Dietary Selection Pressures and Their Impact on the Gut Microbiome

Next generation probiotics for human health: An emerging perspective

Over recent years, the scientific community has acknowledged the crucial role of certain microbial strains inhabiting the intestinal ecosystem in promoting human health, and participating in various beneficial functions for the host. These microorganisms are now referred to as next-generation probiotics and are currently considered as biotherapeutic products and food or nutraceutical supplements. However, the majority of next-generation probiotic candidates pose nutritional demands and exhibit high sensitivity towards aerobic conditions, leading to numerous technological hurdles in large-scale production. This underscores the need for the development of suitable delivery systems capable of enhancing the viability and functionality of these probiotic strains. Currently, potential candidates for next generation probiotics (NGP) are being sought among gut bacteria linked to health, which include strains from the genera Bacteroids, Faecalibacterium, Akkermansia and Clostridium. In contrast to Lactobacillus spp. and Bifidobacterium spp., NGP, particularly Bacteroids spp. and Clostridium spp., appear to exhibit greater ambiguity regarding their potential to induce infectious diseases. The present review provides a comprehensive overview of NGPs in terms of their health beneficial effects, regulation framework and risk assessment targeting relevant criteria for commercialization in food and pharmaceutical markets.

Association of dietary live microbe intake with prevalence of osteoporosis in US postmenopausal women: a cross-sectional study

The association between live microbe intake and osteoporosis in postmenopausal women remains unknown. The research findings indicated that an increased intake of live microbes through dietary sources was associated with a low prevalence of osteoporosis among postmenopausal women.

PURPOSE

To investigate the relationship between the consumption of live microbes in the diet and osteoporosis in postmenopausal women.

METHODS

A cross-sectional investigation using data obtained from the National Health and Nutrition Examination Survey was conducted. Participants were classified into three groups by using the dietary live microbe classification system developed by Sanders. Dual x-ray absorptiometry was used to measure body mineral density, and osteoporosis was diagnosed according to the World Health Organization criteria. We conducted a crude and adjusted multivariate logistic regression analysis, and utilized the restricted cubic splines model to assess the correlation between the consumption of live microbes in the diet and osteoporosis in postmenopausal women.

RESULTS

A total of 1378 women who had undergone menopause were enrolled in the study. After controlling for potential covariates, individuals with a high consumption of live microbes in their diet exhibited a notably low prevalence of osteoporosis in comparison to those with a low intake of dietary live microbes (odd ratio: 0.46, 95% confidence interval: 0.23, 0.93, P = 0.03). Subgroup analysis showed the stability of the results, and restricted cubic splines showed an approximate L-shape curve.

CONCLUSIONS

In this research, a higher consumption of live microbes in the diet was linked to a low prevalence of osteoporosis in postmenopausal women.

The Crucial Roles of Diet, Microbiota, and Postbiotics in Colorectal Cancer

PURPOSE OF REVIEW

Colorectal cancer is the second deadliest cancer in the world, and its prevalence has been increasing alarmingly in recent years. After researchers discovered the existence of dysbiosis in colorectal cancer, they considered the use of probiotics in the treatment of colorectal cancer. However, for various reasons, including the low safety profile of probiotics in susceptible and immunocompromised patient5s, and the risk of developing antibiotic resistance, researchers have shifted their focus to non-living cells, their components, and metabolites. This review aims to comprehensively evaluate the literature on the effects of diet, microbiota, and postbiotics on colorectal cancer and the future of postbiotics.

RECENT FINDINGS

The link between diet, gut microbiota, and colorectal cancer has been established primarily as a relationship rather than a cause-effect relationship. The gut microbiota can convert gastrointestinal tract and dietary factors into either onco-metabolites or tumor suppressor metabolites. There is serious dysbiosis in the microbiota in colorectal cancer. Postbiotics appear to be promising agents in the prevention and treatment of colorectal cancer. It has been shown that various postbiotics can selectively induce apoptosis in CRC, inhibit cell proliferation, growth, invasion, and migration, modulate the immune system, suppress carcinogenic signaling pathways, maintain intestinal epithelial integrity, and have a synergistic effect with chemotherapy drugs. However, it is also reported that some postbiotics are ineffective and may be risky in terms of safety profile in some patients. Many issues need to be researched about postbiotics. Large-scale, randomized, double-blind clinical studies are needed.

A generic approach to infer community-level fitness of microbial genes

The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.

Can essential fatty acids (EFAs) prevent and ameliorate post-COVID-19 long haul manifestations?

It is hypothesized that COVID-19, post-COVID and post-mRNA COVID-19 (and other related) vaccine manifestations including "long haul syndrome" are due to deficiency of essential fatty acids (EFAs) and dysregulation of their metabolism. This proposal is based on the observation that EFAs and their metabolites can modulate the swift immunostimulatory response of SARS-CoV-2 and similar enveloped viruses, suppress inappropriate cytokine release, possess cytoprotective action, modulate serotonin and bradykinin production and other neurotransmitters, inhibit NF-kB activation, regulate cGAS-STING pathway, modulate gut microbiota, inhibit platelet activation, regulate macrophage and leukocyte function, enhance wound healing and facilitate tissue regeneration and restore homeostasis. This implies that administration of EFAs could be of benefit in the prevention and management of COVID-19 and its associated complications.

Detection of typical indigenous gut bacteria related to kanpyo Lagenaria siceraria var. hispida powder in murine caecum and human faecal cultures

Kanpyo (KP) is an edible dried product produced by peeling the fruit of the gourd Lagenaria siceraria var. hispida; it is used in the traditional Japanese cuisine. The health functionality of KP due to its rich dietary fibre is expected to include a possible combined effect of KP-responsive indigenous gut bacteria (KP-RIB). However, its effect on the gut microbiota is unclear. To determine the effects of the KP on the gut microbiota and their host, Institute of Cancer Research mice were fed a high-sucrose diet containing no fibre (NF) or 5% (w/w) KP for 14 days, and their caecal microbiota was analysed by 16S rRNA (V4) amplicon sequencing. Higher faecal frequency and weight and lower spleen weight and spleen tumour necrosis factor-α levels were observed in KP-fed mice than in NF-fed mice (p < 0.05). KP increased and decreased the abundance of short-chain fatty acid producer Lachnospiraceae and obesity-inflammation related Allobaculum species, respectively. In the case of human faecal cultures, stool samples from five healthy volunteers were inoculated and incubated at 37 °C for 24 h anaerobically; 3.2% (w/v) KP suppressed putrefactive compounds (indole, phenol, and ammonia). KP increased butyrate-producer Faecalibacterium, acetate/lactate-producer Bifidobacterium, and Lachnospira. Furthermore, KP cultures showed high antioxidant and RAW264.7 macrophage cell activation capacities. These results suggest that KP-RIB and KP intake may synergistically affect host health. However, further studies are required to clarify the synergistic effects of KP and KP-RIB.

Microbiota Implications in Endocrine-Related Diseases: From Development to Novel Therapeutic Approaches

This comprehensive review article delves into the critical role of the human microbiota in the development and management of endocrine-related diseases. We explore the complex interactions between the microbiota and the endocrine system, emphasizing the implications of microbiota dysbiosis for the onset and progression of various endocrine disorders. The review aims to synthesize current knowledge, highlighting recent advancements and the potential of novel therapeutic approaches targeting microbiota-endocrine interactions. Key topics include the impact of microbiota on hormone regulation, its role in endocrine pathologies, and the promising avenues of microbiota modulation through diet, probiotics, prebiotics, and fecal microbiota transplantation. We underscore the importance of this research in advancing personalized medicine, offering insights for more tailored and effective treatments for endocrine-related diseases.

Probiotic Lactobacillus spp. improves Drosophila memory by increasing lactate dehydrogenase levels in the brain mushroom body neurons

Probiotics are live microorganisms that offer potential benefits to their hosts and can occasionally influence behavioral responses. However, the detailed mechanisms by which probiotics affect the behavior of their hosts and the underlying biogenic effects remain unclear. Lactic acid bacteria, specifically Lactobacillus spp. are known probiotics. Drosophila melanogaster, commonly known as the fruit fly, is a well-established model organism for investigating the interaction between the host and gut microbiota in translational research. Herein, we showed that 5-day administration of Lactobacillus acidophilus (termed GMNL-185) or Lacticaseibacillus rhamnosus (termed GMNL-680) enhances olfactory-associative memory in Drosophila. Moreover, a combined diet of GMNL-185 and GMNL-680 demonstrated synergistic effects on memory functions. Live brain imaging revealed a significant increase in calcium responses to the training odor in the mushroom body β and γ lobes of flies that underwent mixed feeding with GMNL-185 and GMNL-680. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and whole-mount brain immunohistochemistry revealed significant upregulation of lactate dehydrogenase (LDH) expression in the fly brain following the mixed feeding. Notably, the genetic knockdown of Ldh in neurons, specifically in mushroom body, ameliorated the beneficial effects of mixed feeding with GMNL-185 and GMNL-680 on memory improvement. Altogether, our results demonstrate that supplementation with L. acidophilus and L. rhamnosus enhances memory functions in flies by increasing brain LDH levels.

The Role of the Microbiome in the Pathogenesis and Treatment of Ulcerative Colitis-A Literature Review

Ulcerative colitis (UC) is a chronic inflammatory bowel disease affecting the colon and rectum. UC's pathogenesis involves colonic epithelial cell abnormalities and mucosal barrier dysfunction, leading to recurrent mucosal inflammation. The purpose of the article is to show the complex interplay between ulcerative colitis and the microbiome. The literature search was conducted using the PubMed database. After a screening process of studies published before October 2023, a total of 136 articles were selected. It has been discovered that there is a fundamental correlation of a robust intestinal microbiota and the preservation of gastrointestinal health. Dysbiosis poses a grave risk to the host organism. It renders the host susceptible to infections and has been linked to the pathogenesis of chronic diseases, with particular relevance to conditions such as ulcerative colitis. Current therapeutic strategies for UC involve medications such as aminosalicylic acids, glucocorticoids, and immunosuppressive agents, although recent breakthroughs in monoclonal antibody therapies have significantly improved UC treatment. Furthermore, modulating the gut microbiome with specific compounds and probiotics holds potential for inflammation reduction, while fecal microbiota transplantation shows promise for alleviating UC symptoms. This review provides an overview of the gut microbiome's role in UC pathogenesis and treatment, emphasizing areas for further research.

Association of dietary live microbe intake with abdominal aortic calcification in US adults: a cross-sectional study of NHANES 2013-2014

OBJECT

To explore the potential association between dietary live microbe intake and abdominal aortic calcification (AAC).

METHODS

We conducted a cross-section study based on the National Health and Nutrition Examination Survey (NHANES). We categorized the participants into three groups (low, medium, and high dietary intake of live microbes) according to Sanders's dietary live microbe classification system and participants' 24-h dietary recall data. AAC was quantified by using dual-energy X-ray absorptiometry (DXA) and diagnosed by using the Kauppila AAC-24 score system. The analyses utilized weighted logistic regression and weighted linear regression.

RESULTS

A total of 2,586 participants were included. After the full adjustment for covariates, compared to participants with a low dietary live microbe intake, participants with a high dietary live microbe intake had a significantly lower risk of severe AAC (OR: 0.39, 95% CI: 0.22, 0.68, p = 0.003), and the AAC score was also significantly decreased (β:-0.53, 95% CI: -0.83, -0.23, p = 0.002).

CONCLUSION

In this study, more dietary live microbial intake was associated with lower AAC scores and a lower risk of severe AAC. However, more research is needed to verify this.

Nutri-microbiome epidemiology, an emerging field to disentangle the interplay between nutrition and microbiome for human health

Diet and nutrition have a substantial impact on the human microbiome, and interact with the microbiome, especially gut microbiome, to modulate various diseases and health status. Microbiome research has also guided the nutrition field to a more integrative direction, becoming an essential component of the rising area of precision nutrition. In this review, we provide a broad insight into the interplay among diet, nutrition, microbiome, and microbial metabolites for their roles in the human health. Among the microbiome epidemiological studies regarding the associations of diet and nutrition with microbiome and its derived metabolites, we summarize those most reliable findings and highlight evidence for the relationships between diet and disease-associated microbiome and its functional readout. Then, the latest advances of the microbiome-based precision nutrition research and multidisciplinary integration are described. Finally, we discuss several outstanding challenges and opportunities in the field of nutri-microbiome epidemiology.

Oral Microbiota: The Influences and Interactions of Saliva, IgA, and Dietary Factors in Health and Disease

Recent advances in metagenomic analyses have made it easier to analyze microbiota. The microbiota, a symbiotic community of microorganisms including bacteria, archaea, fungi, and viruses within a specific environment in tissues such as the digestive tract and skin, has a complex relationship with the host. Recent studies have revealed that microbiota composition and balance particularly affect the health of the host and the onset of disease. Influences such as diet, food preferences, and sanitation play crucial roles in microbiota composition. The oral cavity is where the digestive tract directly communicates with the outside. Stable temperature and humidity provide optimal growth environments for many bacteria. However, the oral cavity is a unique environment that is susceptible to pH changes, salinity, food nutrients, and external pathogens. Recent studies have emphasized the importance of the oral microbiota, as changes in bacterial composition and balance could contribute to the development of systemic diseases. This review focuses on saliva, IgA, and fermented foods because they play critical roles in maintaining the oral bacterial environment by regulating its composition and balance. More attention should be paid to the oral microbiota and its regulatory factors in oral and systemic health.

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study

The relationship between microbiota, short chain fatty acids (SCFAs), and obesity remains enigmatic. We employ amplicon sequencing and targeted metabolomics in a large (n = 1904) African origin cohort from Ghana, South Africa, Jamaica, Seychelles, and the US. Microbiota diversity and fecal SCFAs are greatest in Ghanaians, and lowest in Americans, representing each end of the urbanization spectrum. Obesity is significantly associated with a reduction in SCFA concentration, microbial diversity, and SCFA synthesizing bacteria, with country of origin being the strongest explanatory factor. Diabetes, glucose state, hypertension, obesity, and sex can be accurately predicted from the global microbiota, but when analyzed at the level of country, predictive accuracy is only universally maintained for sex. Diabetes, glucose, and hypertension are only predictive in certain low-income countries. Our findings suggest that adiposity-related microbiota differences differ between low-to-middle-income compared to high-income countries. Further investigation is needed to determine the factors driving this association.

Building better barriers: how nutrition and undernutrition impact pediatric intestinal health

Chronic undernutrition is a major cause of death for children under five, leaving survivors at risk for adverse long-term consequences. This review focuses on the role of nutrients in normal intestinal development and function, from the intestinal epithelium, to the closely-associated mucosal immune system and intestinal microbiota. We examine what is known about the impacts of undernutrition on intestinal physiology, with focus again on the same systems. We provide a discussion of existing animal models of undernutrition, and review the evidence demonstrating that correcting undernutrition alone does not fully ameliorate effects on intestinal function, the microbiome, or growth. We review efforts to treat undernutrition that incorporate data indicating that improved recovery is possible with interventions focused not only on delivery of sufficient energy, macronutrients, and micronutrients, but also on efforts to correct the abnormal intestinal microbiome that is a consequence of undernutrition. Understanding of the role of the intestinal microbiome in the undernourished state and correction of the phenotype is both complex and a subject that holds great potential to improve recovery. We conclude with critical unanswered questions in the field, including the need for greater mechanistic research, improved models for the impacts of undernourishment, and new interventions that incorporate recent research gains. This review highlights the importance of understanding the mechanistic effects of undernutrition on the intestinal ecosystem to better treat and improve long-term outcomes for survivors.

Microbial circadian clocks: host-microbe interplay in diel cycles

BACKGROUND

Circadian rhythms, observed across all domains of life, enable organisms to anticipate and prepare for diel changes in environmental conditions. In bacteria, a circadian clock mechanism has only been characterized in cyanobacteria to date. These clocks regulate cyclical patterns of gene expression and metabolism which contribute to the success of cyanobacteria in their natural environments. The potential impact of self-generated circadian rhythms in other bacterial and microbial populations has motivated extensive research to identify novel circadian clocks.

MAIN TEXT

Daily oscillations in microbial community composition and function have been observed in ocean ecosystems and in symbioses. These oscillations are influenced by abiotic factors such as light and the availability of nutrients. In the ocean ecosystems and in some marine symbioses, oscillations are largely controlled by light-dark cycles. In gut systems, the influx of nutrients after host feeding drastically alters the composition and function of the gut microbiota. Conversely, the gut microbiota can influence the host circadian rhythm by a variety of mechanisms including through interacting with the host immune system. The intricate and complex relationship between the microbiota and their host makes it challenging to disentangle host behaviors from bacterial circadian rhythms and clock mechanisms that might govern the daily oscillations observed in these microbial populations.

CONCLUSIONS

While the ability to anticipate the cyclical behaviors of their host would likely be enhanced by a self-sustained circadian rhythm, more evidence and further studies are needed to confirm whether host-associated heterotrophic bacteria possess such systems. In addition, the mechanisms by which heterotrophic bacteria might respond to diel cycles in environmental conditions has yet to be uncovered.

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome Study

The relationship between gut microbiota, short chain fatty acid (SCFA) metabolism, and obesity is still not well understood. Here we investigated these associations in a large (n=1904) African origin cohort from Ghana, South Africa, Jamaica, Seychelles, and the US. Fecal microbiota diversity and SCFA concentration were greatest in Ghanaians, and lowest in the US population, representing the lowest and highest end of the epidemiologic transition spectrum, respectively. Obesity was significantly associated with a reduction in SCFA concentration, microbial diversity and SCFA synthesizing bacteria. Country of origin could be accurately predicted from the fecal microbiota (AUC=0.97), while the predictive accuracy for obesity was inversely correlated to the epidemiological transition, being greatest in Ghana (AUC = 0.57). The findings suggest that the microbiota differences between obesity and non-obesity may be larger in low-to-middle-income countries compared to high-income countries. Further investigation is needed to determine the factors driving this association.
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The Role of the Gut Microbiota in the Relationship Between Diet and Human Health

The interplay between diet, the gut microbiome, and host health is complex. Diets associated with health have many similarities: high fiber, unsaturated fatty acids, and polyphenols while being low in saturated fats, sodium, and refined carbohydrates. Over the past several decades, dietary patterns have changed significantly in Westernized nations with the increased consumption of calorically dense ultraprocessed foods low in fiber and high in saturated fats, salt, and refined carbohydrates, leading to numerous negative health consequences including obesity, metabolic syndrome, and cardiovascular disease. The gut microbiota is an environmental factor that interacts with diet and may also have an impact on health outcomes, many of which involve metabolites produced by the microbiota from dietary components that can impact the host. This review focuses on our current understanding of the complex relationship between diet, the gut microbiota, and host health, with examples of how diet can support health, increase an individual's risk for disease, and be used as a therapy for specific diseases.

Measuring food insecurity: An introduction to tools for human biologists and ecologists

OBJECTIVE

Food insecurity is a significant and growing concern undermining the wellbeing of 30% of the global population. Food in/security is a complex construct consisting of four dimensions: availability, access, utilization, and stability, making it challenging to measure. We provide a toolkit human biologists/ecologists can use to advance research on this topic.

METHODS

We review the strengths and limitations of common tools used to measure food access and utilization, the two dimensions most proximate to people's lived experience, and emphasize tools that provide data needed to best link food security with human biological outcomes. We also discuss methods that provide contextual data human biologists/ecologists will find useful for study design, ensuring instrument validity, and improving data quality.

RESULTS

Food access is principally measured using experience-based instruments that emphasize economic access. Social access, such as food sharing, is under-studied and we recommend using social network analysis to explore this dimension. In terms of utilization, emphasis has been on food choice measured as dietary diversity. Food preparation and intrahousehold distribution, also part of the utilization dimension, are less studied and standardized instruments for measuring both are lacking. The embodiment of food insecurity has focused on child growth, although a growing literature addresses adult mental wellbeing and chronic and infectious disease risk.

CONCLUSIONS

We see the potential to expand outcomes to include reproductive and immune function, physical activity, and the gut microbiome. Human biologists/ecologists are well-positioned to advance understanding of the human health impacts of food insecurity and provide data to support intervention efforts.

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample

Voluntary caloric restriction (e.g., eating disorders) often results in alterations in the gut microbiota composition and function. However, these findings may not translate to food insecurity, where an individual experiences inconsistent access to healthy food options. In this study we compared the fecal microbiome and metabolome of racially and ethnically diverse first year college students (n = 60) experiencing different levels of food access. Students were dichotomized into food secure (FS) and food insecure (FI) groups using a validated, 2-question screener assessing food security status over the previous 30 days. Fecal samples were collected up to 5 days post survey-completion. Gut microbiome and metabolome were established using 16S rRNA amplicon sequencing, targeted liquid chromatography-tandem mass spectrometry, and gas chromatography-mass spectrometry. FI students experienced significantly greater microbial diversity with increased abundance of Enterobacteriaceae and Eisenbergiella, while FS students had greater abundance of Megasphaera and Holdemanella. Metabolites related to energy transfer and gut–brain-axis communication (picolinic acid, phosphocreatine, 2-pyrrolidinone) were elevated in FI students (q < 0.05). These findings suggest that food insecurity is associated with differential gut microbial and metabolite composition for which the future implications are unknown. Further work is needed to elucidate the longitudinal metabolic effects of food insecurity and how gut microbes influence metabolic outcomes.

Individual Nutrition Is Associated with Altered Gut Microbiome Composition for Adults with Food Insecurity

Diet is widely recognized as a key contributor to human gut microbiome composition and function. However, overall nutrition can be difficult to compare across a population with varying diets. Moreover, the role of food security in the relationship with overall nutrition and the gut microbiome is unclear. This study aims to investigate the association between personalized nutrition scores, variation in the adult gut microbiome, and modification by food insecurity. The data originate from the Survey of the Health of Wisconsin and the Wisconsin Microbiome Study. Individual nutrition scores were assessed using My Nutrition Index (MNI), calculated using data from food frequency questionnaires, and additional health history and demographic surveys. Food security and covariate data were measured through self-reported questionnaires. The gut microbiome was assessed using 16S amplicon sequencing of DNA extracted from stool samples. Associations, adjusted for confounding and interaction by food security, were estimated using Weighted Quantile Sum (WQS) regression models with Random Subset and Repeated Holdout extensions (WQSRSRH), with bacterial taxa used as components in the weighted index. Of 643 participants, the average MNI was 66.5 (SD = 31.9), and 22.8% of participants were food insecure. Increased MNI was significantly associated with altered gut microbial composition (β = 2.56, 95% CI = 0.52−4.61), with Ruminococcus, Oscillospira, and Blautia among the most heavily weighted of the 21 genera associated with the MNI score. In the stratified interaction WQSRSRH models, the bacterial taxa most heavily weighted in the association with MNI differed by food security, but the level of association between MNI and the gut microbiome was not significantly different. More bacterial genera are important in the association with higher nutrition scores for people with food insecurity versus food security, including Streptococcus, Parabacteroides Faecalibacterium, and Desulfovibrio. Individual nutrition scores are associated with differences in adult gut microbiome composition. The bacterial taxa most associated with nutrition vary by level of food security. While further investigation is needed, results showed a higher nutrition score was associated with a wider range of bacterial taxa for food insecure vs. secure, suggesting nutritional quality in food insecure individuals is important in maintaining health and reducing disparities.

Unpacking determinants and consequences of food insecurity for insulin resistance among people living with HIV: Conceptual framework and protocol for the NOURISH-OK study

Background:

Over the past four decades, advances in HIV treatment have contributed to a longer life expectancy for people living with HIV (PLWH). With these gains, the prevention and management of chronic co-morbidities, such as diabetes, are now central medical care goals for this population. In the United States, food insecurity disproportionately impacts PLWH and may play a role in the development of insulin resistance through direct and indirect pathways. The Nutrition to Optimize, Understand, and Restore Insulin Sensitivity in HIV for Oklahoma (NOURISH-OK) will use a novel, multi-level, integrated framework to explore how food insecurity contributes to insulin resistance among PLWH. Specifically, it will explore how food insecurity may operate as an intermediary risk factor for insulin resistance, including potential linkages between upstream determinants of health and downstream consequences of poor diet, other behavioral risk factors, and chronic inflammation.

Methods/design:

This paper summarizes the protocol for the first aim of the NOURISH-OK study, which involves purposeful cross-sectional sampling of PLWH (n=500) across four levels of food insecurity to test our conceptual framework. Developed in collaboration with community stakeholders, this initial phase involves the collection of anthropometrics, fasting blood samples, non-blood biomarkers, 24-hour food recall to estimate the Dietary Inflammatory Index (DII^®) score, and survey data. A 1-month, prospective observational sub-study (total n=100; n=25 for each food security group) involves weekly 24-hour food recalls and stool samples to identify temporal associations between food insecurity, diet, and gut microbiome composition. Using structural equation modeling, we will explore how upstream risk factors, including early life events, current discrimination, and community food access, may influence food insecurity and its potential downstream impacts, including diet, other lifestyle risk behaviors, and chronic inflammation, with insulin resistance as the ultimate outcome variable. Findings from these analyses of observational data will inform the subsequent study aims, which involve qualitative exploration of significant pathways, followed by development and testing of a low-DII^® food as medicine intervention to reverse insulin resistance among PLWH (ClinicalTrials.gov Identifier: NCT05208671).

Discussion:

The NOURISH-OK study will address important research gaps to inform the development of food as medicine interventions to support healthy aging for PLWH.

Stitching together a healthy gut microbiome with fiber

Inter-individual variability in the gut microbiome confounds efforts to understand host responses to dietary fiber. In this issue of Cell Host & Microbe, Lancaster et al. report individual and generalized host and microbiome responses in an interventional study of fiber supplements, motivating consideration of an alternative classification of fiber.

Profiling of the Conjunctival Bacterial Microbiota Reveals the Feasibility of Utilizing a Microbiome-Based Machine Learning Model to Differentially Diagnose Microbial Keratitis and the Core Components of the Conjunctival Bacterial Interaction Network

Both healthy and diseased human ocular surfaces possess their own microbiota. If allowed, opportunistic pathogens within the ocular microbiota may cause microbial keratitis (MK). However, the nonpathogenic component of the ocular microbiota has been proven to undermine the performance of culture, the gold standard of the etiological diagnosis for MK. As the conjunctival bacterial microbiota generates unique alterations with various oculopathies, this study aimed to evaluate the feasibility of distinguishing MK using machine learning based on the characteristics of the conjunctival bacterial microbiome associated with various types of MK. This study also aimed to reveal which bacterial genera constitute the core of the interaction network of the conjunctival bacterial microbiome. Conjunctival swabs collected from the diseased eyes of MK patients and the randomly chosen normal eyes of healthy volunteers were subjected for high-throughput 16S rDNA sequencing. The relative content of each bacterial genus and the composition of bacterial gene functions in every sample were used to establish identification models with the random forest algorithm. Tenfold cross validation was adopted. Accuracy was 96.25% using the bacterial microbiota structure and 93.75% using the bacterial gene functional composition. Therefore, machine learning with the conjunctival bacterial microbiome characteristics might be used for differentiation of MKs as a noninvasive supplementary approach. In addition, this study found that Actinobacteria, Lactobacillus, Clostridium, Helicobacter, and Sphingomonas constitute the core of the interaction network of the conjunctival bacterial microbiome.

Host-microbe circadian dynamics: Finding a rhythm and hitting a groove in scientific inquiry

Gut microbes are mediators of organismal-level circadian rhythms, responding to and transducing environmental cues. Gut microbes also exhibit rhythms, yet their contribution to a healthy microbiome remains unclear. We present our path to identifying host-microbe circadian dynamics related to health and outline a series of forward-thinking questions requiring further exploration.

The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status

This proof-of-principle study analyzed fecal samples from 30 infants who participated in a randomized controlled trial on the effects of the macronutrient composition of infant formula on growth and energy balance. In that study, infants randomized to be fed cow milk formula (CMF) had faster weight-gain velocity during the first 4 months and higher weight-for-length Z scores up to 11.5 months than those randomized to an isocaloric extensive protein hydrolysate formula (EHF). Here we examined associations among infant formula composition, gut microbial composition and maturation, and children’s weight status. Fecal samples collected before and monthly up to 4.5 months after randomization were analyzed by shotgun metagenomic sequencing and targeted metabolomics. The EHF group had faster maturation of gut microbiota than the CMF group, and increased alpha diversity driven by Clostridia taxa. Abundance of Ruminococcus gnavus distinguished the two groups after exclusive feeding of the assigned formula for 3 months. Abundance of Clostridia at 3–4 months negatively correlated with prior weight-gain velocity and body weight phenotypes when they became toddlers. Macronutrient differences between the formulas likely led to the observed divergence in gut microbiota composition that was associated with differences in transient rapid weight gain, a well-established predictor of childhood obesity and other comorbidities.

Outlook on next-generation probiotics from the human gut

Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored reservoir of potentially beneficial microbes. For this reason, academic and industrial research is focused on identifying and testing novel microbial strains of gut origin for the development of next-generation probiotics. Although several of these are promising for the prevention and treatment of many chronic diseases, studies on human subjects are still scarce and approval from regulatory agencies is, therefore, rare. In addition, some issues need to be overcome before implementing their wide application on the market, such as the best methods for cultivation and storage of these oxygen-sensitive taxa. This review summarizes the most recent evidence related to NGPs and provides an outlook to the main issues that still limit their wide employment.

Possible role of gut microbes and host's immune response in gut-lung homeostasis

The vast diversity of microbial communities reside in various locations of the human body, and they are collectively named as the 'Human Microbiota.' The majority of those microbes are found in the gastrointestinal and respiratory tracts. The microorganisms present in the gastrointestinal and the respiratory tracts are called the gut microbiota and the airway microbiota, respectively. These microbial communities are known to affect both the metabolic functions and the immune responses of the host. Among multiple factors determining the composition of gut microbiota, diet has played a pivotal role. The gut microbes possess enzymatic machinery for assimilating dietary fibers and releasing different metabolites, primarily short-chain fatty acids (SCFAs). The SCFAs modulate the immune responses of not only the gut but other distal mucosal sites as well, such as the lungs. Dysbiosis in normal gut flora is one of the factors involved in the development of asthma and other respiratory disorders. Of note, several human and murine studies have indicated significant cross-talk between gut microbiota and lung immunity, known as the gut-lung axis. Here, in this review, we summarize the recent state of the field concerning the effect of dietary metabolites, particularly SCFAs, on the "gut-lung axis" as well as discuss its impact on lung health. Moreover, we have highlighted the role of the "gut-lung axis" in SARS-CoV-2 mediated inflammation. Also, to analyze the global research progress on the gut-lung axis and to identify the knowledge gap in this field, we have also utilized the bibliographic tools Dimension database and VOS viewer analysis software. Through network mapping and visualization analysis, we can predict the present research trend and the possibility to explore new directions.

OUP accepted manuscript

Organismal survival depends on a well-balanced immune system and maintenance of host–microbe mutualism. The fine-tuned relationship between the gut microbiota and host immunity is constantly challenged by opportunistic bacteria testing the integrity of gastrointestinal (GI) barrier defenses. Barrier dysfunction reduces immunological tolerance towards otherwise innocuous microbes; it is a process that may instigate chronic inflammation. Paradoxically, sustained inflammation further diminishes barrier function, enabling bacterial translocation to extra-intestinal tissues. Once translocated, these bacteria stimulate systemic inflammation, thereby compromising organ function. While genetic risk alleles associate with barrier dysfunction, environmental stressors are key triggers of GI inflammation and associated breakdown in immune tolerance towards resident gut microbes. As dietary components dictate substrate availability, they also orchestrate microbiota composition and function, including migratory and pro-inflammatory potential, thus holding the capacity to fuel both GI and extra-intestinal inflammation. Additionally, Western diet consumption may weaken barrier defenses via curbed Paneth cell function and diminished host-defense peptide secretion. This review focuses on intervenable niches of host–microbe interactions and mucosal immunity with the ambition to provide a framework of plausible strategies to improve barrier function and regain tolerance in the inflamed mucosa via nutritional intervention.