Emerging connections between gut microbiome bioenergetics and chronic metabolic diseases

Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes

Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.

Anti-Biofilm Effects of Z102-E of Lactiplantibacillus plantarum against Listeria monocytogenes and the Mechanism Revealed by Transcriptomic Analysis

Lactic acid bacteria (LAB) are the most common probiotics, and they present excellent inhibitory effects on pathogenic bacteria. This study aimed to explore the anti-biofilm potential of the purified active substance of Lactiplantibacillus plantarum, named Z102-E. The effects of Z102-E on Listeria monocytogenes were investigated in detail, and a transcriptomic analysis was conducted to reveal the anti-biofilm mechanism. The results indicated that the sub-MIC of Z102-E (3.2, 1.6, and 0.8 mg/mL) decreased the bacterial growth and effectively reduced the self-aggregation, surface hydrophobicity, sugar utilization, motility, biofilm formation, AI-2 signal molecule, contents of extracellular polysaccharides, and extracellular protein of L. monocytogenes. Moreover, the inverted fluorescence microscopy observation confirmed the anti-biofilm effect of Z102-E. The transcriptomic analysis indicated that 117 genes were up-regulated and 214 were down-regulated. Z102-E regulated the expressions of genes related to L. monocytogenes quorum sensing, biofilm formation, etc. These findings suggested that Z102-E has great application potential as a natural bacteriostatic agent.

Is There Evidence to Support Probiotic Use for Healthy People?

Probiotics are typically marketed as foods and dietary supplements, categories for products intended to maintain health in generally healthy populations and which, unlike drugs, cannot claim to treat or cure disease. This review addresses the existing evidence that probiotics are beneficial to healthy people. Our approach was to perform a descriptive review of efficacy evidence that probiotics can prevent urinary, vaginal, gastrointestinal, and respiratory infections, and improve risk factors associated with cardiovascular health or reduce antibiotic use. Other endpoints such as mental, dental, or immune health were not specifically addressed. We concluded that there is sufficient evidence of efficacy and safety for clinicians and consumers to consider using specific probiotics for some indications - such as the use of probiotics to support gut function during antibiotic use or to reduce the risk of respiratory tract infections - for certain people. However, we did not find a sufficiently high level of evidence to support unconditional, population-wide recommendations for other preventive endpoints we reviewed for healthy people. Although evidence for some indications is suggestive of the preventive benefits of probiotics, additional research is needed.

Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis

BACKGROUND

The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the composition and function of microbial communities, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations.

METHODS

A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive/athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed.

RESULTS

Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. Most of studies reported an increase in short-chain fatty acid-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella or Roseburia in active individuals and after physical activity interventions.

CONCLUSIONS

Physical activity levels were positively associated with the relative abundance of short-chain fatty acid-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids obtaining conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome.

Exploring the interaction and impact of probiotic and commensal bacteria on vitamins, minerals and short chain fatty acids metabolism

There is increasing evidence that probiotic and commensal bacteria play a role in substrate metabolism, energy harvesting and intestinal homeostasis, and may exert immunomodulatory activities on human health. In addition, recent research suggests that these microorganisms interact with vitamins and minerals, promoting intestinal and metabolic well-being while producing vital microbial metabolites such as short-chain fatty acids (SCFAs). In this regard, there is a flourishing field exploring the intricate dynamics between vitamins, minerals, SCFAs, and commensal/probiotic interactions. In this review, we summarize some of the major hypotheses beyond the mechanisms by which commensals/probiotics impact gut health and their additional effects on the absorption and metabolism of vitamins, minerals, and SCFAs. Our analysis includes comprehensive review of existing evidence from preclinical and clinical studies, with particular focus on the potential interaction between commensals/probiotics and micronutrients. Finally, we highlight knowledge gaps and outline directions for future research in this evolving field.

Dissecting mechanisms of fecal microbiota transplantation efficacy in disease

Fecal microbiota transplantation (FMT) has emerged as an alternative or adjunct experimental therapy for microbiome-associated diseases following its success in the treatment of recurrent Clostridioides difficile infections (rCDIs). However, the mechanisms of action involved remain relatively unknown. The term 'dysbiosis' has been used to describe microbial imbalances in relation to disease, but this traditional definition fails to consider the complex cross-feeding networks that define the stability of the microbiome. Emerging research transitions toward the targeted restoration of microbial functional networks in treating different diseases. In this review, we explore potential mechanisms responsible for the efficacy of FMT and future therapeutic applications, while revisiting definitions of 'dysbiosis' in favor of functional network restoration in rCDI, inflammatory bowel diseases (IBDs), metabolic diseases, and cancer.

The untapped potential of cell culture in disentangling insect-microbial relationships

Cell culture is a powerful technique for the investigation of molecular mechanisms fundamental to health and disease in a diverse array of organisms. Cell lines offer several advantages, namely their simplistic approach and high degree of reproducibility. One field where cell culture has proven particularly useful is the study of the microbiome, where cell culture has led to the illumination of microbial influences on host immunity, nutrition, and physiology. Thus far, researchers have focused cell culture work predominantly on humans, but the growing field of insect microbiome research stands to benefit greatly from its application. Insects constitute one of Earth's most diverse and ancient life forms and, just as with humans, possess microbiomes with great significance to their health. Insects, which play critical roles in supporting food security and ecological stability, are facing increasing threats from agricultural intensification, climate change, and pesticide use. As the microbiome is closely tied to host health, gaining a more robust understanding is of increasing importance. In this review, we assert that the cultivation and utilization of insect gut cell lines in microbiome research will bridge critical knowledge gaps essential for informing insect management practices in a world under pressure.

The effects of whole grain cereals on tryptophan metabolism and intestinal barrier function: underlying factors of health impact

This review aims to investigate the relationship between the health impact of whole grains mediated via the interaction with intestinal microbiota and intestinal barrier function with special interest on tryptophan metabolism, focusing on the role of the intestinal microbiota and their impact on barrier function. Consuming various types of whole grains can lead to the growth of different microbiota species, which in turn leads to the production of diverse metabolites, including those derived from tryptophan metabolism, although the impact of whole grains on intestinal microbiota composition results remains inconclusive and vary among different studies. Whole grains can exert an influence on tryptophan metabolism through interactions with the intestinal microbiota, and the presence of fibre in whole grains plays a notable role in establishing this connection. The impact of whole grains on intestinal barrier function is closely related to their effects on the composition and activity of intestinal microbiota, and SCFA and tryptophan metabolites serve as potential links connecting whole grains, intestinal microbiota and the intestinal barrier function. Tryptophan metabolites affect various aspects of the intestinal barrier, such as immune balance, mucus and microbial barrier, tight junction complexes and the differentiation and proliferation of epithelial cells. Despite the encouraging discoveries in this area of research, the evidence regarding the effects of whole grain consumption on intestine-related activity remains limited. Hence, we can conclude that we are just starting to understand the actual complexity of the intestinal factors mediating in part the health impacts of whole grain cereals.

Rapid adaptation of the rainbow trout intestinal microbiota to the use of a high-starch 100% plant-based diet

Short-term adaptation of the microbiota could promote nutrient degradation and the host health. While numerous studies are currently undertaking feeding trials using sustainable diets for the aquaculture industry, the extent to which the microbiota adapts to these novel diets is poorly described. The incorporation of carbohydrates (CHO) within a 100% plant-based diet could offer a novel, cost-effective energy source that is readily available, potentially replacing the protein component in the diets. In this study, we investigated the short-term (3 weeks) effects of a high CHO, 100% plant-based diet on the mucosal and digesta associated microbiota diversity and composition, as well as several metabolic parameters in rainbow trout. We highlighted that the mucosa is dominated by Mycoplasma (44.86%). While the diets did not have significant effects on the main phyla (Proteobacteria, Firmicutes, and Actinobacteria), after 3 weeks, a lower abundance of Bacillus genus, and higher abundances of four lactic-acid bacteria were demonstrated in digesta. In addition, no post-prandial hyperglycemia was observed with high carbohydrate intake. These results provide evidence for the rapid adaptation of the gut microbiota and host metabolism to high CHO in combination with 100% plant ingredients in rainbow trout.

The health benefits of dietary short-chain fatty acids in metabolic diseases

Short-chain fatty acids (SCFAs) are a subset of fatty acids that play crucial roles in maintaining normal physiology and developing metabolic diseases, such as obesity, diabetes, cardiovascular disease, and liver disease. Even though dairy products and vegetable oils are the direct dietary sources of SCFAs, their quantities are highly restricted. SCFAs are produced indirectly through microbial fermentation of fibers. The biological roles of SCFAs in human health and metabolic diseases are mainly due to their receptors, GPR41 and GPR43, FFAR2 and FFAR3. Additionally, it has been demonstrated that SCFAs modulate DNMTs and HDAC activities, inhibit NF-κB-STAT signaling, and regulate G(i/o)βγ-PLC-PKC-PTEN signaling and PPARγ-UCP2-AMPK autophagic signaling, thus mitigating metabolic diseases. Recent studies have uncovered that SCFAs play crucial roles in epigenetic modifications of DNAs, RNAs, and post-translational modifications of proteins, which are critical regulators of metabolic health and diseases. At the same time, dietary recommendations for the purpose of SCFAs have been proposed. The objective of the review is to summarize the most recent research on the role of dietary SCFAs in metabolic diseases, especially the signal transduction of SCFAs in metabolic diseases and their functional efficacy in different backgrounds and models of metabolic diseases, at the same time, to provide dietary and nutritional recommendations for using SCFAs as food ingredients to prevent metabolic diseases.

Multi-site microbiota alteration is a hallmark of kidney stone formation

BACKGROUND

Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD.

RESULTS

Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism.

CONCLUSIONS

We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.

Effects of maternal probiotic supplementation on breast milk microbiome and infant gut microbiome and health: a systematic review and meta-analysis of randomized controlled trials

OBJECTIVE

The early-life microbiome is formed during the perinatal period and is critical for infants' lifelong health. This is established by maternal-infant microbiome crosstalk, which is mediated by the breast milk microbiome. The milk microbiome is dependent on the maternal gut microbiome, suggesting that it could potentially be restored through oral probiotic supplements. Therefore, we conducted this systematic review and meta-analysis to summarize the effect of maternal probiotic supplements on breast milk and infant gut microbiome composition and on infant health.

DATA SOURCES

The PubMed, EMBASE, Web of Science, Scopus, CINAHL, and Science Direct databases were searched until December 15, 2022.

STUDY ELIGIBILITY CRITERIA

Randomized controlled trials following the population, intervention, comparison, and outcome (population: pregnant or lactating women; intervention: probiotics; control: placebo or follow-up; outcome: breast milk and infant gut microbiome composition and infant health) principles were included.

METHODS

Using a random effect model, the standard mean difference, risk difference, and risk ratio with 95% confidence interval were used to measure each outcome. All analyses were conducted using the intention-to-treat approach. Heterogeneity was evaluated using I2 statistics.

RESULTS

The final data set included 24 randomized controlled trials with a total of 2761 mothers and 1756 infants. The overall effect of probiotics on the beneficial bacteria detection rate in breast milk had a risk difference of 24% (95% confidence interval, 0.1-0.37; P<.001; I2=91.12%). The pooled mean beneficial and pathogenic bacteria abundance in breast milk had a standard mean difference of 1.22 log10 colony forming units/mL (95% confidence interval, 0.48-1.97; P<.001; I2=95.51%) and -1.05 log10 colony forming unites/mL (95% confidence interval, -1.99 to -0.12; P=.03; I2=96.79%), respectively. The overall abundance of beneficial bacteria in the infant gut had a standard mean difference of 0.89 log10 colony forming units/g (95% confidence interval, 0.22-1.56; P=.01; I2=95.01%). It also controlled infant weight gain (standard mean difference, -0.49 kg/equivalent age; 95% confidence interval, -0.82 to -0.17; P<.001; I2=0.00%) and decreased the occurrence of infantile colic (risk ratio, 0.30; 95% confidence interval, 0.16-0.57; P<.001; I2=0.00%).

CONCLUSION

Maternal probiotic supplements effectively orchestrate the breast milk and infant gut microbiome with a wide range of clinical benefits and safety. Lactobacillus, Bifidobacterium, Streptococcus thermophilus, and S. boulardii can be used as maternal supplements to promote infant health.

Acetate and succinate benefit host muscle energetics as exercise-associated post-biotics

Recently, the gut microbiome has emerged as a potent modulator of exercise-induced systemic adaptation and appears to be crucial for mediating some of the benefits of exercise. This study builds upon previous evidence establishing a gut microbiome-skeletal muscle axis, identifying exercise-induced changes in microbiome composition. Metagenomics sequencing of fecal samples from non-exercise-trained controls or exercise-trained mice was conducted. Biodiversity indices indicated exercise training did not change alpha diversity. However, there were notable differences in beta-diversity between trained and untrained microbiomes. Exercise significantly increased the level of the bacterial species Muribaculaceae bacterium DSM 103720. Computation simulation of bacterial growth was used to predict metabolites that accumulate under in silico culture of exercise-responsive bacteria. We identified acetate and succinate as potential gut microbial metabolites that are produced by Muribaculaceae bacterium, which were then administered to mice during a period of mechanical overload-induced muscle hypertrophy. Although no differences were observed for the overall muscle growth response to succinate or acetate administration during the first 5 days of mechanical overload-induced hypertrophy, acetate and succinate increased skeletal muscle mitochondrial respiration. When given as post-biotics, succinate or acetate treatment may improve oxidative metabolism during muscle hypertrophy.

Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis

Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our objective was to investigate associations between respiratory health in Inuit communities and their airway microbiome. Oropharyngeal samples were collected during the Qanuilirpitaa? 2017 Inuit Health Survey and subjected to metagenomic analyses. Participants were assigned to a bronchial obstruction group or a control group based on their clinical history and their pulmonary function, as monitored by spirometry. The Inuit microbiota composition was found to be distinct from other studied populations. Within the Inuit microbiota, differences in diversity measures tend to distinguish the two groups. Bacterial taxa found to be more abundant in the control group included candidate probiotic strains, while those enriched in the bronchial obstruction group included opportunistic pathogens. Crossing taxa affiliation method and machine learning consolidated our finding of distinct core microbiomes between the two groups. More microbial metabolic pathways were enriched in the control participants and these were often involved in vitamin and anti-inflammatory metabolism, while a link could be established between the enriched pathways in the disease group and inflammation. Overall, our results suggest a link between microbial abundance, interactions and metabolic activities and respiratory health in the Inuit population.

Vitamins as regulators of calcium-containing kidney stones - new perspectives on the role of the gut microbiome

Calcium-based kidney stone disease is a highly prevalent and morbid condition, with an often complicated and multifactorial aetiology. An abundance of research on the role of specific vitamins (B6, C and D) in stone formation exists, but no consensus has been reached on how these vitamins influence stone disease. As a consequence of emerging research on the role of the gut microbiota in urolithiasis, previous notions on the contribution of these vitamins to urolithiasis are being reconsidered in the field, and investigation into previously overlooked vitamins (A, E and K) was expanded. Understanding how the microbiota influences host vitamin regulation could help to determine the role of vitamins in stone disease.

Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease

Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune programming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxidative activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (βindirect = -2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.

Gut microbiome alterations in patients with COVID-19-related coagulopathy

COVID-19 is characterized by a predominantly prothrombotic state, which underlies severe disease and poor outcomes. Imbalances of the gut microbiome have been linked with abnormal hemostatic processes. Understanding the relationship between the gut microbiome and abnormal coagulation parameters in COVID-19 could provide a novel framework for the diagnosis and management of COVID-related coagulopathies (CRC). This cross-sectional study used shotgun metagenomic sequencing to examine the gut microbiota of patients with CRC (n = 66) and compared it to COVID control (CCs) (n = 27) and non-COVID control (NCs) (n = 22) groups. Three, 1, and 3 taxa were found enriched in CRCs, CCs, and NCs. Next, random forest models using 7 microbial biomarkers and differential clinical characteristics were constructed and achieved strong diagnostic potential in distinguishing CRC. Specifically, the most promising biomarker species for CRC were Streptococcus thermophilus, Enterococcus faecium, and Citrobacter portucalensis. Conversely, Enterobacteriaceae family and Fusicatenibacter genus are potentially protective against CRC in COVID patients. We further identified 4 species contributing to 20 MetaCyc pathways that were differentially abundant among groups, with S. thermophilus as the main coding species in CRCs. Our findings suggest that the alterations of gut microbiota compositional and functional profiles may influence the pathogenesis of CRC and that microbiota-based diagnosis and treatment could potentially benefit COVID patients in preventing and alleviating thrombosis-related clinical outcomes.

Dynamic changes of inulin utilization associated with longitudinal development of gut microbiota

Inulin is a typical kind of fermentable polysaccharide and has emerged as a promising dietary supplement due to its multiple health-promoting effects. This study aimed to unveil the dynamic change pattern of inulin utilizability as a fermentation substrate during gut microbiota development and illuminate its potential association with gut microbiota in Chinese Jinhua native pig models via longitudinal analyses. Herein, fresh feces were collected at one week pre- and post-weaning as well as 3rd month post-weaning, respectively. Targeted metabolomics and in vitro simulated fermentation revealed increasing concentrations of fecal short-chain fatty acids (SCFAs) and elevating utilizability of inulin as a fermentation substrate. Microbiomic analyses demonstrated the conspicuous longitudinal alteration in gut microbial composition and a significant rise in microbial community diversity during gut microbiota development. Furthermore, gut microbial functional analyses showed a remarkable increase in the relative abundances of carbohydrate metabolism pathways, including pentose phosphate pathway, galactose metabolism pathway, butanoate metabolism pathway as well as fructose and mannose metabolism pathway. Notably, relative abundances of bacterial genera Bifidobacterium, Roseburia, Faecalibacterium and Enterococcus displayed significantly positive correlations with the production of microbial fermentation-derived SCFAs. Collectively, these findings offer novel insights into understanding inulin utilizability variations from the perspective of gut microbiota development.

The Role of Microbiota-Derived Vitamins in Immune Homeostasis and Enhancing Cancer Immunotherapy

Not all cancer patients who receive immunotherapy respond positively and emerging evidence suggests that the gut microbiota may be linked to treatment efficacy. Though mechanisms of microbial contributions to the immune response have been postulated, one likely function is the supply of basic co-factors to the host including selected vitamins. Bacteria, fungi, and plants can produce their own vitamins, whereas humans primarily obtain vitamins from exogenous sources, yet despite the significance of microbial-derived vitamins as crucial immune system modulators, the microbiota is an overlooked source of these nutrients in humans. Microbial-derived vitamins are often shared by gut bacteria, stabilizing bioenergetic pathways amongst microbial communities. Compositional changes in gut microbiota can affect metabolic pathways that alter immune function. Similarly, the immune system plays a pivotal role in maintaining the gut microbiota, which parenthetically affects vitamin biosynthesis. Here we elucidate the immune-interactive mechanisms underlying the effects of these microbially derived vitamins and how they can potentially enhance the activity of immunotherapies in cancer.

The Differing Roles of Flavins and Quinones in Extracellular Electron Transfer in Lactiplantibacillus plantarum

Lactiplantibacillus plantarum is a lactic acid bacterium that is commonly found in the human gut and fermented food products. Despite its overwhelmingly fermentative metabolism, this microbe can perform extracellular electron transfer (EET) when provided with an exogenous quinone, 1,4-dihydroxy-2-naphthoic acid (DHNA), and riboflavin. However, the separate roles of DHNA and riboflavin in EET in L. plantarum have remained unclear. Here, we seek to understand the role of quinones and flavins in EET by monitoring iron and anode reduction in the presence and absence of these small molecules. We found that addition of either DHNA or riboflavin can support robust iron reduction, indicating electron transfer to extracellular iron occurs through both flavin-dependent and DHNA-dependent routes. Using genetic mutants of L. plantarum, we found that flavin-dependent iron reduction requires Ndh2 and EetA, while DHNA-dependent iron reduction largely relies on Ndh2 and PplA. In contrast to iron reduction, DHNA-containing medium supported more robust anode reduction than riboflavin-containing medium, suggesting electron transfer to an anode proceeds most efficiently through the DHNA-dependent pathway. Furthermore, we found that flavin-dependent anode reduction requires EetA, Ndh2, and PplA, while DHNA-dependent anode reduction requires Ndh2 and PplA. Taken together, we identify multiple EET routes utilized by L. plantarum and show that the EET route depends on access to environmental biomolecules and on the electron acceptor. This work expands our molecular-level understanding of EET in Gram-positive microbes and provides additional opportunities to manipulate EET for biotechnology. IMPORTANCE Lactic acid bacteria are named because of their nearly exclusive fermentative metabolism. Thus, the recent observation of EET activity-typically associated with anaerobic respiration-in this class of organisms has forced researchers to rethink the rules governing microbial metabolic strategies. Our identification of multiple routes for EET in L. plantarum that depend on two different redox active small molecules expands our understanding of how microbes metabolically adapt to different environments to gain an energetic edge and how these processes can be manipulated for biotechnological uses. Understanding the role of EET in lactic acid bacteria is of great importance due to the significance of lactic acid bacteria in agriculture, bioremediation, food production, and gut health. Furthermore, the maintenance of multiple EET routes speaks to the importance of this process to function under a variety of environmental conditions.

The Urinary Microbiome; Axis Crosstalk and Short-Chain Fatty Acid

Our knowledge that "urine is sterile" is no longer accepted after the development of a next-generation sequencing (NGS) test. Using NGS, microbiota in the human body were discovered, and it is expected that this will improve our understanding of human diseases. However, the mechanism involved in the effect of the microbiome on diseases is still poorly understood. Associations of gut microbiome with diseases have been recently reported. Based on such associations, bladder-gut-brain axis, gut-bladder axis, gut-vagina-bladder axis, and gut-kidney axis as novel mechanisms of action of the microbiome have been suggested. Each axis can influence the development and progression of disease through interactions. In these interactions, metabolites of the microbiome including short-chain fatty acids (SCFA) and the inflammasome play an important role. Inflammasomes are multiprotein oligomers that can initiate inflammatory responses. Inflammasomes can trigger inflammation and pyroptosis and ultimately contribute to disease development. SCFAs play an important role in immune cell migration, cytokine production, and maintenance of cellular homeostasis. Associations of inflammasomes with systemic diseases such as obesity and insulin resistance have been reported. The roles of inflammasomes and SCFAs in kidney, bladder, and prostate diseases have also been revealed recently.

Developing Strategies to Help Bee Colony Resilience in Changing Environments

Climate change, loss of plant biodiversity, burdens caused by new pathogens, predators, and toxins due to human disturbance and activity are significant causes of the loss of bee colonies and wild bees. The aim of this review is to highlight some possible strategies that could help develop bee resilience in facing their changing environments. Scientists underline the importance of the links between nutrition, microbiota, and immune and neuroendocrine stress resistance of bees. Nutrition with special care for plant-derived molecules may play a major role in bee colony health. Studies have highlighted the importance of pollen, essential oils, plant resins, and leaves or fungi as sources of fundamental nutrients for the development and longevity of a honeybee colony. The microbiota is also considered as a key factor in bee physiology and a cornerstone between nutrition, metabolism, growth, health, and pathogen resistance. Another stressor is the varroa mite parasite. This parasite is a major concern for beekeepers and needs specific strategies to reduce its severe impact on honeybees. Here we discuss how helping bees to thrive, especially through changing environments, is of great concern for beekeepers and scientists.

High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure

Human gut microbiome structure and emergent metabolic outputs impact health outcomes. However, what drives such community characteristics remains underexplored. Here, we rely on high throughput genomic reconstruction modeling, to infer the metabolic attributes and nutritional requirements of 816 gut strains, via a framework termed GEMNAST. This has been performed in terms of a group of human vitamins to examine the role vitamin exchanges have at different levels of community organization. We find that only 91 strains can satisfy their vitamin requirements (prototrophs) while the rest show various degrees of auxotrophy/specialization, highlighting their dependence on external sources, such as other members of the microbial community. Further, 79% of the strains in our sample were mapped to 11 distinct vitamin requirement profiles with low phylogenetic consistency. Yet, we find that human gut microbial community enterotype indicators display marked metabolic differences. Prevotella strains display a metabolic profile that can be complemented by strains from other genera often associated with the Prevotella enterotype and agrarian diets, while Bacteroides strains occupy a prototrophic profile. Finally, we identify pre-defined interaction modules (IMs) of gut species from human and mice predicted to be driven by, or highly independent of vitamin exchanges. Our analysis provides mechanistic grounding to gut microbiome stability and to co-abundance-based observations, a fundamental step toward understanding emergent processes that influence health outcomes. Further, our work opens a path to future explorations in the field through applications of GEMNAST to additional nutritional dimensions.

The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs

The gut microbiota plays a fundamental role in human nutrition and metabolism and may have direct implications for type 2 diabetes and associated preconditions. An improved understanding of relations between human gut microbiota and glucose metabolism could lead to novel opportunities for type 2 diabetes prevention, but human observational studies reporting on such findings have not been extensively reviewed. Here, we review the literature on associations between gut microbiota and markers and stages of glucose dysregulation and insulin resistance in healthy adults and in adults with metabolic disease and risk factors. We present the current evidence for identified key bacteria and their potential roles in glucose metabolism independent of overweight, obesity, and metabolic drugs. We provide support for SCFAs mediating such effects and discuss the role of diet, as well as metabolites derived from diet and gut microbiota interactions. From 5983 initially identified PubMed records, 45 original studies were eligible and reviewed. α Diversity and 45 bacterial taxa were associated with selected outcomes. Six taxa were most frequently associated with glucose metabolism: Akkermansia muciniphila, Bifidobacterium longum, Clostridium leptum group, Faecalibacterium prausnitzii, and Faecalibacterium (inversely associated) and Dorea (directly associated). For Dorea and A. muciniphila, associations were independent of metabolic drugs and body measures. For A. muciniphila and F. prausnitzii, limited evidence supported SCFA mediation of potential effects on glucose metabolism. We conclude that observational studies applying metagenomics sequencing to identify species-level relations are warranted, as are studies accounting for confounding factors and investigating SCFA and postprandial glucose metabolism. Such advances in the field will, together with mechanistic and prospective studies and investigations into diet-gut microbiota interactions, have the potential to bring critical insight into roles of gut microbiota and microbial metabolites in human glucose metabolism and to contribute toward the development of novel prevention strategies for type 2 diabetes, including precision nutrition.

Long-Duration Space Travel Support Must Consider Wider Influences to Conserve Microbiota Composition and Function

The microbiota is important for immune modulation, nutrient acquisition, vitamin production, and other aspects for long-term human health. Isolated model organisms can lose microbial diversity over time and humans are likely the same. Decreasing microbial diversity and the subsequent loss of function may accelerate disease progression on Earth, and to an even greater degree in space. For this reason, maintaining a healthy microbiome during spaceflight has recently garnered consideration. Diet, lifestyle, and consumption of beneficial microbes can shape the microbiota, but the replenishment we attain from environmental exposure to microbes is important too. Probiotics, prebiotics, fermented foods, fecal microbiota transplantation (FMT), and other methods of microbiota modulation currently available may be of benefit for shorter trips, but may not be viable options to overcome the unique challenges faced in long-term space travel. Novel fermented food products with particular impact on gut health, immune modulation, and other space-targeted health outcomes are worthy of exploration. Further consideration of potential microbial replenishment to humans, including from environmental sources to maintain a healthy microbiome, may also be required.

Grape seed and skin extract, a potential prebiotic with anti-obesity effect through gut microbiota modulation

Background

Obesity is a worldwide health problem and a significant risk factor for diabetes and cardiovascular diseases. Gut microbiota (GM) plays an essential role in obesity, and prebiotics such as polyphenols could be one way to improve microbial dysbiosis-induced obesity.

Objective

This study was designed to assess the effectiveness of grape seed and skin extract (GSSE), and/or orlistat on obese rats fed with high fat diet by targeting GM modulations. The impact of treatments was also studied in non-obese rats.

Material and methods

Rats were rendered obese or kept with a standard diet for three months. Then they were treated either with GSSE or orlistat or with the combined treatment (GSOR) during three months and then sacrificed. Adipose tissues, blood and faeces were collected and analyzed.

Results

In obese rats and to a lesser extent in non-obese rats, treatments decreased the weight of various adipose tissues and the serum levels of cholesterol, LDL, triglycerides, lipase, and CRP and increased HDL and adiponectin. GSOR treatment was even more efficient that orlistat. Obese rats had less GM diversity than non-obese rats and orlistat reduced it even more. However, diversity was restored with GSSE and GSOR treatments. Potential pathogenic Streptococcus alactolyticus/gallolyticus species were greatly increased in obese rats and drastically reduced with the treatments, as wells as other potential pathobionts.

Conclusions

GSSE exerts beneficial effects in obese rats and restores, at least partially, the observed dysbiosis. GSOR induced the highest beneficial effect. Moreover, the various treatments could also enhance physiological and GM modifications in non obese rats.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-022-00505-0.

Effect of Moderate Consumption of Different Phenolic-Content Beers on the Human Gut Microbiota Composition: A Randomized Crossover Trial

The moderate consumption of beer has been associated with positive effects on health, and these benefits are driven, in part, by the antioxidant properties of phenolic compounds found in this beverage. However, the potential impact of beer polyphenols on the human gut microbiome and their consequences are yet to be elucidated. In this study, our aim was to evaluate the effect of three different phenolic-content beers on the gut microbiome and the potential role of the induced shifts in the antioxidant capacity of beer polyphenols. In total, 20 subjects (10 healthy volunteers and 10 individuals with metabolic syndrome) were randomly assigned in a crossover design to consume each of the different beers (alcohol-free, lager or dark beer) during a 2-week intervention. Significant changes in the relative abundance of Streptococcaceae and Streptococcus were found after beer consumption. An increased abundance of Streptococcaceae and Streptococcus was observed after the consumption of dark beer, with no detected differences between baseline and alcohol-free/lager beer intervention. Moreover, some of the detected differences appeared to be related to the metabolic status. Finally, a decrease in porphyrin metabolism and heme biosynthesis was found after the intervention, especially after the consumption of dark beer. These results show that the antioxidant capacity of beer polyphenols may induce positive shifts in gut microbiota composition, and some of the observed changes may also boost the antioxidant capacity of these compounds.

Why Are Bifidobacteria Important for Infants?

The presence of Bifidobacterium species in the maternal vaginal and fecal microbiota is arguably an evolutionary trait that allows these organisms to be primary colonizers of the newborn intestinal tract. Their ability to utilize human milk oligosaccharides fosters their establishment as core health-promoting organisms throughout life. A reduction in their abundance in infants has been shown to increase the prevalence of obesity, diabetes, metabolic disorder, and all-cause mortality later in life. Probiotic strains have been developed as supplements for premature babies and to counter some of these ailments as well as to confer a range of health benefits. The ability to modulate the immune response and produce short-chain fatty acids, particularly acetate and butyrate, that strengthen the gut barrier and regulate the gut microbiome, makes Bifidobacterium a core component of a healthy infant through adulthood.

Metabolomic Fingerprinting for the Detection of Early-Stage Lung Cancer: From the Genome to the Metabolome

The five-year survival rate of lung cancer patients is very low, mainly because most newly diagnosed patients present with locally advanced or metastatic disease. Therefore, early diagnosis is key to the successful treatment and management of lung cancer. Unfortunately, early detection methods of lung cancer are not ideal. In this brief review, we described early detection methods such as chest X-rays followed by bronchoscopy, sputum analysis followed by cytological analysis, and low-dose computed tomography (LDCT). In addition, we discussed the potential of metabolomic fingerprinting, compared to that of other biomarkers, including molecular targets, as a low-cost, high-throughput blood-based test that is both feasible and affordable for early-stage lung cancer screening of at-risk populations. Accordingly, we proposed a paradigm shift to metabolomics as an alternative to molecular and proteomic-based markers in lung cancer screening, which will enable blood-based routine testing and be accessible to those patients at the highest risk for lung cancer.