The role of the microbiome for human health: from basic science to clinical applications

Systematically-designed mixtures outperform single fibers for gut microbiota support

Dietary fiber interventions to modulate the gut microbiota have largely relied on isolated fibers or specific fiber sources. We hypothesized that fibers systematically blended could promote more health-related bacterial groups. Initially, pooled in vitro fecal fermentations were used to design dietary fiber mixtures to support complementary microbial groups related to health. Then, microbial responses were compared for the designed mixtures versus their single fiber components in vitro using fecal samples from a separate cohort of 10 healthy adults. The designed fiber mixtures outperformed individual fibers in supporting bacterial taxa across donors resulting in superior alpha diversity and unexpected higher SCFA production. Moreover, unique shifts in community structure and specific taxa were observed for fiber mixtures that were not observed for single fibers, suggesting a synergistic effect when certain fibers are put together. Fiber mixture responses were remarkably more consistent than individual fibers across donors in promoting several taxa, especially butyrate producers from the Clostridium cluster XIVa. This is the first demonstration of synergistic fiber interactions for superior support of a diverse group of important beneficial microbes consistent across people, and unexpectedly high SCFA production. Overall, harnessing the synergistic potential of designed fiber mixtures represents a promising and more efficacious avenue for future prebiotic development.

The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo

Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.

Prenatal PFAS exposure and outcomes related to maternal gut microbiome composition in later pregnancy

The composition of the gut microbiome is dependent on factors including diet, lifestyle, and exposure to environmental chemicals, and has implications for human health. Per- and polyfluoroalkyl substances (PFAS), a class of man-made chemicals that have nonstick and flame-retardant properties may impact on gut microbiome composition. Our objective was to elucidate links between PFAS and maternal gut microbiome composition in two geographically diverse sites of the Environmental Influences on Child Health Outcomes program. The present analysis includes participants in the Atlanta African American Maternal Child Cohort; ATL AA and a predominately non-Hispanic White subsample of the Michigan Archive for Research on Child Health Cohort; MARCH with serum or plasma PFAS concentrations measured in early or late pregnancy and 16s rRNA sequencing from maternal gut microbiome samples available primarily in later pregnancy (2nd-3rd trimester). Linear regression models tested associations between prenatal PFAS levels (separately for the 1st/3rd trimesters) and measures of alpha diversity, bacterial composition differences, and differential taxonomic abundance. Bayesian Kernel Machine Regression and Elastic net regression mixture modeling were also incorporated. In both cohorts, multiple PFAS were significantly associated with the relative abundance of specific microbiome taxa even after adjustment for covariates including maternal diet, age, race, BMI, and smoking; A total of 16 significant family-level associations were identified for ATL AA (e.g., PFOA with Clostridiaceae; natural log fold change = 0.94) and 13 significant family-level associations identified for MARCH e.g., PFOS with Desulfovibrionaceae; natural log fold change = -1.53 (pFDR<0.05), but similarities between cohorts were lacking. Mixture analyses did not identify interactive or combined effects but did provide modest evidence of inclusion of individual PFAS in beta diversity models in both cohorts. In 2 distinct cohorts, there were significant associations between prenatal PFAS and the relative abundance of several bacterial taxa, but these differences were cohort-specific. This work suggests that PFAS may modulate the gut microbiome during pregnancy.

Butyrate: a key mediator of gut-brain communication in Alzheimer's disease

Alzheimer's disease (AD), a prevalent neurodegenerative disorder, represents a significant global health challenge, characterized by cognitive decline and neuroinflammation. Recent investigations have highlighted the critical role of the gut-brain axis in the pathogenesis of AD, particularly focusing on the influence of short-chain fatty acids (SCFAs), metabolites produced by the gut microbiota through the fermentation of dietary fiber. Among SCFAs, butyrate has emerged as a crucial mediator, positively impacting various pathological processes associated with AD, including epigenetic regulation, neuroinflammation modulation, maintenance of the blood-brain barrier (BBB), enhanced intestinal integrity, regulation of brain metabolism, and interference with amyloid protein formation as well as tau protein hyperphosphorylation. Furthermore, distinctions in butyrate profile and microbial communities have been observed between AD patients and healthy individuals, underscoring the importance of gut microbiota in AD progression. This review summarizes the current understanding of the many functions of butyrate in reducing the consequences of AD and emphasizes the possibility of addressing the gut microbiota as a therapeutic approach to managing AD.

Food-Based Interventions as Therapy for Inflammatory Bowel Disease: Important Steps in Diet Trial Design and Reporting of Outcomes

Diet therapy for inflammatory bowel disease (IBD) is an international research priority but guidance for IBD-specific diet trial design is lacking. This review critically evaluates key elements of prospective IBD food-based intervention trials and identifies gaps. Electronic databases were searched for interventional IBD diet studies. Prospective primary studies/trials were included if used food-based dietary strategies. Forty studies/trials evaluating 29 food-based strategies as therapy for IBD were identified. Considerable heterogeneity in diets, trial design, and methodology exists. Thirty-one trials (78%) intended the diet to modulate inflammation but 14/31 (46%) did not have a primary endpoint measuring an objective change in inflammatory activity and 20/31 (65%) controlled for medication stability prior to application of diet at baseline. Higher-quality IBD diet trials used symptom-based assessment tools coupled with an objective evaluation of inflammatory activity. Dietary advice trials are the most common. One-third of trials developed and administered diet education without a dietitian. Evaluation and reporting on adherence to diet therapy occurred in <60% of trials. Failure to include or report on key elements of trial design reduced the interpretability and validity of the results. This is a considerable limitation to advancing scientific knowledge in this area. Diet therapy trials should adhere to similar rigorous quality standards used to develop other IBD therapies. Therefore, a set of practical recommendations was generated to provide the authors' perspective to help inform the future design of high-quality IBD diet trials.

Environmental risk factors of inflammatory bowel disease: toward a strategy of preventative health

The pathogenesis of inflammatory bowel disease (IBD) involves a complex interplay between genetic, environmental, and microbial factors. Many of these environmental determinants are modifiable, offering opportunities to prevent disease or delay its onset. Advances in the study of preclinical IBD cohorts offer the potential to identify biomarkers that predict individuals at high risk of developing IBD, enabling targeted environmental interventions aimed at reducing IBD incidence. This review summarizes findings from 79 meta-analyses on modifiable environmental factors associated with the development of IBD. Identified risk factors include smoking, Western diets, ultra-processed foods, and early life antibiotic use, while protective factors include breastfeeding, Mediterranean diets rich in fiber, plant-based foods, and fish, along with an active physical lifestyle. Despite the promise shown by observational data, interventional or randomized controlled studies evaluating the efficacy of modifying environmental risk factors remain limited and mostly focus on dietary intervention. This review aims to inform the design of higher quality interventional and randomized controlled studies for disease prevention while providing actionable guidance to healthcare providers on reducing the risk of developing IBD through environmental modifications.

Microbiome and climate: skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate

The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Understanding these effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to higher climate variability, particularly in temperature fluctuations. Additionally, the functional traits of microbial communities changed in parallel with shifts in community diversity and composition. The significant correlations of the functional redundancy index with climatic factors suggest that environmental filtering driven by climate change impacts microbial community functional stability. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.IMPORTANCEThis study is important in understanding the association between climate variability, microbial diversity, and host adaptation in amphibians, which are particularly vulnerable to environmental changes due to their poikilothermic nature. Amphibians rely on their skin microbiome for key functions like disease resistance, yet little is known about how climate fluctuations impact these microbial communities. By analyzing the microbiome of Polypedates megacephalus across different climatic regimes, our analysis reveals that warmer climates could reduce the microbial diversity and community functional redundancy, indicating the functional stability of skin microbiome could be susceptible to climate variability, particularly in hosts adapted to relatively cooler conditions. These findings highlight the potential ecological consequences of climate change and emphasize the need to integrate microbiome health into amphibian conservation strategies.

Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome

Oncologists increasingly recognize the microbiome as an important facilitator of health as well as a contributor to disease, including, specifically, cancer. Our knowledge of the etiologies, mechanisms, and modulation of microbiome states that ameliorate or promote cancer continues to evolve. The progressive refinement and adoption of "omic" technologies (genomics, transcriptomics, proteomics, and metabolomics) and utilization of advanced computational methods accelerate this evolution. The academic cancer center network, with its immediate access to extensive, multidisciplinary expertise and scientific resources, has the potential to catalyze microbiome research. Here, we review our current understanding of the role of the gut microbiome in cancer prevention, predisposition, and response to therapy. We underscore the promise of operationalizing the academic cancer center network to uncover the structure and function of the gut microbiome; we highlight the unique microbiome-related expert resources available at the City of Hope of Comprehensive Cancer Center as an example of the potential of team science to achieve novel scientific and clinical discovery.

Retrieval of conditioned immune response in male mice is mediated by an anterior-posterior insula circuit

To protect the body from infections, the brain has evolved the ability to coordinate behavioral and immunological responses. The conditioned immune response (CIR) is a form of Pavlovian conditioning wherein a sensory (for example, taste) stimulus, when paired with an immunomodulatory agent, evokes aversive behavior and an anticipatory immune response after re-experiencing the taste. Although taste and its valence are represented in the anterior insular cortex and immune response in the posterior insula and although the insula is pivotal for CIRs, the precise circuitry underlying CIRs remains unknown. Here, we demonstrated that a bidirectional circuit connecting the anterior and posterior (aIC-pIC) insula mediates the CIR in male mice. Retrieving the behavioral dimension of the association requires activity of aIC-to-pIC neurons, whereas modulating the anticipatory immunological dimension requires bidirectional projections. These results illuminate a mechanism by which experience shapes interactions between sensory internal representations and the immune system. Moreover, this newly described intrainsular circuit contributes to the preservation of brain-dependent immune homeostasis.

Exploring the microbiota-gut-brain axis: impact on brain structure and function

The microbiota-gut-brain axis (MGBA) plays a significant role in the maintenance of brain structure and function. The MGBA serves as a conduit between the CNS and the ENS, facilitating communication between the emotional and cognitive centers of the brain via diverse pathways. In the initial stages of this review, we will examine the way how MGBA affects neurogenesis, neuronal dendritic morphology, axonal myelination, microglia structure, brain blood barrier (BBB) structure and permeability, and synaptic structure. Furthermore, we will review the potential mechanistic pathways of neuroplasticity through MGBA influence. The short-chain fatty acids (SCFAs) play a pivotal role in the MGBA, where they can modify the BBB. We will therefore discuss how SCFAs can influence microglia, neuronal, and astrocyte function, as well as their role in brain disorders such as Alzheimer's disease (AD), and Parkinson's disease (PD). Subsequently, we will examine the technical strategies employed to study MGBA interactions, including using germ-free (GF) animals, probiotics, fecal microbiota transplantation (FMT), and antibiotics-induced dysbiosis. Finally, we will examine how particular bacterial strains can affect brain structure and function. By gaining a deeper understanding of the MGBA, it may be possible to facilitate research into microbial-based pharmacological interventions and therapeutic strategies for neurological diseases.

Using metabolomics to investigate the relationship between the metabolomic profile of the intestinal microbiota derivatives and mental disorders in inflammatory bowel diseases: a narrative review

Individuals with inflammatory bowel disease (IBD) are at a higher risk of developing mental disorders, such as anxiety and depression. The imbalance between the intestinal microbiota and its host, known as dysbiosis, is one of the factors, disrupting the balance of metabolite production and their signaling pathways, leading to disease progression. A metabolomics approach can help identify the role of gut microbiota in mental disorders associated with IBD by evaluating metabolites and their signaling comprehensively. This narrative review focuses on metabolomics studies that have comprehensively elucidated the altered gut microbial metabolites and their signaling pathways underlying mental disorders in IBD patients. The information was compiled by searching PubMed, Web of Science, Scopus, and Google Scholar from 2005 to 2023. The findings indicated that intestinal microbial dysbiosis in IBD patients leads to mental disorders such as anxiety and depression through disturbances in the metabolism of carbohydrates, sphingolipids, bile acids, neurotransmitters, neuroprotective, inflammatory factors, and amino acids. Furthermore, the reduction in the production of neuroprotective factors and the increase in inflammation observed in these patients can also contribute to the worsening of psychological symptoms. Analyzing the metabolite profile of the patients and comparing it with that of healthy individuals using advanced technologies like metabolomics, aids in the early diagnosis and prevention of mental disorders. This approach allows for the more precise identification of the microbes responsible for metabolite production, enabling the development of tailored dietary and pharmaceutical interventions or targeted manipulation of microbiota.

Synergistic interactions between gut microbiota and short chain fatty acids: Pioneering therapeutic frontiers in chronic disease management

Microorganisms in the gut play a pivotal role in human health, influencing various pathophysiological processes. Certain microorganisms are particularly essential for maintaining intestinal homeostasis, reducing inflammation, supporting nervous system function, and regulating metabolic processes. Short-chain fatty acids (SCFAs) are a subset of fatty acids produced by the gut microbiota (GM) during the fermentation of indigestible polysaccharides. The interaction between GM and SCFAs is inherently bidirectional: the GM not only shapes SCFAs composition and metabolism but SCFAs also modulate microbiota's diversity, stability, growth, proliferation, and metabolism. Recent research has shown that GM and SCFAs communicate through various pathways, mainly involving mechanisms related to inflammation and immune responses, intestinal barrier function, the gut-brain axis, and metabolic regulation. An imbalance in GM and SCFA homeostasis can lead to the development of several chronic diseases, including inflammatory bowel disease, colorectal cancer, systemic lupus erythematosus, Alzheimer's disease, and type 2 diabetes mellitus. This review explores the synergistic interactions between GM and SCFAs, and how these interactions directly or indirectly influence the onset and progression of various diseases through the regulation of the mechanisms mentioned above.

The Role of Gut Microbiota Dysbiosis in Erectile Dysfunction: From Pathophysiology to Treatment Strategies

Erectile dysfunction (ED) is a prevalent male sexual disorder characterized by the persistent inability to achieve or maintain an erection sufficient for satisfactory sexual performance. While its etiology is multifactorial, encompassing vascular, neurological, hormonal, and psychological components, emerging evidence suggests a significant role for gut microbiota dysbiosis in its development. The gut microbiota influences various metabolic, inflammatory, and neuropsychological processes critical to erectile function. Dysbiosis can lead to systemic inflammation, endothelial dysfunction, hormonal imbalances, and altered neurotransmitter production, all of which are key factors in ED pathogenesis. This narrative review synthesizes current research on the association between gut microbiota alterations and ED, highlighting specific bacterial taxa implicated in ED through mechanisms involving inflammation, metabolic disturbances, and hormonal regulation. This review explores potential mechanisms linking gut microbiota and ED, including pro-inflammatory cytokines, gut barrier integrity disruption, metabolic disorders, psychological factors via the gut-brain axis, and hormonal regulation. Furthermore, the gut microbiota offers promising avenues for developing non-invasive biomarkers and therapeutic interventions such as probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation. Future research should focus on longitudinal studies, mechanistic explorations, and clinical trials to validate these findings and translate them into clinical practice. Understanding the interplay between the gut microbiota and erectile function could unveil novel diagnostic biomarkers and pave the way for innovative treatments targeting the microbiota, ultimately improving men's sexual and overall health.

Shaping oral and intestinal microbiota and the immune system during the first 1,000 days of life

The first 1, 000 days of life, from the fetal stage of a woman's pregnancy to 2 years of age after the baby is born, is a critical period for microbial colonization of the body and development of the immune system. The immune system and microbiota exhibit great plasticity at this stage and play a crucial role in subsequent development and future health. Two-way communication and interaction between immune system and microbiota is helpful to maintain human microecological balance and immune homeostasis. Currently, there is a growing interest in the important role of the microbiota in the newborn, and it is believed that the absence or dysbiosis of human commensal microbiota early in life can have lasting health consequences. Thus, this paper summarizes research advances in the establishment of the oral and intestinal microbiome and immune system in early life, emphasizing the substantial impact of microbiota diversity in the prenatal and early postnatal periods, and summarizes that maternal microbes, mode of delivery, feeding practices, antibiotics, probiotics, and the environment shape the oral and intestinal microbiota of infants in the first 1, 000 days of life and their association with the immune system.

Influence of ESBL colonization status on gut microbiota composition during allogenic hematopoietic stem cell transplantation

After allogeneic HSCT (allo-HSCT), the diversity of the intestinal microbiota significantly decreases. The changes can be rapid and are thought to be caused by chemotherapy, antibiotics, or intestinal inflammation. Most patients are exposed to prophylactic and therapeutic antibiotics during neutropenia and several patients are colonized by ESBL bacteria. We investigated the changes in gut microbiota composition in allo-HSCT, aiming at investigating if the acquisition of ESBL colonization may affect gut microbiome diversity during allo-HSCT. This was a single-center prospective pilot study. All patients consecutively admitted to the Haematological Unit of the City of Health and Science, Molinette Hospital in Turin, Italy, and undergoing allo-HSCT between August 2017 to August 2020 were enrolled in the study. Microbiome analysis on fecal samples were collected every 7 days from hospital admission to discharge and until 1 year after HSCT. 48 patients were enrolled in the study. At baseline 14 patients (29.16%) were colonized by MDR bacteria, mostly extended-spectrum beta-lactamase (ESBL)-producing gram negatives (N = 11; 78.57%). During allo-HSCT, one patient had a positive rectal swab for a carbapenemase-producing Klebsiella pneumoniae and eight patients lost the colonization during the hospital stay. Microbiota composition was compared between patients colonized by ESBL at baseline and non-colonized patients. Patients colonized by ESBL had a greater abundances of Bifidobacterium, Blautia, Clostridium, Coprococcus, L-Ruminococcus Mogibacteriaceae, Peptostreptococceae and Oscillospira, while non-colonized ESBL patients had a greater abundance of Actinomycetales, Staphylococcus and Sutterella. Moreover, microbiota composition of colonized by ESBL that retained colonization after HSCT showed an increased in abundances of Akkermansia, Dialister, Erysipelotrichaceae and Methanobrevibacter when compared with patients that become negative at rectal swabs. From a clinical perspective, the evolution of this prospective pilot study will be to investigate markers of gut barrier functions, SCFA productions and to correlate the predictivity of these parameters with risk of invasive infections and clinical outcomes in allo-HSCT population.

The non-nutritive sweetener rebaudioside a enhances phage infectivity

Non-nutritive sweeteners (NNS) are widely employed in foodstuffs. However, it has become increasingly evident that their consumption is associated with bacterial dysbiosis, which, in turn, is linked to several health conditions, including a higher risk of type 2 diabetes and cancer. Among the NNS, stevia, whose main component is rebaudioside A (rebA), is gaining popularity in the organic food market segment. While the effect of NNS on bacteria has been established, the impact of these sweeteners on bacterial viruses (phages) has been neglected, even though phages are crucial elements in maintaining microbial eubiosis. The present study sought to provide a proof-of-concept of the impact of NNS on phage infectivity by assessing the binding of rebA to phage proteins involved in the infection process of enteropathogenic bacteria, namely the fiber protein gp17 of Yersinia enterocolitica phage φYeO3-12 and the tubular baseplate protein gp31 of Klebsiella pneumoniae phage 32. We employed docking analysis and a panel of in vitro confirmatory tests (microscale thermophoresis, RedStarch™ depolymerization, adsorption, and lysis rates). Docking analysis indicated that NNS can bind to both fiber and baseplate proteins. Confirmatory assays demonstrated that rebA can bind gp31 and that such binding increased the protein's enzymatic activity. Moreover, the binding of rebA to gp17 resulted in a decrease in the adsorption rate of the recombinant protein to its host but increased the Yersinia bacteriolysis caused by the whole phage compared to unexposed controls. These results support the hypothesis that NNS can impair phage infectivity, albeit the resulting effect on the microbiome remains to be elucidated.

Fish gut microbiome and its application in aquaculture and biological conservation

Understanding the diversity and function of fish gut microbiomes has advanced substantially, yet many aspects remain poorly understood, particularly the interplay among microbiota, host species, and environmental factors in the context of conservation. This review explores the composition and abundance of gut bacterial communities in key aquaculture fish groups-cyprinids, ictalurids (catfish), salmonids, and cichlids (tilapia)-alongside the model organism zebrafish, across diverse geographic regions. The findings highlight environmental habitats and host species as primary determinants of gut microbiome structure, offering a global perspective on these microbial communities. Across all fish groups, the phyla Firmicutes, Fusobacteria, and Proteobacteria consistently dominated, while temperate, sub-equatorial, and sub-tropical regions exhibited the highest microbiome diversity, underscoring the contribution of taxonomic and environmental factors. The gut bacterial diversity of farm-raised fish shows a significant divergence from that of wild-caught fish, reflecting the impacts of ecological and management differences. Understanding the dynamic responses of fish gut microbiota is vital for guiding conservation efforts, safeguarding aquatic biodiversity, and advancing sustainable aquaculture practices. Future research should leverage innovative techniques and integrative approaches, both experimental and theoretical, to uncover the functional roles of microbiomes and predict their responses to environmental changes. Expanding geographic and taxonomic coverage will be critical for creating a comprehensive framework to inform global aquaculture and conservation strategies. Collectively, this perspective highlights the transformative potential of microbiome research in addressing global challenges in aquaculture and conservation biology.

An interdisciplinary perspective of the built-environment microbiome

The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.

Fecal microbiota transplantation, a tool to transfer healthy longevity

The complex gut microbiome influences host aging and plays an important role in the manifestation of age-related diseases. Restoring a healthy gut microbiome via Fecal Microbiota Transplantation (FMT) is receiving extensive consideration to therapeutically transfer healthy longevity. Herein, we comprehensively review the benefits of gut microbial rejuvenation - via FMT - to promote healthy aging, with few studies documenting life length properties. This review explores how preconditioning donors via standard - lifestyle and pharmacological - antiaging interventions reshape gut microbiome, with the resulting benefits being also FMT-transferable. Finally, we expose the current clinical uses of FMT in the context of aging therapy and address FMT challenges - regulatory landscape, protocol standardization, and health risks - that require refinement to effectively utilize microbiome interventions in the elderly.

Gut microbiome strain-sharing within isolated village social networks

When humans assemble into face-to-face social networks, they create an extended social environment that permits exposure to the microbiome of others, thereby shaping the composition and diversity of the microbiome at individual and population levels1-6. Here we use comprehensive social network mapping and detailed microbiome sequencing data in 1,787 adults within 18 isolated villages in Honduras7 to investigate the relationship between network structure and gut microbiome composition. Using both species-level and strain-level data, we show that microbial sharing occurs between many relationship types, notably including non-familial and non-household connections. Furthermore, strain-sharing extends to second-degree social connections, suggesting the relevance of a person's broader network. We also observe that socially central people are more microbially similar to the overall village than socially peripheral people. Among 301 people whose microbiome was re-measured 2 years later, we observe greater convergence in strain-sharing in connected versus otherwise similar unconnected co-villagers. Clusters of species and strains occur within clusters of people in village social networks, meaning that social networks provide the social niches within which microbiome biology and phenotypic impact are manifested.

What Veterinarians Need to Know About the Newly-Emerging Field of Insects-as-Food-and-Feed

Over the last two decades, the insects-as-food-and-feed industry has rapidly emerged. Its growth is largely because insects require substantially less resources (water, food, and energy) to produce than traditional sources of animal protein, making it a sustainable alternative food option. As this industry continues to grow, veterinarians will likely be called upon to assist in identifying food safety concerns, assessing animal health, implementing biosecurity measures, and formulating/prescribing treatment protocols comparable to what we have seen with the honeybee industry and the institution of veterinary feed directives (VFDs). Similar to other agricultural markets, high animal densities and management practices put insects at high risk for infectious diseases. Veterinarians interested in working with these species will need to become knowledgeable regarding the diseases afflicting the feeder insect industry and how best to diagnose and treat pathogens of concern. Using the edible cricket industry as an example, this review will highlight health and production issues while drawing similarities to other traditional livestock operations. If the insects-as-feed-and-food industry is going to be viable, veterinary involvement will be essential to ensure that insects can be used as a safe source of food for all.

Short-Term Supplementation of Sauerkraut Induces Favorable Changes in the Gut Microbiota of Active Athletes: A Proof-of-Concept Study

BACKGROUND

Since the gut microbiota is important for athlete health and performance, its optimization is increasingly gaining attention in sports nutrition, for example, with whole fermented foods. Sauerkraut is a traditional fermented food rich in pro-, pre-, and postbiotics, which has not yet been investigated in the field of sports nutrition.

METHODS

To determine whether sauerkraut could be used for gut microbiota optimization in sports nutrition, a proof-of-concept study was conducted. The microbiota composition of organic pasteurized sauerkraut was analyzed, and then healthy active athletes were provided with the same sauerkraut for 10 days as an intervention. The effects of sauerkraut on the athlete's gut microbiota, laboratory parameters, and bowel function were assessed.

RESULTS

Significant changes in the gut microbiota composition were seen on taxonomic and functional levels, independent of baseline microbiota composition, even after short-term supplementation. Most notably, there was an increase in several health-promoting genera of the family Lachnospiraceae, as well as significant alterations in metabolic pathways regarding cell wall synthesis and the metabolism of nucleotide bases. An increase in the proportion of lymphocytes and a decrease in B12 vitamin levels was observed, as well as a risk of indigestion in certain athletes, which significantly resolved after seven days of supplementation in all athletes. It is unclear whether the observed effects are attributable to the sauerkraut's own microbiome or its pre- and postbiotics since it is a whole food.

CONCLUSIONS

Our study has demonstrated that the concept of whole fermented foods, such as sauerkraut, could potentially be feasible and effective in sports nutrition for gut microbiota optimization.

The role for ω-3 polyunsaturated and short chain fatty acids in hypertension: An updated view on the interaction with gut microbiota

As of 2024, arterial hypertension is still considered the leading modifiable cardiovascular risk factor and, due to high rates of undertreatment and poor blood pressure control, the major contributor to human morbidity and mortality. Development of new treatment options and better interventions in lifestyle correction have become a priority of experimental and clinical research. In the last decades, dietary supplementation of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) and generation of gut microbiota-derived short chain fatty acids (SCFAs) have surged as potential and promising interventions for hypertension and cardiovascular prevention. ω-3 PUFAs are considered "essential" fatty acids that can be obtained only from dietary sources. Although previous intervention trials were not consistent in reporting a significant benefit of ω-3 PUFAs, the recent REDUCE-IT trial has provided robust evidence in support of their role in cardiovascular prevention. Recent studies have also identified the intestinal microbiota as a potential player in the pathophysiology and progression of hypertension. Although this might occur through many pathways, generation of SCFAs that is highly dependent on dietary fiber intake is primarily involved, providing an additional target for the development of novel therapeutic strategies. For these reasons, some scientific societies currently recommend dietary supplementation of ω-3 PUFAs and fiber-containing foods in patients with hypertension. In this narrative review, we summarize the results of studies that examined the effects of ω-3 PUFAs and SCFAs on blood pressure, highlighting the mechanisms of action on the vascular system and their possible impact on hypertension, hypertension-related organ damage and, ultimately, cardiovascular outcomes.

DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis

Microbial data analysis poses significant challenges due to its high dimensionality, sparsity, and compositionality. Recent advances have shown that integrating abundance and phylogenetic information is an effective strategy for uncovering robust patterns and enhancing the predictive performance in microbiome studies. However, existing methods primarily focus on the hierarchical structure of phylogenetic trees, overlooking the evolutionary distances embedded within them. This study introduces DeepPhylo, a novel method that employs phylogeny-aware amplicon embeddings to effectively integrate abundance and phylogenetic information. DeepPhylo improves both the unsupervised discriminatory power and supervised predictive accuracy of microbiome data analysis. Compared to the existing methods, DeepPhylo demonstrates superiority in informing biologically relevant insights across five real-world microbiome use cases, including clustering of skin microbiomes, prediction of host chronological age and gender, diagnosis of inflammatory bowel disease (IBD) across 15 studies, and multilabel disease classification.

Effects of Polyvinyl Chloride (PVC) Microplastic Particles on Gut Microbiota Composition and Health Status in Rabbit Livestock

The widespread use of polyvinyl chloride (PVC) and its entry into humans and livestock is of serious concern. In our study, we investigated the impact of PVC treatments on physiological, pathological, hormonal, and microbiota changes in female rabbits. Trend-like alterations in weight were observed in the spleen, liver, and kidney in both low (P1) and high dose (P2) PVC treatment groups. Histopathological examination revealed exfoliation of the intestinal mucosa in the treated groups compared to the control, and microplastic particles were penetrated and embedded in the spleen. Furthermore, both P1 and P2 showed increased 17-beta-estradiol (E2) hormone levels, indicating early sexual maturation. Moreover, the elevated tumor necrosis factor alpha (TNF-α) levels suggest inflammatory reactions associated with PVC treatment. Genus-level analyses of the gut microbiota in group P2 showed several genera with increased or decreased abundance. In conclusion, significant or trend-like correlations were demonstrated between the PVC content of feed and physiological, pathological, and microbiota parameters. To our knowledge, this is the first study to investigate the broad-spectrum effects of PVC microplastic exposure in rabbits. These results highlight the potential health risks associated with PVC microplastic exposure, warranting further investigations in both animals and humans.

Role of Microbiota-Derived Hydrogen Sulfide (H2S) in Modulating the Gut-Brain Axis: Implications for Alzheimer's and Parkinson's Disease Pathogenesis

Microbiota-derived hydrogen sulfide (H2S) plays a crucial role in modulating the gut-brain axis, with significant implications for neurodegenerative diseases such as Alzheimer's and Parkinson's. H2S is produced by sulfate-reducing bacteria in the gut and acts as a critical signaling molecule influencing brain health via various pathways, including regulating inflammation, oxidative stress, and immune responses. H2S maintains gut barrier integrity at physiological levels and prevents systemic inflammation, which could impact neuroinflammation. However, as H2S has a dual role or a Janus face, excessive H2S production, often resulting from gut dysbiosis, can compromise the intestinal barrier and exacerbate neurodegenerative processes by promoting neuroinflammation and glial cell dysfunction. This imbalance is linked to the early pathogenesis of Alzheimer's and Parkinson's diseases, where the overproduction of H2S exacerbates beta-amyloid deposition, tau hyperphosphorylation, and alpha-synuclein aggregation, driving neuroinflammatory responses and neuronal damage. Targeting gut microbiota to restore H2S homeostasis through dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation presents a promising therapeutic approach. By rebalancing the microbiota-derived H2S, these strategies may mitigate neurodegeneration and offer novel treatments for Alzheimer's and Parkinson's diseases, underscoring the critical role of the gut-brain axis in maintaining central nervous system health.

Protocol for the collection, packaging, and transportation of preterm newborn stool samples

BACKGROUND

The newborn's intestinal microbiota can vary with gestational age. Reliable analyses of stool samples require establishing the steps of collection, packaging, transportation, and storage.

OBJECTIVE

To describe the development of a protocol and test an algorithm for the sequence of actions and procedures for the collection, packaging, transportation, and storage of stool samples from Preterm Newborn (PTNB) admitted to a Neonatal Intensive Care Unit (NICU).

MATERIALS AND METHODS

This is a descriptive, observational study linked to a non-randomized controlled clinical trial conducted in the NICU of two public hospitals covenanted to the Unified Health System of a large city in inland northeastern Brazil. The methodology adopted in its development followed the Brazilian Ministry of Health Preparation Guide recommendations.

RESULTS

The flow of actions and procedures was consistent with scientific evidence. The sequence of work process steps to implement the proposed protocol was tested and resulted in a graphical representation of an algorithm compatible with the reality of Brazilian public hospitals.

CONCLUSION

Following the protocol steps with the description of the rules of conduct and recommendations regarding the collection, packaging, transportation, and storage of stool samples from PTNBs ensured the preservation and integrity of the bacterial DNA in the stools sample. The details of the recommendations will allow their reproducibility and improvement by professionals and researchers with similar study objects.

TRIAL REGISTRATION

World Health Organization (WHO) under Universal Trial Number (UTN) code U1111-1266-2295, under register RBR-3mm7cs in the Brazilian Registry of Clinical Trials (REBEC).

Comparison of the urinary microbiome in men who have sex with men with and without Chlamydia trachomatis infection

PURPOSE

The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.

METHODS

This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.

RESULTS

Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).

CONCLUSION

Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.

Dietary Sugar and Saturated Fat Consumption Associated with the Gastrointestinal Microbiome during Pregnancy

BACKGROUND

Growing evidence supports changes in the gastrointestinal microbiome over the course of pregnancy may have an impact on the short- and long-term health of both the mother and the child.

OBJECTIVE

Our objective was to explore the association of diet quality, as measured by the Healthy Eating Index (HEI), with the composition and gene ontology (GO) representation of microbial function in the maternal gastrointestinal microbiome during pregnancy.

METHODS

We conducted a retrospective, observational analysis of n = 185 pregnant participants in the Pregnancy Eating Attributes Study. Maternal dietary intake was assessed in the first trimester using the automated self-administered 24-h recall method, from which the HEI 2015 was calculated. Rectal swabs were obtained in the second trimester and sequenced using the NovaSeq 6000 system shotgun platform. We used unsupervised clustering to identify microbial enterotypes representative of maternal taxa and GO functional term composition. Multivariable linear models were used to identify associations between taxa, functional terms, and food components while controlling for relevant covariates. Multinomial regression was then used to predict enterotype membership based on a participant's HEI food component score.

RESULTS

Those in the high diet quality tertile had a lower early pregnancy BMI [mean (M) = 23.48 kg/m2, SD = 3.38] compared with the middle (M = 27.35, SD = 6.01) and low (M = 27.49, SD = 6.99) diet quality tertiles (P < 0.01). There were no statistically significant associations between the HEI components or the total HEI score and the 4 alpha diversity measures. Differences in taxa and GO term enterotypes were found in participants with, but not limited to, a higher saturated fat component score (β = 1.35, P = 0.01), added sugar HEI component (β = 0.07, P < 0.001), and higher total dairy score (β = 1.58, P = 0.01).

CONCLUSIONS

Specific dietary components are associated with microbial composition and function in the second trimester of pregnancy. These findings provide a foundation for future testable hypotheses.

A cross-systems primer for synthetic microbial communities

The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.

Gut-brain axis and neurodegeneration: mechanisms and therapeutic potentials

This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors.

Bacterial and clinical metabolic signatures and their interactions in obese patients post-bariatric surgery

BACKGROUND

Obesity is a growing health concern in China, closely linked to metabolic disorders such as type 2 diabetes. Laparoscopic Sleeve Gastrectomy (LSG) is effective in promoting weight loss and improving metabolic outcomes. Emerging evidence highlights the role of gut microbiota in metabolic regulation, yet the specific alterations in gut microbiota and their association with metabolic changes post-surgery in Chinese patients remain unclear. Understanding these shifts could provide key insights into optimizing treatment strategies for metabolic improvement following bariatric surgery.

METHODS

Stool samples and clinical data were collected from 30 obese patients before and 6 months after surgery. The composition of the gut microbiota was analyzed through 16S rRNA sequencing, and Spearman correlation analysis was used to determine the association between gut microbiota and clinical indicators.

RESULTS

The analysis of 30 patients showed a significant decrease in Body Mass Index (BMI) (36.75 ± 4.09 kg/m2 vs 26.37 ± 3.47 kg/m2, p < 0.0001). Glucose metabolism, including Hemoglobin A1C levels, improved significantly (6.05 ± 0.96 vs 5.05 ± 0.25, p < 0.0001), and liver function as well as serum lipid levels were also notably improved. LSG increased the richness and composition of gut microbiota in obese patients post-surgery. These changes in gut microbiota were closely associated with improved clinical metabolic parameters.

CONCLUSION

LSG not only significantly reduces body weight while also alleviating metabolic syndrome and comorbidities by altering gut microbiota.

The diversity of the microbiome impacts chronic lymphocytic leukemia development in mice and humans

The gut microbiota plays a critical role in maintaining a healthy human body and its dysregulation is associated with various diseases. In this study, we investigated the influence of gut microbiome diversity on the development of chronic lymphocytic leukemia (CLL). Analysis of stool samples from 59 CLL patients revealed individual and heterogeneous microbiome compositions, but allowed for grouping of patients according to their microbiome diversity. Interestingly, CLL patients with lower microbiome diversity and an enrichment of bacteria linked to poor health suffered from a more advanced or aggressive form of CLL. In the Eµ-TCL1 mouse model of CLL, we observed a faster course of disease when mice were housed in high hygiene conditions. Shotgun DNA sequencing of fecal samples showed that this was associated with a lower microbiome diversity which was dominated by Mucispirillum and Parabacteroides genera in comparison to mice kept under lower hygiene conditions. In conclusion, we applied taxonomic microbiome analyses to demonstrate a link between gut microbiome diversity and the clinical course of CLL in humans, as well as the development of CLL in mice. Our novel data serve as a basis for further investigations to decipher the pathological and mechanistic role of intestinal microbiota in CLL development.

Microbiota-immune-brain interactions: A new vision in the understanding of periodontal health and disease

This review highlights the significance of interactions between the microbiota, immune system, nervous and hormonal systems, and the brain on periodontal health and disease. Microorganisms in the microbiota, immune cells, and neurons communicate via homeostatic nervous and hormonal systems, regulating vital body functions. By modulating pro-inflammatory and anti-inflammatory adaptive immune responses, these systems control the composition and number of microorganisms in the microbiota. The strength of these brain-controlled responses is genetically determined but is sensitive to early childhood stressors, which can permanently alter their responsiveness via epigenetic mechanisms, and to adult stressors, causing temporary changes. Clinical evidence and research with humans and animal models indicate that factors linked to severe periodontitis enhance the responsiveness of these homeostatic systems, leading to persistent hyperactivation. This weakens the immune defense against invasive symbiotic microorganisms (pathobionts) while strengthening the defense against non-invasive symbionts at the gingival margin. The result is an increased gingival tissue load of pathobionts, including Gram-negative bacteria, followed by an excessive innate immune response, which prevents infection but simultaneously destroys gingival and periodontal tissues. Thus, the balance between pro-inflammatory and anti-inflammatory adaptive immunity is crucial in controlling the microbiota, and the responsiveness of brain-controlled homeostatic systems determines periodontal health.

Disrupted gut harmony in attention-deficit/hyperactivity disorder: Dysbiosis and decreased short-chain fatty acids

Background

Attention-Deficit Hyperactivity Disorder (ADHD) is a prevalent neurodevelopmental disorder with complex genetic and environmental underpinnings. Emerging evidence suggests a significant role of gut microbiota in ADHD pathophysiology. This study investigates variations in gut microbiota composition and Short-Chain Fatty Acid (SCFA) profiles between children and adolescents with ADHD and healthy controls.

Methods

The study included 42 ADHD patients and 31 healthy controls, aged 6-18 years. Fecal samples were analyzed for microbial composition using 16S rRNA gene sequencing and for SCFA profiles through gas chromatography-mass spectrometry (GC-MS). The study assessed both α and β diversity of gut microbiota and quantified various SCFAs to compare between the groups.

Results

ADHD subjects demonstrated significantly reduced gut microbiota diversity, as indicated by lower α-diversity indices (Shannon index, Observed species, Faith PD index) and a trend towards significance in β-diversity (Weighted UniFrac). Notably, the ADHD group exhibited significantly lower levels of key SCFAs, including acetic, propionic, isobutyric, isovaleric, and valeric acids, highlighting a distinct microbial and metabolic profile in these individuals.

Conclusion

This study uncovers significant alterations in gut microbiota and SCFA profiles in children with ADHD, compared to healthy controls. The observed changes in SCFAs, known for their associations with other behavioral and neurologic pathologies, and for their role in neural signaling. These findings offer a metabolite fingerprint that could potentially lead to novel diagnostic and treatment approaches for ADHD, emphasizing the importance of gut microbiota in the disorder's pathogenesis and management.

Synthetic Colonic Mucus Enables the Development of Modular Microbiome Organoids

The human colon is home to trillions of microorganisms that modulate gastrointestinal physiology. Our understanding of how this gut ecosystem impacts human health, although evolving, has been slowed by the lack of accessible tools suitable to studying complex host-mucus-microbe interactions. Here, we report a synthetic gel-like material capable of recapitulating the varied structural, mechanical, and biochemical profiles of native human colonic mucus to develop compositionally simple microbiome screening platforms with utility in microbiology and drug discovery. The viscous fibrillar material is realized through templated assembly of a fluorine-rich amino acid at liquid-liquid interphases. The fluorine-assisted mucus surrogate (FAMS) can be decorated with mucins to serve as a habitat for microbial colonization and integrated with human colorectal cells to generate artificial mucosae, referred to as a microbiome organoid. Notably, FAMS are made with inexpensive and commercially available materials, and can be generated using simple protocols and standard laboratory hardware. As a result, this platform can be broadly incorporated into various laboratory settings to advance probiotic research and inform in vivo approaches. If implemented into high throughput screening approaches, FAMS may represent a valuable tool to study compound metabolism and gut permeability, with an exemplary demonstration of this utility presented here.

Bowel Inflammation and Nutrient Supplementation: Effects of a Fixed Combination of Probiotics, Vitamins, and Herbal Extracts in an In Vitro Model of Intestinal Epithelial Barrier Dysfunction

The gut microbiota is a very important factor in the state of health of an individual, its alteration implies a situation of "dysbiosis," which can be connected to functional gastrointestinal disorders and pathological conditions, such as Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), Ulcerative Colitis (UC) and Crohn's Disease (CD), and Colorectal Cancer (CRC). In this work, we studied the effect of a food supplement called ENTERO-AD containing a mix of probiotics (Lactobacillus acidophilus LA1, L. reuteri LR92, Bifidobacterium breve Bbr8), Matricaria Chamomilla, and B group vitamins (B1, B2, B6) on intestinal inflammation. The in vitro model used for the study is the Caco-2 cell, a culture derived from human intestinal adenocarcinoma; the inflammatory condition was achieved with treatment with Lipopolysaccharide (LPS) and the association between Tumor necrosis factor α/Interferon γ (TNF-α/IFN-γ) [1,2]. The effect of ENTERO-AD was evaluated by cell viability, measures of Transepithelial Electrical Resistance (TEER), paracellular permeability, and immunofluorescence. Results of the study have shown that ENTERO-AD has a favorable effect on Caco-2 cells in inflammatory conditions. It improves the integrity of Occludin and Zonula Occludens-1 (ZO-1) proteins, leading to an improvement in terms of TEER values and a reduction of paracellular permeability. This evidence underlines the protective effect of ENTERO-AD and its components in intestinal inflammation.

Environmental Factors Associated With Risk of Crohn's Disease Development in the Crohn's and Colitis Canada - Genetic, Environmental, Microbial Project

BACKGROUND & AIMS

To date, it is unclear how environmental factors influence Crohn's disease (CD) risk and how they interact with biological processes. This study investigates the association between environmental exposures and CD risk and evaluates their association with pre-disease biomarkers.

METHODS

We studied 4289 healthy first-degree relatives (FDRs) of patients with CD from the Crohn's and Colitis Canada - Genetic, Environmental, Microbial (CCC-GEM) project. Regression models identified environmental factors associated with future CD onset and their association with pre-disease biological factors, including altered intestinal permeability measured by urinary fractional excretion of lactulose to mannitol ratio (LMR); gut inflammation via fecal calprotectin (FCP) levels; and fecal microbiome composition through 16S rRNA sequencing.

RESULTS

Over a 5.62-year median follow-up, 86 FDRs developed CD. Living with a dog between ages 5 and 15 (hazard ratio [HR], 0.62; 95% confidence interval [CI], 0.40-0.96; P = .034), and living with a large family size in the first year of life (HR, 0.43; 95% CI, 0.21-0.85; P = .016) were associated with decreased CD risk, whereas having a bird at the time of recruitment (HR, 2.78; 95% CI, 1.36-5.68; P = .005) was associated with an increased CD risk. Furthermore, living with a dog was associated with reduced LMR, altered relative abundance of multiple bacterial genera, and increased Chao1 diversity, whereas bird owners had higher FCP levels. Large family during participants' first year of life was associated with altered microbiota composition without affecting FCP or LMR.

CONCLUSION

This study identifies environmental variables associated with CD risk. These variables were also associated with altered barrier function, subclinical inflammation, and gut microbiome composition shifts, suggesting potential roles in CD pathogenesis.

Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults

PURPOSE

Population-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the consumption of plant-based foods (vegetables, potatoes, fruits, cereals), red and processed meat (RPM) or dairy (fermented milk, cheese, other dairy products) are related to gut microbiome in Finnish adults.

METHODS

We utilized data from the National FINRISK/FINDIET 2002 Study (n = 1273, aged 25-64 years, 55% women). Diet was assessed with 48-hour dietary recalls. Gut microbiome was analyzed using shallow shotgun sequencing. We applied multivariate analyses with linear models and permutational ANOVAs adjusted for relevant confounders.

RESULTS

Fruit consumption was positively (beta = 0.03, SE = 0.01, P = 0.04), while a dairy subgroup including milk, cream and ice-creams was inversely associated (beta=-0.03, SE 0.01, P = 0.02) with intra-individual gut microbiome diversity (alpha-diversity). Plant-based foods (R2 = 0.001, P = 0.03) and dairy (R2 = 0.002, P = 0.01) but not RPM (R2 = 0.001, P = 0.38) contributed to the compositional differences in gut microbiome (beta-diversity). Plant-based foods were associated with several butyrate producers/cellulolytic species including Roseburia hominis. RPM associations included an inverse association with R. hominis. Dairy was positively associated with several lactic producing/probiotic species including Lactobacillus delbrueckii and potentially opportunistic pathogens including Citrobacter freundii. Dairy, fermented milk, vegetables, and cereals were associated with specific microbial functions.

CONCLUSION

Our results suggest a potential association between plant-based foods and dairy or their subgroups with microbial diversity measures. Furthermore, our findings indicated that all the food groups were associated with distinct overall microbial community compositions. Plant-based food consumption particularly was associated with a larger number of putative beneficial species.

A comprehensive review of Bifidobacterium spp: as a probiotic, application in the food and therapeutic, and forthcoming trends

Recently, more consumers are interested in purchasing probiotic food and beverage products that may improve their immune health. The market for functional foods and beverages that include Bifidobacterium is expanding because of their potential uses in both food and therapeutic applications. However, maintaining Bifidobacterium's viability during food processing and storage remains a challenge. Microencapsulation technique has been explored to improve the viability of Bifidobacterium. Despite the technical, microbiological, and economic challenges, the market potential for immune-supporting functional foods and beverages is significant. Additionally, there is a shift toward postbiotics as a solution for product innovation, a promising postbiotic product that can be incorporated into various food and beverage formats is also introduced in this review. As consumers become more health-conscious, future developments in the functional food and beverage market discussed in this review could serve as a reference for researchers and industrialist.

Effect of green banana and pineapple fibre powder consumption on host gut microbiome

Purpose

To determine whether green banana powder (GBP) and pineapple fibre powder (PFP) promote beneficial bacterial species, directly improve human gut health and modulate the gut microbiome and understand their utility as functional foods and dietary supplements.

Methods

Over 14 days, 60 adults followed protocol requirements, completed food diaries and study questionnaires, avoided consuming supplements with prebiotics, probiotics or postbiotics, and ingested food containing 5 g of total daily fibre [placebo (10.75 g), GBP (10.75 g) or PFP (7.41 g)]. Participants' medical and baseline wellness histories, as well as stool samples, were collected at baseline, day 7 and 14. Stool DNA was processed for sequencing.

Results

Dietary fibre and resistant starches (RS) in GBP and PFP promoted temporal increases in beneficial bacteria. GBP significantly elevated 7 species (F. prausnitzii, B. longum, B. bifidum, B. adolescentis, B. pseudocatenulatum, B. obeum, and R. inulinivorans), while PFP enriched 6 species (B. ovatus, B. cellulosilyticus, B. bifidum, B. intestinalis, R. inulinivorans, and E. siraeum). These bacteria, found to be deficient in younger adults, were promoted by both powders. PFP benefitted both genders aged 16-23, while GBP benefitted overweight/obese individuals, including females. GBP and PFP fiber and RS improved bowel regularity and health as well as metabolism by promoting histidine, branched-chain amino acids, short-chain fatty acids, and biotin production. The additional fiber caused "low" bloatedness and reduced "fairly bad" sleep disruptions, without affecting sleep durations.

Conclusion

GBP and PFP supplementation increased beneficial bacteria and metabolites, improved host gut health, and present a valuable nutritional strategy for enhancing human health.

Clinical trial registration

AMILI Institutional Review Board, Identifier 2023/0301.

Measures of nutrition status and health for weight-inclusive patient care: A narrative review

In healthcare, weight is often equated to and used as a marker for health. In examining nutrition and health status, there are many more effective markers independent of weight. In this article, we review practical and emerging clinical applications of technologies and tools used to collect non-weight-related data in nutrition assessment, monitoring, and evaluation in the outpatient setting. The aim is to provide clinicians with new ideas about various types of data to evaluate and track in nutrition care.

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort

INTRODUCTION

Our understanding of particular gut microbiota members such as Bifidobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level beneficial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; comparing their genomic characteristics with strains isolated from infants across North America, Europe, and other regions of Africa.

MATERIALS AND METHOD

From 110 infant stool samples collected in Harare, Zimbabwe, 20 randomly selected samples were used to isolate dominant early-life gut microbiota members Bifidobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbohydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibiotic resistance genes (ARGs).

RESULTS

The study observed some location-based clustering within the main five identified taxonomic groups. Furthermore, there were varying and overall species-specific numbers of genes belonging to different GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specific variances were identified in the potential of Bifidobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifidobacterium, while Enterococcus genomes exhibited a high abundance of aspartyl peptidases. Both genera harboured resistance genes against multiple classes of antimicrobial drugs, with Enterococcus genomes containing a higher number of ARGs compared to Bifidobacterium, on average.

CONCLUSION

This study identified promising probiotic strains within Zimbabwean isolates, offering the potential for early-life diet and microbial therapies. However, the presence of antibiotic resistance genes in infant-associated microbes raises concerns for infection risk and next-stage probiotic development. Further investigation in larger cohorts, particularly in regions with limited existing data on antibiotic and probiotic use, is crucial to validate these initial insights.

IMPACT STATEMENT

This research represents the first investigation of its kind in the Zimbabwean context, focusing on potential probiotic strains within the early-life gut microbiota. By identifying local probiotic strains, this research can contribute to the development of probiotic interventions that are tailored to the Zimbabwean population, which can help address local health challenges and promote better health outcomes for infants. Another essential aspect of the study is the investigation of antimicrobial resistance genes present in Zimbabwean bacterial strains. Antimicrobial resistance is a significant global health concern, and understanding the prevalence and distribution of resistance genes in different regions can help inform public health policies and interventions.

The Link between Inflammation, Lipid Derivatives, and Microbiota Metabolites in COVID-19 Patients: Implications on Eating Behaviors and Nutritional Status

Extreme inflammation that continues even after infections can lead to a cytokine storm. In recent times, one of the most common causes of cytokine storm activation has been SARS-CoV-2 infection. A cytokine storm leads to dysregulation and excessive stimulation of the immune system, producing symptoms typical of post-COVID syndrome, including chronic fatigue, shortness of breath, joint pain, trouble concentrating (known as "brain fog"), and even direct organ damage in the heart, lungs, kidneys, and brain. This work summarizes the current knowledge regarding inflammation and the cytokine storm related to SARS-CoV-2 infection. Additionally, changes in lipid metabolism and microbiota composition under the influence of inflammation in COVID-19, along with the possible underlying mechanisms, are described. Finally, this text explores potential health implications related to changes in eating behaviors and nutritional status in COVID-19 patients. Although research on the cytokine storm is still ongoing, there is convincing evidence suggesting that severe immune and inflammatory responses during the acute phase of COVID-19 may lead to long-term health consequences. Understanding these links is key to developing treatment strategies and supporting patients after infection.

Association of maternal constipation and risk of atopic dermatitis in offspring

Objectives: Atopic dermatitis (AD) is a chronic and relapsing dermatologic disease that can affect individuals of all ages, including children and adults. The prevalence of AD has increased dramatically over the past few decades. AD may affect children's daily activities, increase their parents' stress, and increase health expenditure. Constipation is a worldwide issue and may affect the gut microbiome. Some research has indicated that constipation might be associated with risk of atopic disease. The primary objective of this retrospective cohort study was to extend and to explore the link between maternal constipation and risk of atopic dermatitis in offspring. Methods: Using the Longitudinal Health Insurance Database, a subset of Taiwan's National Health Insurance Research Database, we identified 138,553 mothers with constipation and 138,553 matched controls between 2005 and 2016. Propensity score analysis was used matching birth year, child's sex, birth weight, gestational weeks, mode of delivery, maternal comorbidities, and antibiotics usage, with a ratio of 1:1. Multiple Cox regression and subgroup analyses were used to estimate the adjusted hazard ratio of child AD. Results: The incidence of childhood AD was 66.17 per 1,000 person-years in constipated mothers. By adjusting child's sex, birth weight, gestational weeks, mode of delivery, maternal comorbidities, and received antibiotics, it was found that in children whose mother had constipation, there was a 1.26-fold risk of AD compared to the children of mothers without constipation (adjusted hazard ratio [aHR]: 1.26; 95% CI, 1.25-1.28). According to subgroup analyses, children in the maternal constipation group had a higher likelihood of AD irrespective of child's sex, birth weight, gestational weeks, mode of delivery, and with or without comorbidities, as well as usage of antibiotics during pregnancy. Compared to the non-constipated mothers, the aHR for the constipated mothers with laxative prescriptions <12 and ≥12 times within one year before the index date were 1.26; 95% CI, 1.24 -1.28 and 1.40; 95% CI, 1.29-1.52, respectively. Conclusion: Maternal constipation was associated with an elevated risk of AD in offspring. Clinicians should be aware of the potential link to atopic dermatitis in the children of constipation in pregnant women and should treat gut patency issues during pregnancy. More study is needed to investigate the mechanisms of maternal constipation and atopic diseases in offspring.

Rebalancing the Gut: Glucagon-Like Peptide-1 Agonists as a Strategy for Obesity and Metabolic Health

Obesity significantly impacts gut microbial composition, exacerbating metabolic dysfunction and weight gain. Traditional treatment methods often fall short, underscoring the need for innovative approaches. Glucagon-like peptide-1 (GLP-1) agonists have emerged as promising agents in obesity management, demonstrating significant potential in modulating gut microbiota. These agents promote beneficial bacterial populations, such as Bacteroides, Lactobacillus, and Bifidobacterium, while reducing harmful species like Enterobacteriaceae. By influencing gut microbiota composition, GLP-1 agonists enhance gut barrier integrity, reducing permeability and systemic inflammation, which are hallmarks of metabolic dysfunction in obesity. Additionally, GLP-1 agonists improve metabolic functions by increasing the production of short-chain fatty acids like butyrate, propionate, and acetate, which serve as energy sources for colonocytes, modulate immune responses, and enhance the production of gut hormones that regulate appetite and glucose homeostasis. By increasing microbial diversity, GLP-1 agonists create a more resilient gut microbiome capable of resisting pathogenic invasions and maintaining metabolic balance. Thus, by shifting the gut microbiota toward a healthier profile, GLP-1 agonists help disrupt the vicious cycle of obesity-induced gut dysbiosis and inflammation. This review highlights the intricate relationship between obesity, gut microbiota, and GLP-1 agonists, providing valuable insights into their combined role in effective obesity treatment and metabolic health enhancement.

Understanding how pre- and probiotics affect the gut microbiome and metabolic health

The gut microbiome, a complex assembly of microorganisms, significantly impacts human health by influencing nutrient absorption, the immune system, and disease response. These microorganisms form a dynamic ecosystem that is critical to maintaining overall well-being. Prebiotics and probiotics are pivotal in regulating gut microbiota composition. Prebiotics nourish beneficial bacteria and promote their growth, whereas probiotics help maintain balance within the microbiome. This intricate balance extends to several aspects of health, including maintaining the integrity of the gut barrier, regulating immune responses, and producing metabolites crucial for metabolic health. Dysbiosis, or an imbalance in the gut microbiota, has been linked to metabolic disorders such as type 2 diabetes, obesity, and cardiovascular disease. Impaired gut barrier function, endotoxemia, and low-grade inflammation are associated with toll-like receptors influencing proinflammatory pathways. Short-chain fatty acids derived from microbial fermentation modulate anti-inflammatory and immune system pathways. Prebiotics positively influence gut microbiota, whereas probiotics, especially Lactobacillus and Bifidobacterium strains, may improve metabolic outcomes, such as glycemic control in diabetes. It is important to consider strain-specific effects and study variability when interpreting these findings, highlighting the need for further research to optimize their therapeutic potential. The aim of this report is therefore to review the role of the gut microbiota in metabolic health and disease and the effects of prebiotics and probiotics on the gut microbiome and their therapeutic role, integrating a broad understanding of physiological mechanisms with a clinical perspective.

Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis

BACKGROUND/PURPOSE(S)

The gut microbiota and its metabolites play crucial roles in pathogenesis of arthritis, highlighting gut microbiota as a promising avenue for modulating autoimmunity. However, the characterization of the gut virome in arthritis patients, including osteoarthritis (OA) and gouty arthritis (GA), requires further investigation.

METHODS

We employed virus-like particle (VLP)-based metagenomic sequencing to analyze gut viral community in 20 OA patients, 26 GA patients, and 31 healthy controls, encompassing a total of 77 fecal samples.

RESULTS

Our analysis generated 6819 vOTUs, with a considerable proportion of viral genomes differing from existing catalogs. The gut virome in OA and GA patients differed significantly from healthy controls, showing variations in diversity and viral family abundances. We identified 157 OA-associated and 94 GA-associated vOTUs, achieving high accuracy in patient-control discrimination with random forest models. OA-associated viruses were predicted to infect pro-inflammatory bacteria or bacteria associated with immunoglobulin A production, while GA-associated viruses were linked to Bacteroidaceae or Lachnospiraceae phages. Furthermore, several viral functional orthologs displayed significant differences in frequency between OA-enriched and GA-enriched vOTUs, suggesting potential functional roles of these viruses. Additionally, we trained classification models based on gut viral signatures to effectively discriminate OA or GA patients from healthy controls, yielding AUC values up to 0.97, indicating the clinical utility of the gut virome in diagnosing OA or GA.

CONCLUSION

Our study highlights distinctive alterations in viral diversity and taxonomy within gut virome of OA and GA patients, offering insights into arthritis etiology and potential treatment and prevention strategies.

Immune and Microbial Signatures Associated with PD-1 Blockade Sensitivity in a Preclinical Model for HPV+ Oropharyngeal Cancer

The United States is suffering from an epidemic associated with high-risk strains of the Human Papillomavirus (HPV) predominantly responsible for the development of head and neck squamous cell carcinoma (HNSCC). Treatment with immune checkpoint inhibitors targeting programmed death 1 (PD-1) or its ligand PD-L1 has shown poor efficacy in HNSCC patients, observing only a 20-30% response. Therefore, biological marker identification associated with PD-1 blockade response is important to improve prognosis and define novel therapeutics for HNSCC patients. Therapy response was associated with increased frequencies of activated CD27+T cells, activated CD79a+ B cells, antigen-presenting CD74+ dendritic and B cells, and PD-L1+ and PD-L2+ myeloid-derived suppressor cells (MDSCs). The oral microbiota composition differed significantly in mice bearing tongue tumors and treated with anti-PD-1. A higher abundance of Allobaculum, Blautia, Faecalibacterium, Dorea, or Roseburia was associated with response to the therapy. However, an increase in Enterococcus was attributed to tongue tumor-bearing non-responding mice. Our findings indicate that differences in immune phenotypes, protein expression, and bacterial abundance occur as mice develop tongue tumors and are treated with anti-PD-1. These results may have a clinical impact as specific bacteria and immune phenotype could serve as biomarkers for treatment response in HNSCC.

Microbiome-Modifiers for Cancer-Related Fatigue Management: A Systematic Review

OBJECTIVES

This study systematically investigates the evidence regarding the use of probiotics in managing cancer-related fatigue (CRF).

STUDY DESIGN

We conducted a systematic review of randomized controlled trials.

DATA SOURCES

The systematic search encompassed six databases: PubMed, CINHAL, Cochrane Database of Systematic Reviews, Web of Science, Scopus, and EMBASE, covering the period from inception to December 2023. The assessment of risk of bias employed the Cochrane risk of bias tool (RoB 2). A narrative synthesis and an exploratory meta-analysis were conducted to summarize the evidence.

RESULTS

Among 460 records, three studies met the eligibility criteria and were included in the review. These studies involved a total of 284 participants with colorectal and breast cancer. One study demonstrated a marginal improvement in CRF postchemotherapy in colorectal cancer patients using probiotics. Another study, also using probiotics, reported a significant reduction in CRF among colorectal cancer patients undergoing chemotherapy. Additionally, a study employing synbiotics showed a substantial decrease in CRF severity in breast cancer patients receiving chemotherapy.

CONCLUSION

The study presents initial but varied evidence suggesting the potential of probiotics and synbiotics as adjunctive therapies in managing CRF alongside anticancer treatments.

IMPLICATIONS FOR NURSING PRACTICE

In nursing practice, large-scale clinical trials are urgently needed to evaluate the effectiveness of probiotics in treating cancer-related fatigue during cancer therapy. Insights from this review could guide nurses in selecting appropriate probiotic strains and integrating microbiome modifiers into comprehensive care plans, potentially enhancing the quality of life for cancer patients.