609). HM was supported by the Wellcome's Institutional Strategic Support Fund (grant number 204928/Z/16/Z).

Heat-killed Mycolicibacterium aurum Aogashima: An environmental nonpathogenic actinobacteria under development as a safe novel food ingredient

Over the last few decades, a wealth of evidence has formed the basis for "the Old Friends hypothesis" suggesting that, in contrast to the past, increasingly people are living in environments with limited and less diverse microbial exposure, with potential consequences for their health. Hence, including safe live or heat-killed microbes in the diet may be beneficial in promoting and maintaining human health. In order to assess the safety of microbes beyond the current use of standardized cultures and probiotic supplements, new approaches are being developed. Here, we present evidence for the safety of heat-killed Mycolicibacterium aurum Aogashima as a novel food, utilizing the decision tree approach developed by Pariza and colleagues (2015). We provide evidence that the genome of M. aurum Aogashima is free of (1) genetic elements associated with pathogenicity or toxigenicity, (2) transferable antibiotic resistance gene DNA, and (3) genes coding for antibiotics used in human or veterinary medicine. Moreover, a 90-day oral toxicity study in rats showed that (4) the no observed adverse effect level (NOAEL) was the highest concentration tested, namely 2000 μg/kg BW/day. We conclude that oral consumption of heat-killed M. aurum Aogashima is safe and warrants further evaluation as a novel food ingredient.

Fecal microbiota transplantation in human metabolic diseases: From a murky past to a bright future?

Fecal microbiota transplantation (FMT) is gaining considerable traction as a therapeutic approach to influence the course of a plethora of chronic conditions, ranging from metabolic syndrome and malignancies to auto-immune and neurological diseases, and helped to establish the contribution of the gut microbiome to these conditions. Although FMT procedures have yielded important mechanistic insights, their use in clinical practice may be limited due to practical objections in the setting of metabolic diseases. While its applicability is established to treat recurrent Clostridiodes difficile, FMT is emerging in ulcerative colitis and various other diseases. A particularly new insight is that FMTs may not only alter insulin sensitivity but may also alter the course of type 1 diabetes by attenuating underlying auto-immunity. In this review, we will outline the major principles and pitfalls of FMT and where optimization of study design and the procedure itself will further advance the field of cardiometabolic medicine.

Hygiene hypothesis and autoimmune diseases: A narrative review of clinical evidences and mechanisms

Since the start of the "modern era", characterized by the increase in urbanization, a progressive attention to hygiene and autoimmune conditions has considerably grown. Although these diseases are often multifactorial, it was demonstrated that environment factors such as pollution, diet and lifestyles may play a crucial role together with genetic signature. Our research, based on the newest and most significant literature of this topic, highlights that the progressive depletion of microbes and parasites due to increased socioeconomic improvement, may lead to a derangement of immunoregulatory mechanisms. Moreover, special attention was given to the complex interplay between microbial agents, as gut microbiome, diet and vitamin D supplementation with the aim of identifying promising future therapeutic options. In conclusion, autoimmunity cannot be limited to hygiene-hypothesis, but from the point of view of precision medicine, this theory represents a fundamental element together with the study of genomics, the microbiome and proteomics, in order to understand the complex functioning of the immune system.

Hitchhiking microbes: Declining biodiversity & emerging zoonoses

The connection between nature conservation and human wellbeing is well known, however, the role of declining biodiversity and emerging diseases is relatively less studied. The presence of a thriving biological diversity is known to have therapeutic effects on human health. On the other hand, human economic activities have contributed to a sharp decline in species, resulting in poor ecosystem health. Several studies have shown how microorganisms have switched from animals to humans, leading to novel diseases. This review describes studies on zoonotic diseases and biodiversity, with examples from India. It is argued that conservation of biodiversity and ecosystems and changes in economic activities must be made to ward off new diseases, and why cooperation between ministries is critical to restrict the decline of biological diversity in a megadiverse country like India.

Dysbiosis From a Microbial and Host Perspective Relative to Oral Health and Disease

The significance of microbiology and immunology with regard to caries and periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related to several simple but elegant experiments illustrating the relevance of bacteria to oral infections. Since that point, the understanding of oral diseases has become increasingly sophisticated and many of the original hypotheses related to disease causality have either been abandoned or amplified. The COVID pandemic has reminded us of the importance of history relative to infectious diseases and in the words of Churchill "those who fail to learn from history are condemned to repeat it." This review is designed to present an overview of broad general directions of research over the last 60 years in oral microbiology and immunology, reviewing significant contributions, indicating emerging foci of interest, and proposing future directions based on technical advances and new understandings. Our goal is to review this rich history (standard microbiology and immunology) and point to potential directions in the future (omics) that can lead to a better understanding of disease. Over the years, research scientists have moved from a position of downplaying the role of bacteria in oral disease to one implicating bacteria as true pathogens that cause disease. More recently it has been proposed that bacteria form the ecological first line of defense against "foreign" invaders and also serve to train the immune system as an acquired host defensive stimulus. While early immunological research was focused on immunological exposure as a modulator of disease, the "hygiene hypothesis," and now the "old friends hypothesis" suggest that the immune response could be trained by bacteria for long-term health. Advanced "omics" technologies are currently being used to address changes that occur in the host and the microbiome in oral disease. The "omics" methodologies have shaped the detection of quantifiable biomarkers to define human physiology and pathologies. In summary, this review will emphasize the role that commensals and pathobionts play in their interaction with the immune status of the host, with a prediction that current "omic" technologies will allow researchers to better understand disease in the future.

SARS-CoV-2 and immune-microbiome interactions: Lessons from respiratory viral infections

By the beginning of 2020, infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had rapidly evolved into an emergent worldwide pandemic, an outbreak whose unprecedented consequences highlighted many existing flaws within public healthcare systems across the world. While coronavirus disease 2019 (COVID-19) is bestowed with a broad spectrum of clinical manifestations, involving the vital organs, the respiratory system transpires as the main route of entry for SARS-CoV-2, with the lungs being its primary target. Of those infected, up to 20% require hospitalization on account of severity, while the majority of patients are either asymptomatic or exhibit mild symptoms. Exacerbation in the disease severity and complications of COVID-19 infection have been associated with multiple comorbidities, including hypertension, diabetes mellitus, cardiovascular disorders, cancer, and chronic lung disease. Interestingly, a recent body of evidence indicated the pulmonary and gut microbiomes as potential modulators for altering the course of COVID-19, potentially via the microbiome-immune system axis. While the relative concordance between microbes and immunity has yet to be fully elucidated with regards to COVID-19, we present an overview of our current understanding of COVID-19-microbiome-immune cross talk and discuss the potential contributions of microbiome-related immunity to SARS-CoV-2 pathogenesis and COVID-19 disease progression.

Gut Microbiota Bacterial Species Associated with Mediterranean Diet-Related Food Groups in a Northern Spanish Population

The MD (Mediterranean diet) is recognized as one of the healthiest diets worldwide and is associated with the prevention of cardiovascular and metabolic diseases. Dietary habits are considered one of the strongest modulators of gut microbiota, which seem to play a significant role in health status of the host. The purpose of the present study was to evaluate interactive associations between gut microbiota composition and habitual dietary intake in 360 Spanish adults from the Obekit cohort (normal weight, overweight, and obese participants). Dietary intake and adherence to the MD tests were administered and fecal samples were collected from each participant. Fecal 16S rRNA (ribosomal Ribonucleic Acid) gene sequencing was performed and checked against the dietary habits. MetagenomeSeq was the statistical tool applied to analyze data at the species taxonomic level. Results from this study identified several beneficial bacteria that were more abundant in the individuals with higher adherence to the MD. Bifidobacterium animalis was the species with the strongest association with the MD. Some SCFA (Short Chain Fatty Acids) -producing bacteria were also associated with MD. In conclusion, this study showed that MD, fiber, legumes, vegetable, fruit, and nut intake are associated with an increase in butyrate-producing taxa such as Roseburia faecis, Ruminococcus bromii, and Oscillospira (Flavonifractor) plautii.

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a "Two Hit" Stressor Model

Previous studies demonstrate that Mycobacterium vaccae NCTC 11659 (M. vaccae), a soil-derived bacterium with anti-inflammatory and immunoregulatory properties, is a potentially useful countermeasure against negative outcomes to stressors. Here we used male C57BL/6NCrl mice to determine if repeated immunization with M. vaccae is an effective countermeasure in a "two hit" stress exposure model of chronic disruption of rhythms (CDR) followed by acute social defeat (SD). On day -28, mice received implants of biotelemetric recording devices to monitor 24-h rhythms of locomotor activity. Mice were subsequently treated with a heat-killed preparation of M. vaccae (0.1 mg, administered subcutaneously on days -21, -14, -7, and 27) or borate-buffered saline vehicle. Mice were then exposed to 8 consecutive weeks of either stable normal 12:12 h light:dark (LD) conditions or CDR, consisting of 12-h reversals of the LD cycle every 7 days (days 0-56). Finally, mice were exposed to either a 10-min SD or a home cage control condition on day 54. All mice were exposed to object location memory testing 24 h following SD. The gut microbiome and metabolome were assessed in fecal samples collected on days -1, 48, and 62 using 16S rRNA gene sequence and LC-MS/MS spectral data, respectively; the plasma metabolome was additionally measured on day 64. Among mice exposed to normal LD conditions, immunization with M. vaccae induced a shift toward a more proactive behavioral coping response to SD as measured by increases in scouting and avoiding an approaching male CD-1 aggressor, and decreases in submissive upright defensive postures. In the object location memory test, exposure to SD increased cognitive function in CDR mice previously immunized with M. vaccae. Immunization with M. vaccae stabilized the gut microbiome, attenuating CDR-induced reductions in alpha diversity and decreasing within-group measures of beta diversity. Immunization with M. vaccae also increased the relative abundance of 1-heptadecanoyl-sn-glycero-3-phosphocholine, a lysophospholipid, in plasma. Together, these data support the hypothesis that immunization with M. vaccae stabilizes the gut microbiome, induces a shift toward a more proactive response to stress exposure, and promotes stress resilience.

Mycobacterium-Induced Th1, Helminths-Induced Th2 Cells and the Potential Vaccine Candidates for Allergic Asthma: Imitation of Natural Infection

Bronchial asthma is one of the most chronic pulmonary diseases and major public health problems. In general, asthma prevails in developed countries than developing countries, and its prevalence is increasing in the latter. For instance, the hygiene hypothesis demonstrated that this phenomenon resulted from higher household hygienic standards that decreased the chances of infections, which would subsequently increase the occurrence of allergy. In this review, we attempted to integrate our knowledge with the hygiene hypothesis into beneficial preventive approaches for allergic asthma. Therefore, we highlighted the studies that investigated the correlation between allergic asthma and the two different types of infections that induce the two major antagonizing arms of T cells. This elucidation reflects the association between various types of natural infections and the immune system, which is predicted to support the main objective of the current research on investigating of the benefits of natural infections, regardless their immune pathways for the prevention of allergic asthma. We demonstrated that natural infection with Mycobacterium tuberculosis (Mtb) prevents the development of allergic asthma, thus Bacille Calmette-Guérin (BCG) vaccine is suggested at early age to mediate the same prevention particularly with increasing its efficiency through genetic engineering-based modifications. Likewise, natural helminth infections might inhabit the allergic asthma development. Therefore, helminth-derived proteins at early age are good candidates for designing vaccines for allergic asthma and it requires further investigation. Finally, we recommend imitation of natural infections as a general strategy for preventing allergic asthma that increased dramatically over the past decades.

Vaccination and Immunotherapy for Major Depression

Depression is a very common disease with increasing incidence resulting from complex interactions of genetic, environmental, and immunological processes. To this day, the etiopathogenesis and treatment of depression unfortunately seem to be stuck in the synaptic gap. Despite highly potent antidepressants, the treatment rate cannot reach 100%, the treatment resistant group cannot be eliminated, and relapse cannot be prevented. These problems lead researchers to further and different research to understand and treat psychopathology. Immune dysfunction and neuroinflammation have been one of the main issues that psychiatry has focused on in recent years and helps us to understand depression. Extraneuronal components of all neuropsychiatric disorders, especially depression, have begun to be revealed in detail thanks to a better understanding of the immune system and an increase in experimental and technological possibilities. There is increasing evidence of a causal relationship between the etiopathogenesis of major depression and low-level chronic neuroinflammation. In this article, the role of neuroinflammation in the etiopathogenesis of depression and the possibilities of vaccination and immunotherapy are discussed.

Oxygen and Metabolism: Digesting Determinants of Antibiotic Susceptibility in the Gut

Microbial metabolism is a major determinant of antibiotic susceptibility. Environmental conditions that modify metabolism, notably oxygen availability and redox potential, can directly fine-tune susceptibility to antibiotics. Despite this, relatively few studies have discussed these modifications within the gastrointestinal tract and their implication on in vivo drug activity and the off-target effects of antibiotics in the gut. In this review, we discuss the environmental and biogeographical complexity of the gastrointestinal tract in regard to oxygen availability and redox potential, addressing how the heterogeneity of gut microhabitats may modify antibiotic activity in vivo. We contextualize the current literature surrounding oxygen availability and antibiotic efficacy and discuss empirical treatments. We end by discussing predicted patterns of antibiotic activity in prominent microbiome taxa, given gut heterogeneity, oxygen availability, and polymicrobial interactions. We also propose additional work required to fully elucidate the role of oxygen metabolism on antibiotic susceptibility in the context of the gut.