Bacteria as vitamin suppliers to their host: a gut microbiota perspective

The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential

This review explores the emerging term "gut-skin axis" (GSA), describing the bidirectional signaling that occurs between the skin and the gastrointestinal tract under both homeostatic and disease conditions. Central to GSA communication are the gut and skin microbiota, the microbial communities that colonize these barrier surfaces. By influencing diverse host pathways, including innate immune, vitamin D receptor, and Aryl hydrocarbon receptor signaling, a balanced microbiota contributes to both tissue homeostasis and host defense. In contrast, microbiota imbalance, or dysbiosis at one site, can lead to local barrier dysfunction, resulting in the activation of signaling pathways that can disrupt tissue homeostasis at the other site, potentially leading to inflammatory skin conditions such as atopic dermatitis and psoriasis, or gut diseases like Inflammatory Bowel Disease. To date, most research on the GSA has examined the impact of the gut microbiota and diet on skin health, but recent studies show that exposing the skin to ultraviolet B-light can beneficially modulate both the gut microbiome and intestinal health. Thus, despite the traditional focus of clinicians and researchers on these organ systems as distinct, the GSA offers new opportunities to better understand the pathogenesis of cutaneous and gastrointestinal diseases and promote health at both sites.

The impact of novel probiotics isolated from the human gut on the gut microbiota and health

The gut microbiota plays a pivotal role in influencing the metabolism and immune responses of the body. A balanced microbial composition promotes metabolic health through various mechanisms, including the production of beneficial metabolites, which help regulate inflammation and support immune functions. In contrast, imbalance in the gut microbiota, known as dysbiosis, can disrupt metabolic processes and increase the risk of developing diseases, such as obesity, type 2 diabetes, and inflammatory disorders. The composition of the gut microbiota is dynamic and can be influenced by environmental factors such as diet, medication, and the consumption of live bacteria. Since the early 1900s, bacteria isolated from food and have been used as probiotics. However, the human gut also offers an enormous reservoir of bacterial strains, and recent advances in microbiota research have led to the discovery of strains with probiotic potentials. These strains, derived from a broad spectrum of microbial taxa, differ in their ecological properties and how they interact with their hosts. For most probiotics bacterial structural components and metabolites, such as short-chain fatty acids, contribute to the maintenance of metabolic and immunological homeostasis by regulating inflammation and reinforcing gut barrier integrity. Metabolites produced by probiotic strains can also be used for bacterial cross-feeding to promote a balanced microbiota. Despite the challenges related to safety, stability, and strain-specific properties, several newly identified strains offer great potential for personalized probiotic interventions, allowing for targeted health strategies.

Whole Genome Sequencing and In Silico Analysis of the Safety and Probiotic Features of Lacticaseibacillus paracasei FMT2 Isolated from Fecal Microbiota Transplantation (FMT) Capsules

Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2,838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3,358 orthologous clusters, including 1,775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.

Gut Microbiome, Diet and Depression: Literature Review of Microbiological, Nutritional and Neuroscientific Aspects

PURPOSE OF REVIEW

This review explores the intricate relationships among the gut microbiota, dietary patterns, and mental health, focusing specifically on depression. It synthesizes insights from microbiological, nutritional, and neuroscientific perspectives to understand how the gut-brain axis influences mood and cognitive function.

RECENT FINDINGS

Recent studies underscore the central role of gut microbiota in modulating neurological and psychological health via the gut-brain axis. Key findings highlight the importance of dietary components, including probiotics, prebiotics, and psychobiotics, in restoring microbial balance and enhancing mood regulation. Different dietary patterns exhibit a profound impact on gut microbiota composition, suggesting their potential as complementary strategies for mental health support. Furthermore, mechanisms like tryptophan metabolism, the HPA axis, and microbial metabolites such as SCFAs are implicated in linking diet and microbiota to depression. Clinical trials show promising effects of probiotics in alleviating depressive symptoms. This review illuminates the potential of diet-based interventions targeting the gut microbiota to mitigate depression and improve mental health. While the interplay between microbial diversity, diet, and brain function offers promising therapeutic avenues, further clinical research is needed to validate these findings and establish robust, individualized treatment strategies.

Short-Chain Fatty Acids and Their Metabolic Interactions in Heart Failure

Short-chain fatty acids (SCFAs), produced through fermentation of dietary fibers by gut bacteria, play a central role in modulating cardiovascular function and heart failure (HF) development. The progression of HF is influenced by intestinal barrier dysfunction and microbial translocation, where SCFAs serve as key mediators in the gut-heart axis. This review examines the complex metabolic interactions between SCFAs and other gut microbiota metabolites in HF, including their relationships with trimethylamine N-oxide (TMAO), aromatic amino acids (AAAs), B vitamins, and bile acids (BAs). We analyze the associations between SCFA production and clinical parameters of HF, such as left ventricular ejection fraction (LVEF), N-terminal pro-B-type natriuretic peptide (NT-proBNP), and glomerular filtration rate (GFR). Gaining insights into metabolic networks offers new potential therapeutic targets and prognostic markers for managing heart failure, although their clinical significance needs further exploration.

Effects of traditional Chinese medicine Zuo-Gui-Wan on gut microbiota in an osteoporotic mouse model

BACKGROUND

The target and mechanism of oral traditional Chinese medicine (TCM) have been important research directions for a long time. The close relationship between osteoporosis and gut microbiota (GM) has been confirmed. However, the relevance of oral TCM and the "Gut-Bone Axis" is still poorly understood.

METHODS

Twenty-one SPF C57BL/6J female mice were divided into sham (Sham), ovariectomized (OVX), and Zuo-Gui-Wan-treated (ZGW, 1.4 g/kg) groups. The osteoporosis mouse model was established through ovariectomy. After eight weeks of Zuo-Gui-Wan treatment via gavage, serum calcium, phosphorus, ALT, AST, CREA, and other biochemical indicators were measured. Subsequently, Micro-CT, HE staining, and analysis of gut microbiota were conducted to further explore the potential mechanism.

RESULTS

The anti-osteoporotic effects of ZGW were confirmed through micro-CT, histological, and biochemical tests in an OVX-induced osteoporosis mouse model. ZGW treatment also alters the diversity and composition of the gut microbiota and altered the Firmicutes/Bacteroidetes ratio. Further analysis reveals a correlation between specific bacterial groups and serum indicators. Mfuzz clustering analysis and metagenomeSeq analysis identified important microbiota species that were rescued or modulated by ZGW treatment.

CONCLUSION

These findings suggest that changes in gut microbiota abundance may be linked to ZGW's ability to improve osteoporosis. This study provides new insights into how ZGW treats osteoporosis, though further research is needed to clarify the mechanisms by which specific gut microbiota influence bone health.

The Interplay of Nutrition, the Gut Microbiota and Immunity and Its Contribution to Human Disease

Nutrition, the gut microbiota and immunity are all important factors in the maintenance of health. However, there is a growing realization of the complex interplay between these elements coalescing in a nutrition-gut microbiota-immunity axis. This regulatory axis is critical for health with disruption being implicated in a broad range of diseases, including autoimmune disorders, allergies and mental health disorders. This new perspective continues to underpin a growing number of innovative therapeutic strategies targeting different elements of this axis to treat relevant diseases. This review describes the inter-relationships between nutrition, the gut microbiota and immunity. It then details several human diseases where disruption of the nutrition-gut microbiota-immunity axis has been identified and presents examples of how the various elements may be targeted therapeutically as alternate treatment strategies for these diseases.

Effects of the Curcuminoid and Non-Curcuminoid Compounds of Turmeric on the Gut Microbiome and Inflammation: Potential Use in the Treatment and Prevention of Disease

The gut microbiome is a complex system that directly interacts with and influences many systems in the body. This delicate balance of microbiota plays an important role in health and disease and is highly influenced by lifestyle factors and the surrounding environment. As further research emerges, understanding the full potential of the gut microbiome and the impact of using nutraceuticals to positively influence its function may open the door to greater therapeutic outcomes in the treatment and prevention of disease. Curcumin, a bioactive compound derived from the turmeric rhizome, has been studied in depth for its influence on human health as a potent anti-inflammatory and antioxidant properties. However, the therapeutic activity of curcumin is limited by its low oral bioavailability. While most available research has primarily focused on the curcuminoid compounds of turmeric, the non-curcuminoid compounds hold promise to offer therapeutic benefits while synergistically enhancing the bioavailability of curcumin and supporting the gut microbiome. This review summarizes current knowledge of the relationship between the gut and the various systems within the body, and how dysbiosis, or disruption in the gut microbial balance, leads to inflammation and increased risk of chronic disease. The review also summarizes recent research that focuses on the bioactivity of both the curcuminoid and non-curcuminoid compounds that comprise the whole turmeric root and their synergistic role in enhancing bioavailability to support a healthy gut microbiome and promising use in the treatment and prevention of disease.

Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient

The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R2 value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.

The gut microbiota and its role in the development of cardiovascular disease

INTRODUCTION

The pathophysiology of cardiovascular diseases encompasses a complex interplay of genetic and environmental risk factors. Even if traditional risk factors are treated to target, there remains a residual risk.

AREAS COVERED

This manuscript reviews the potential role of gut microbiota in the development of cardiovascular disease, and as potential target. A systematic search was conducted until 30 October 2024 on PubMed (MEDLINE), using the MeSH terms [Gut microbiota] + [Dysbiosis] + [Cardiovascular] + [TMAO] + [bile acids] + [short-chain fatty acids].

EXPERT OPINION

The term dysbiosis implies changes in equilibrium, with modifications in the composition and functionality of microbiota and a series of additional factors: reduced diversity and uniformity of microorganisms; reduced short-chain fatty acid-producing bacteria; increased gut permeability; release of metabolites, such as trimethylamine N-oxide, betaine, phenylalanine, tryptophan-kynurenine, phenylacetylglutamine, and lipopolysaccharides; and reduced secondary bile acid excretion, leading to inflammation, oxidative stress, and endothelial dysfunction and facilitating the onset of pathological conditions, including obesity, hypertension, diabetes, atherosclerosis, and heart failure. Attempts to restore gut microbiota balance through different interventions, mainly changes in diet, have been shown to positively affect individual components and metabolites and reduce the risk of cardiovascular disease. In addition, probiotics and prebiotics are potentially useful. Fecal microbiota transplantation is a promising therapy.

A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates

Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.

The involvement of the microbiota-gut-brain axis in the pathophysiology of mood disorders and therapeutic implications

INTRODUCTION

There is a growing body of evidence implicating gut-brain axis dysfunction in the pathophysiology of mood disorders. Accordingly, gut microbiota has become a promising target for the development of biomarkers and novel therapeutics for bipolar and depressive disorders.

AREAS COVERED

We describe the observed changes in the gut microbiota of patients with mood disorders and discuss the available studies assessing microbiota-based strategies for their treatment.

EXPERT OPINION

Microbiota-targeted interventions, such as symbiotics, prebiotics, paraprobiotics, and fecal microbiota transplants seem to attenuate the severity of depressive symptoms. The available results must be seen as preliminary and need to be replicated and/or confirmed in larger and independent studies, also considering the pathophysiological and clinical heterogeneity of mood disorders.

Gut-microbiota-brain Axis and post-traumatic epilepsy

There has been growing evidence that perturbations in gut-microbiota-brain axis (GMBA) are involved in mechanisms of chronic sequelae of traumatic brain injury (TBI). This review discusses the connection between GMBA and post-traumatic epilepsy (PTE), the latter being a common outcome of TBI. The focus is on two aspects of post-TBI GMBA dysfunction that are relevant to epilepsy. First are impairments in intestinal permeability with subsequent translocation of gut bacteria into the bloodstream. Specifically, endotoxemia following TBI may have a serendipitous protective effect against PTE through lipopolysaccharide conditioning, which may be leveraged for the development of therapeutic interventions. Second are changes in microbial composition (i.e., dysbiosis). Here, the GMBA-PTE connection is explored from predictive biomarker perspective, whereby the risk of PTE can be stratified based on specific microbial profiles. Finally, microbiota transplantation is discussed both as a tool to examine the role of gut microbiota in PTE and as a prelude to novel approaches for PTE therapy and prevention.

The Hygienic Significance of Microbiota and Probiotics for Human Wellbeing

The human body can be viewed as a combination of ecological niches inhabited by trillions of bacteria, viruses, fungi, and parasites, all united by the microbiota concept. Human health largely depends on the nature of these relationships and how they are built and maintained. However, personal hygiene practices have historically been focused on the wholesale elimination of pathogens and "hygiene-challenging microorganisms" without considering the collateral damage to beneficial and commensal species. The microbiota can vary significantly in terms of the qualitative and quantitative composition both between different people and within one person during life, and the influence of various environmental factors, including age, nutrition, bad habits, genetic factors, physical activity, medication, and hygienic practices, facilitates these changes. Disturbance of the microbiota is a predisposing factor for the development of diseases and also greatly influences the course and severity of potential complications. Therefore, studying the composition of the microbiota of the different body systems and its appropriate correction is an urgent problem in the modern world. The application of personal hygiene products or probiotics must not compromise health through disruption of the healthy microbiota. Where changes in the composition or metabolic functions of the microbiome may occur, they must be carefully evaluated to ensure that essential biological functions are unaffected. As such, the purpose of this review is to consider the microbiota of each of the "ecological niches" of the human body and highlight the importance of the microbiota in maintaining a healthy body as well as the possibility of its modulation through the use of probiotics for the prevention and treatment of certain human diseases.

Impact of gestational diabetes mellitus in gut and human breast milk microbiome in Colombian women and their infants

Human breast milk (HBM) is a vital source of macronutrients and micronutrients that are crucial for an infant's development. Recent studies have shown that HBM contains diverse microorganisms, including bacteria, viruses, protozoa, and anaerobic fungi. Additionally, novel research has revealed that individuals with metabolic disorders, such as diabetes mellitus, are prone to dysbiosis in their gut microbiome. Our study aimed to investigate the impact of gestational diabetes mellitus (GDM) on HBM and the pair mother-infant gut microbiota. We conducted a comprehensive analysis of two groups from Pereira, Colombia: a GDM group and a non-GDM group. Each group consisted of five infants and their mothers. HBM and stool samples were collected from GDM and non-GDM mother-infant pairs. DNA was purified, and the 16S V3-V4 region was amplified and sequenced. Reads obtained were quality filtered and classified by homology according to the Ribosomal Small Subunit SILVA database. We found significant differences in the relative abundances of gut bacteria between GDM and non-GDM groups. Notably, Bifidobacterium, Serratia and Sutterella were negatively associated in women's gut with GDM. In HBM, Sutterella, Serratia and Lactococcus were found in low RA in the GDM group. Moreover, in the infants, Bifidobacterium, Lactobacillus, Sutterella, Serratia, Streptococcus, and Veillonella had a low presence in GDM. Our findings indicate that there are variations in gut bacteriome profiles between healthy women and those with GDM. These variations may impact the bacterial diversity in HBM, potentially leading to gut bacterial dysbiosis in their infants.

Adaptive Laboratory Evolution of Flavin Functionality Identifies Dihydrolipoyl Dehydrogenase as One of the Critical Points for the Activity of 7,8-Didemethyl-Riboflavin as a Surrogate for Riboflavin in Escherichia coli

Riboflavin analogs lacking one methyl group (7α or 8α) can still serve as a surrogate for riboflavin in riboflavin-deficient microorganisms or animals. The absence of both methyl groups at once completely abolishes this substitution capability. To elucidate the molecular mechanisms behind this phenomenon, we performed an adaptive laboratory evolution experiment (in triplicate) on an E. coli strain auxotrophic for riboflavin. As a result, the riboflavin requirement of the E. coli strain was reduced ~10-fold in the presence of 7,8-didemethyl-riboflavin. The whole genome sequencing of E. coli strains isolated from three experiments revealed two mutation hotspots: lpdA coding for the flavoenzyme dihydrolipoyl dehydrogenase (LpdA), and ompF coding for the major outer membrane protein. In order to investigate the essentiality of flavin's methyl groups to LpdA, the wild type and mutant variants of lpdA were cloned. At least two lpdA mutants increased the fitness of E. coli, and when 7,8-didemethyl-flavin was added to the growth medium, the increase was significant. To the best of our knowledge, an adaptive laboratory evolution experiment running in triplicate as a tool for the identification of mutation hotspots in the genome of microorganisms exposed to metabolic stress challenges is described here for the first time.

Phytobiotics in poultry: revolutionizing broiler chicken nutrition with plant-derived gut health enhancers

As the global population continues to expand, the demand for broiler chicken production to supply safe and high-quality meat is increasing. To meet this ever-growing demand, broiler chickens with enhanced growth performance are being developed, but they often face challenges related to oxidative stress, which can adversely affect gut health. Phytobiotics, which are plant-derived feed additives known for their antimicrobial, antioxidant, immune-modulating, and growth-promoting properties, have emerged as promising natural alternatives to synthetic antibiotics. This review consolidates recent advancements in the use of phytobiotics-derived products from leaves, roots, seeds, flowers, and their extracts in broiler diets reared under standard experimental conditions, without the introduction of stressors. The focus is on elucidating the key mechanisms through which phytobiotics improve gut health, including their effects on gut morphology, integrity, microflora composition, antioxidant capacity, and immune function. The review highlights the potential of phytobiotics to revolutionize broiler nutrition by acting as natural enhancers of gut health. Research findings reveal that phytobiotics significantly improve intestinal health, and boost growth performance, offering a sustainable approach to managing to gut dysfunction. These findings indicate a potential shift in how gut-health related challenges in broilers can be addressed, moving towards natural phytobiotic therapy. However, several challenges persist. Optimizing the dosage of phytobiotics, ensuring consistent performance, and overcoming the limitations related to their extraction and application are key areas requiring further investigation. The review emphasizes the importance of continued research to refine phytobiotic formulations, explore synergistic effects, and incorporate advanced technologies such as AI-driven methods and precision nutrition to tailor feeding strategies more effectively. Additionally, the development of innovative delivery systems, such as nanoencapsulation, is suggested as a way to enhance the effectiveness and reliability of phytobiotics. By highlighting the potential of phytobiotics to revolutionize broiler nutrition, this review supports the poultry industry's shift towards antibiotic-free and sustainable dietary solutions, offering new perspectives on the future of broiler chicken production.

Exploring the Connections: Autophagy, Gut Microbiota, and Inflammatory Bowel Disease Pathogenesis

Inflammatory Bowel Disease (IBD), which includes Crohn's disease and ulcerative colitis, represents a complex and growing global health issue with a multifaceted origin. This review delves into the intricate relationship between gut microbiota, autophagy, and the development of IBD. The gut microbiota, a diverse community of microorganisms, plays a vital role in maintaining gut health, while imbalances in this microbial community, known as dysbiosis, are linked to IBD. Autophagy, a process by which cells recycle their components, is essential for gut homeostasis and the regulation of immune responses. When autophagy is impaired and dysbiosis occurs, they individually contribute to IBD, with their combined impact intensifying inflammation. The interconnectedness of gut microbiota, autophagy, and the host's immune system is central to the onset of IBD. The review also examines how diet influences gut microbiota and its subsequent effects on IBD. It highlights the therapeutic potential of targeting the microbiota and modulating autophagic pathways as treatment strategies for IBD. Understanding these interactions could lead to personalized therapies within the rapidly advancing fields of microbiome research and immunology.

Integrating fruit by-products and whey for the design of folate-bioenriched innovative fermented beverages safe for human consumption

Global concerns over folate deficiency, the risks of excessive synthetic folic acid consumption, and food loss implications for environmental sustainability and food security drive needs of innovative approaches that align food by-product valorisation with folate bio-enrichment. This study explored the use of three fruit by-products extracts (grape, passion fruit, and pitaya) and whey to develop a folate bio-enriched fermented whey-based beverage. Three strains (Lacticaseibacillus rhamnosus LGG, Bifidobacterium infantis BB-02, and Streptococcus thermophilus TH-4) were tested for folate production in different fermentation conditions in modified MRS medium and in a whey-based matrix prepared with water extracts of these fruit by-products. B. infantis BB-02 and S. thermophilus TH-4, alone and in co-culture, were the best folate producers. The selection of cultivation conditions, including the presence of different substrates and pH, with grape by-product water extract demonstrating the most substantial effect on folate production among the tested extracts, was crucial for successfully producing a biofortified fermented whey-based beverage (FWBB). The resulting FWBB provided 40.7 μg of folate per 100 mL after 24 h of fermentation at 37 °C, effectively leveraging food by-products. Moreover, the beverage showed no cytotoxicity in mouse fibroblast cells tests. This study highlights the potential for valorising fruit by-products and whey for the design of novel bioenriched foods, promoting health benefits and contributing to reduced environmental impact from improper disposal.

Advances in characterization of probiotics and challenges in industrial application

An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.

Intestine bacterial community affects the growth of the Pacific white shrimp (Litopenaeus vannamei)

Increasing evidence suggests that intestine microorganisms are closely related to shrimp growth, but there is no existing experiment to prove this hypothesis. Here, we compared the intestine bacterial community of fast- and slow-growing shrimp at the same developmental stage with a marked difference in body size. Our results showed that the intestine bacterial communities of slow-growing shrimp exhibited less diversity but were more heterogeneous than those of fast-growing shrimp. Uncultured_bacterium_g_Candidatus Bacilloplasma, Tamlana agarivorans, Donghicola tyrosinivorans, and uncultured_bacterium_f_Flavobacteriaceae were overrepresented in the intestines of fast-growing shrimp, while Shimia marina, Vibrio sp., and Vibrio campbellii showed the opposite trends. We further found that the bacterial community composition was significantly correlated with shrimp length, and some bacterial species abundances were found to be significantly correlated with shrimp weight and length, including T. agarivorans and V. campbellii, which were chosen as indicators for a reverse gavage experiment. Finally, T. agarivorans was found to significantly promote shrimp growth after the experiment. Collectively, these results suggest that intestine bacterial community could be important factors in determining the growth of shrimp, indicating that specific bacteria could be tested in further studies against shrimp growth retardation. KEY POINTS: • A close relationship between intestine bacterial community and shrimp growth was proven by controllable experiments. • The bacterial signatures of the intestine were markedly different between slow- and fast-growing shrimp, and the relative abundances of some intestine bacterial species were correlated significantly with shrimp body size. • Reverse gavage by Tamlana agarivorans significantly promoted shrimp growth.

Therapeutic success in primary biliary cholangitis and gut microbiota: a safe highway?

Primary biliary cholangitis (PBC) is a chronic, cholestatic, autoimmune disease, characterized by destruction of bile ducts. PBC predominantly affects women between 40 and 60 years of age. The presence of antimitochondrial antibodies (AMA) is a serological feature of PBC. These highly specific antibodies are found in about 95% of patients with the disease. The family of enzymes located in the inner membrane of the mitochondria, called the 2-oxo-acid dehydrogenase complex represents the target of the AMA. Ursodeoxycholic acid (UDCA) is a synthetic bile acid capable of protecting cholangiocytes from cholestatic damage caused by the accumulation of bile acids with a mechanism of action not yet well clarified. UDCA represents the gold standard therapy for PBC patients with recommended dose of 13-15 mg/kg/day. However, not every patient responds to therapy. On the other hand, the gut microbiota plays a key role in the onset of PBC through still unclear biochemical pathways. Less is known about its role as a potential biomarker after drug treatment. Actually, few studies analyzed the changes in gut microbiota composition before and after UDCA treatment. For this reason, this review represents an examination of the studies carried out on changes in gut microbiota composition in patients affected by PBC before and after treatment.

Harnessing Oxidative Stress to Obtain Natural Riboflavin Secreting Lactic Acid Bacteria for Use in Biofortification

Lactococcus lactis suffers from oxidative stress and riboflavin starvation at elevated temperatures due to dissolved oxygen, which can be relieved partially by exogenously supplied riboflavin. Here we explore whether this phenomenon can be harnessed to obtain riboflavin overproducing mutants. Using a riboflavin auxotrophic L. lactis strain as a riboflavin biosensor, we screened L. lactis cultures that had been exposed to temperature induced oxidative stress for up to one year. Riboflavin secreting mutants could readily be identified, some of which had arisen after just two weeks of exposure to oxidative stress. Whole genome sequencing revealed mutations in the riboswitch, which regulate riboflavin biosynthesis. Riboflavin secretion conferred a significant increase in tolerance to oxidative stress and enabled growth at high temperatures in the presence of dissolved oxygen. It was subsequently demonstrated that vigorous aeration at high temperature (37 °C) could prompt rapid emergence of riboflavin secreting mutants. The protective effect provided by riboflavin against oxidative stress may explain the natural occurrence of lactic acid bacteria (LAB) secreting riboflavin. By optimizing fermentation conditions and eliminating lactate formation, we achieved 64 mg/L riboflavin, the highest reported titer so far for LAB, which indicates great potential for use as a riboflavin fortification agent in food.

Research advancements on the diversity and host interaction of gut microbiota in chickens

The maintenance of host health and immune function is heavily dependent on the gut microbiota. However, the precise contribution of individual microbial taxa to regulating the overall functionality of the gut microbiome remains inadequately investigated. Chickens are commonly used as models for studying poultry gut microbiota, with high-throughput 16S rRNA sequencing has emerged as a valuable tool for assessing both its composition and functionality. The interactions between the gut's microbial community and its host significantly influence health outcomes, disease susceptibility, and various mechanisms affecting gastrointestinal function. Despite substantial research efforts, the dynamic nature of this microbial ecosystem has led to inconsistencies in findings related to chicken gut microbiota, which is largely attributed to variations in rearing conditions. Consequently, the interaction between the chickens' gut microflora and its host remains inadequately explored. This review highlights recent advances in understanding these relationships, with a specific focus on microbial composition, diversity, functional mechanisms, and their potential implications for improving poultry production.

The riboflavin biosynthetic pathway as a novel target for antifungal drugs against Candida species

In recent decades, there has been an increase in the occurrence of fungal infections; yet, the arsenal of drugs available to fight invasive infections remains very limited. The development of new antifungal agents is hindered by the restricted number of molecular targets that can be exploited, given the shared eukaryotic nature of fungi and their hosts which often leads to host toxicity. In this paper, we examine the riboflavin biosynthetic pathway as a potential novel drug target. Riboflavin is an essential nutrient for all living organisms. Its biosynthetic pathway does not exist in humans, who obtain riboflavin through their diet. Our findings demonstrate that all enzymes in the pathway are essential for Candida albicans, Candida glabrata, and Saccharomyces cerevisiae. Auxotrophic strains, which mimic a drug targeting the biosynthesis pathway, experience rapid mortality in the absence of supplemented riboflavin. Furthermore, RIB1 is essential for virulence in both C. albicans and C. glabrata in a systemic mouse model. The fungal burden of a RIB1 deletion strain is significantly reduced in the kidneys and brain of infected mice, and this reduction becomes more pronounced over time. Nevertheless, auxotrophic cells can still take up external riboflavin when supplemented. We identified Orf19.4337 as the riboflavin importer in C. albicans and named it Rut1. We found that Rut1 only facilitates growth at external riboflavin concentrations that exceed the physiological concentrations in the human body. This suggests that riboflavin uptake is unlikely to serve as a resistance mechanism against drugs targeting the biosynthesis pathway. Interestingly, the uptake system in S. cerevisiae is more effective than in C. albicans and C. glabrata, enabling an auxotrophic S. cerevisiae strain to outcompete an auxotrophic C. albicans strain in lower riboflavin concentrations.

IMPORTANCE

Candida species are a common cause of invasive fungal infections. Candida albicans, in particular, poses a significant threat to immunocompromised individuals. This opportunistic pathogen typically lives as a commensal on mucosal surfaces of healthy individuals but it can also cause invasive infections associated with high morbidity and mortality. Currently, there are only three major classes of antifungal drugs available to treat these infections. In addition, the efficacy of these antifungal agents is restricted by host toxicity, suboptimal pharmacokinetics, a narrow spectrum of activity, intrinsic resistance of fungal species, such as Candida glabrata, to certain drugs, and the acquisition of resistance over time. Therefore, it is crucial to identify new antifungal drug targets with novel modes of action to add to the limited armamentarium.

Hedgehog Signalling Pathway and Its Role in Shaping the Architecture of Intestinal Epithelium

The hedgehog (Hh) signalling pathway plays a key role in both embryonic and postnatal development of the intestine and is responsible for gut homeostasis. It regulates stem cell renewal, formation of the villous-crypt axis, differentiation of goblet and Paneth cells, the cell cycle, apoptosis, development of gut innervation, and lipid metabolism. Ligands of the Hh pathway, i.e., Indian hedgehog (Ihh) and Sonic hedgehog (Shh), are expressed by superficial enterocytes but act in the mesenchyme, where they are bound by a Patched receptor localised on myofibroblasts and smooth muscle cells. This activates a cascade leading to the transcription of target genes, including those encoding G1/S-specific cyclin-D2 and -E1, B-cell lymphoma 2, fibroblast growth factor 4, and bone morphogenetic protein 4. The Hh pathway is tightly connected to Wnt signalling. Ihh is the major ligand in the Hh pathway. Its activation inhibits proliferation, while its blocking induces hyperproliferation and triggers a wound-healing response. Thus, Ihh is a negative feedback regulator of cell proliferation. There are data indicating that diet composition may affect the expression of the Hh pathway genes and proteins, which in turn, induces changes in mucosal architecture. This was shown for fat, vitamin A, haem, berberine, and ovotransferrin. The Hh signalling is also affected by the intestinal microbiota, which affects the intestinal barrier integrity. This review highlights the critical importance of the Hh pathway in shaping the intestinal mucosa and summarises the results obtained so far in research on the effect of dietary constituents on the activity of this pathway.

Developmental programming of tissue-resident macrophages

Macrophages are integral components of the innate immune system that colonize organs early in development and persist into adulthood through self-renewal. Their fate, whether they are replaced by monocytes or retain their embryonic origin, depends on tissue type and integrity. Macrophages are influenced by their environment, a phenomenon referred to as developmental programming. This influence extends beyond the local tissue microenvironment and includes soluble factors that can reach the macrophage niche. These factors include metabolites, antibodies, growth factors, and cytokines, which may originate from maternal diet, lifestyle, infections, or other developmental triggers and perturbations. These influences can alter macrophage transcriptional, epigenetic, and metabolic profiles, affecting cell-cell communication and tissue integrity. In addition to their crucial role in tissue immunity, macrophages play vital roles in tissue development and homeostasis. Consequently, developmental programming of these long-lived cells can modulate tissue physiology and pathology throughout life. In this review, we discuss the ontogeny of macrophages, the necessity of developmental programming by the niche for macrophage identity and function, and how developmental perturbations can affect the programming of macrophages and their subtissular niches, thereby influencing disease onset and progression in adulthood. Understanding these effects can inform targeted interventions or preventive strategies against diseases. Finally, understanding the consequences of developmental programming will shed light on how maternal health and disease may impact the well-being of future generations.

Genetics, diet, microbiota, and metabolome: partners in crime for colon carcinogenesis

Colorectal cancer (CRC) ranks among the most prevalent malignant tumors worldwide, with a multifactorial etiology encompassing genetic, environmental, and life-style factors, as well as the intestinal microbiota and its metabolome. These risk factors often work together in specific groups of patients, influencing how CRC develops and progresses. Importantly, alterations in the gut microbiota act as a critical nexus in this interplay, significantly affecting susceptibility to CRC. This review highlights recent insights into unmodifiable and modifiable risk factors for CRC and how they might interact with the gut microbiota and its metabolome. Understanding the mechanisms of these interactions will help us develop targeted, precision-medicine strategies that can adjust the composition of the gut microbiota to meet individual health needs, preventing or treating CRC more effectively.

Orally administered recombinant Lactobacillus expressing PEDV neutralizing antibody protects piglets against PEDV infection

Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus, causing fatal acute diarrhea in suckling pigs, with mortality rates as high as 100 % in 7-day-old piglets. Due to the challenge of quickly establishing effective active immunity, the main strategy for protecting piglets from PEDV infection relies on antibodies, particularly neutralizing antibodies, to provide passive immune protection. In this study, a recombinant Lactobacillus strain for secreting the Fab fragment of neutralizing antibody against PEDV was constructed (pPG-Fab/J31). The results showed that the Fab antibody was stably expressed by pPG-Fab/J31, and exhibit specific neutralizing effect against PEDV. Then, pPG-Fab/J31 was used for the oral administration of newborn piglets to test the protective effect against PEDV challenge. The findings demonstrated that piglets in the antibody administration group exhibited an alleviation of clinical symptoms, a smaller decrease in weight, significant reduction in viral shedding, and attenuation of intestinal lesions. Additionally, the survival rate of piglets orally administered pPG-Fab/J31 was 100 %. Thus, PEDV neutralizing antibody expressed by recombinant Lactobacillus hold promise as a passive protective candidate, providing a new idea for the prevention and treatment of viral infections.

Determinants of raffinose family oligosaccharide use in Bacteroides species

Bacteroides species are successful colonizers of the human colon and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in polysaccharide utilization loci (PULs). While recent work has uncovered the PULs required for the use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under the control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron. Examining the genomes of other Bacteroides species, we found homologs of BT1871 in a subset and showed that representative strains of species with a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.

IMPORTANCE

The gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the microbiota in the colon since they remain undigested by the host. Here, we study how the model commensal organism, Bacteroides thetaiotaomicron utilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.

Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge

Coccidiosis, caused by Eimeria parasites, significantly impacts poultry farm economics and animal welfare. Beyond its direct impact on health, Eimeria infection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused by Clostridium perfringens. The impact of Eimeria infection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with a Saccharomyces cerevisiae-vectored anticoccidial vaccine and challenged with 15,000 Eimeria tenella oocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and caecal metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficial Bifidobacterium. Using a multi-omics factor analysis, data on caecal microbiota and metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.IMPORTANCEAdvances in anticoccidial vaccines have garnered significant attention in poultry health management. However, the intricacies of vaccine-induced alterations in the chicken gut microbiome and its subsequent impact on host metabolism remain inadequately explored. This study delves into the metabolic and microbiotic shifts in chickens post-vaccination, employing a multi-omics integration analysis. Our findings highlight a notable synergy between the microbiome composition and host-microbe interacted metabolic pathways in vaccinated chickens, differentiating them from infected or non-vaccinated cohorts. These insights pave the way for more targeted and efficient approaches in poultry disease control, enhancing both the efficacy of vaccines and the overall health of poultry populations.

MKAN-MMI: empowering traditional medicine-microbe interaction prediction with masked graph autoencoders and KANs

The growing microbial resistance to traditional medicines necessitates in-depth analysis of medicine-microbe interactions (MMIs) to develop new therapeutic strategies. Widely used artificial intelligence models are limited by sparse observational data and prevalent noise, leading to over-reliance on specific data for feature extraction and reduced generalization ability. To address these limitations, we integrate Kolmogorov-Arnold Networks (KANs), independent subspaces, and collaborative decoding techniques into the masked graph autoencoder (Mask GAE) framework, creating an innovative MMI prediction model with enhanced accuracy, generalization, and interpretability. First, we apply Bernoulli distribution to randomly mask parts of the medicine-microbe graph, advancing self-supervised training and reducing noise impact. Additionally, the independent subspace technique enables graph neural networks (GNNs) to learn weights independently across different feature subspaces, enhancing feature expression. Fusing the multi-layer outputs of GNNs effectively reduces information loss caused by masking. Moreover, using KANs for advanced nonlinear mapping enhances the learnability and interpretability of weights, deepening the understanding of complex MMIs. These measures significantly enhanced the accuracy, generalization, and interpretability of our model in MMI prediction tasks. We validated our model on three public datasets with results showing that our model outperformed existing leading models. The relevant data and code are publicly accessible at: https://github.com/zhuoninnin1992/MKAN-MMI.

Riboflavin for women's health and emerging microbiome strategies

Riboflavin (vitamin B2) is an essential water-soluble vitamin that serves as a precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). FMN and FAD are coenzymes involved in key enzymatic reactions in energy metabolism, biosynthesis, detoxification and electron scavenging pathways. Riboflavin deficiency is prevalent worldwide and impacts women's health due to riboflavin demands linked to urogenital and reproductive health, hormonal fluctuations during the menstrual cycle, pregnancy, and breastfeeding. Innovative functional foods and nutraceuticals are increasingly developed to meet women's riboflavin needs to supplement dietary sources. An emerging and particularly promising strategy is the administration of riboflavin-producing lactic acid bacteria, combining the health benefits of riboflavin with those of probiotics and in situ riboflavin production. Specific taxa of lactobacilli are of particular interest for women, because of the crucial role of Lactobacillus species in the vagina and the documented health effects of other Lactobacillaceae taxa in the gut and on the skin. In this narrative review, we synthesize the underlying molecular mechanisms and clinical benefits of riboflavin intake for women's health, and evaluate the synergistic potential of riboflavin-producing lactobacilli and other microbiota.

Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles' heel to target?

Salmonella is a pathogenic bacterium, being the second most commonly reported foodborne pathogen in Europe, due to the ability of its different serovars to contaminate a wide variety of foods, with differences among countries. Common chemical or physical control methods are not always effective, eco-sustainable and adapted to the diversity of Salmonella serovars. Thus, great attention is given to developing complementary or alternative control methods that can be tailor made for specific situations. One of these methods is biopreservation using lactic acid bacteria, with most studies on their antagonistic activity focused on the production of antimicrobials. Less attention has been given to competition by exploitation of nutrients. This review is thus set to investigate and highlight limiting resources that may be involved in the competitive exclusion of Salmonella in food matrices. To do this the needs for nutrients and microelements and the known homeostatic pathways of Salmonella and lactic acid bacteria are examined. Finally, milk, intended for the manufacture of fermented dairy foods, is pointed out as an example of food to investigate the bioavailable macronutrients, metals and vitamins that could be involved in competition between the different species and serovars, and could be exploited for targeted biopreservation.

Investigation of the fermentation filtrate from soapberry (Sapindus mukorossi Gaertn.) pericarp on improving the microbial diversity and composition of the human scalp

Introduction

Microorganisms as a component of scalp ecosystem play a vital role in human scalp health. Soapberry pericarp is employed in improving scalp health, and its content of active ingredients could be enhanced resulted in fermentation. This study aims to investigate the effect of the fermentation filtrate from soapberry pericarp on the diversity of scalp microorganisms.

Methods

The components in fermentation filtrate from soapberry pericarp were analyzed by HPLC-Q-Orbitrap HRMS, and 16S and ITS sequences of 198 samples from three different used stages (Day 0, Day 7, Day 28) were sequenced using the Illumina Novaseq platform. Microbial diversity was assessed using alpha diversity (Chao1 and Shannon indexes) and beta diversity (weighted unifrac and unweighted unifrac). Principal coordinate analysis (PCoA) and linear discriminant analysis (LDA) effect size analysis (LEfSe) were used to visualize microbial variation among different stages.

Results

There were 22 components were identified in the fermentation filtrate from soapberry pericarp by HPLC-Q-Orbitrap HRMS. The alpha-diversity and beta-diversity analyses showed that scalp microbial diversity and composition were influenced by the fermentation filtrate of soapberry pericarp. Based on functional analysis, this study found an enrichment of healthy scalp-related bacterial pathways, such as amino acid, nucleoside, and nucleotide biosynthesis, while a decrease in fungal pathogenesis pathways, specifically saprotroph and symbiotroph pathways, was observed.

Discussion

The study described about the complex community dynamics of human scalp microorganisms during the stages of using the fermentation filtrate from soapberry pericarp. This result will help rationally utilize the fermentation filtrate from soapberry pericarp to keep or improve human scalp health.

Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community

Animal guts contain numerous microbes, which are critical for nutrient assimilation and pathogen defence. While corals and other Cnidaria lack a true differentiated gut, they possess semi-enclosed gastrovascular cavities (GVCs), where vital processes such as digestion, reproduction and symbiotic exchanges take place. The microbiome harboured in GVCs is therefore likely key to holobiont fitness, but remains severely understudied due to challenges of working in these small compartments. Here, we developed minimally invasive methodologies to sample the GVC of coral polyps and characterise the microbial communities harboured within. We used glass capillaries, low dead volume microneedles, or nylon microswabs to sample the gastrovascular microbiome of individual polyps from six species of corals, then applied low-input DNA extraction to characterise the microbial communities from these microliter volume samples. Microsensor measurements of GVCs revealed anoxic or hypoxic micro-niches, which persist even under prolonged illumination with saturating irradiance. These niches harboured microbial communities enriched in putatively microaerophilic or facultatively anaerobic taxa, such as Epsilonproteobacteria. Some core taxa found in the GVC of Lobophyllia hemprichii from the Great Barrier Reef were also detected in conspecific colonies held in aquaria, indicating that these associations are unlikely to be transient. Our findings suggest that the coral GVC is chemically and microbiologically similar to the gut of higher Metazoa. Given the importance of gut microbiomes in mediating animal health, harnessing the coral "gut microbiome" may foster novel active interventions aimed at increasing the resilience of coral reefs to the climate crisis.

A novel clinically relevant human fecal microbial transplantation model in humanized mice

The intact immune system of mice exhibits resistance to colonization by exogenous microorganisms, but the gut microbiota profiles of the humanized mice and the patterns of human fecal microbiota colonization remain unexplored. Humanized NCG (huNCG) mice were constructed by injected CD34 +stem cells. 16S rRNA sequencing and fecal microbiota transplantation (FMT) technologies were used to detect the differences in microbiota and selective colonization ability for exogenous community colonization among three mice cohorts (C57BL/6J, NCG, and huNCG). Flow cytometry analysis showed that all huNCG mice had over 25% hCD45 +in peripheral blood. 16S rRNA gene sequence analysis showed that compared with NCG mice, the gut microbiota of huNCG mice were significantly altered. After FMT, the principal coordinates analysis (PCoA) showed that the gut microbial composition of huNCG mice (huNCG-D9) was similar to that of donors. The relative abundance of Firmicutes and Bacteroidetes were significantly increased in huNCG mice compared to NCG mice. Further comparison of ASV sequences revealed that Bacteroides plebeius, Bacteroides finegoldii, Escherichia fergusonii, Escherichia albertii, Klebsiella pneumoniae, and Klebsiella variicola exhibited higher abundance and stability in huNCG mice after FMT. Furthermore, PICRUSt2 analysis showed that huNCG mice had significantly enhanced metabolism and immunity. This study demonstrated that humanized mice are more conducive to colonization within the human gut microbiota, which provides a good method for studying the association between human diseases and microbiota.IMPORTANCEThe gut microbiota and biomarkers of humanized mice are systematically revealed for the first time. The finding that human fecal microbiota colonize humanized mice more stably provides new insights into the study of interactions between immune responses and gut microbiota.

Host-diet-microbiota interplay in intestinal nutrition and health

The intestine is populated by a complex and dynamic assortment of microbes, collectively called gut microbiota, that interact with the host and contribute to its metabolism and physiology. Diet is considered a key regulator of intestinal microbiota, as ingested nutrients interact with and shape the resident microbiota composition. Furthermore, recent studies underscore the interplay of dietary and microbiota-derived nutrients, which directly impinge on intestinal stem cells regulating their turnover to ensure a healthy gut barrier. Although advanced sequencing methodologies have allowed the characterization of the human gut microbiome, mechanistic studies assessing diet-microbiota-host interactions depend on the use of genetically tractable models, such as Drosophila melanogaster. In this review, we first discuss the similarities between the human and fly intestines and then we focus on the effects of diet and microbiota on nutrient-sensing signaling cascades controlling intestinal stem cell self-renewal and differentiation, as well as disease. Finally, we underline the use of the Drosophila model in assessing the role of microbiota in gut-related pathologies and in understanding the mechanisms that mediate different whole-body manifestations of gut dysfunction.

L-shaped association of thiamine intake and risk for peripheral artery disease in US adults: a cross-sectional study

Background

The relationship between thiamine intake and risk for peripheral artery disease (PAD) is unknown. We aimed to clarify the role of thiamine intake on risk for PAD and the implications of this relationship. The secondary objective of this study is to explore the potential non-linear dose-response relationship between exposure to thiamine intake and outcome risk for PAD.

Methods

We conducted a cross-sectional study involving 6,112 participants with US adults from the National Health and Nutrition Examination Survey (1999-2004). Logistic regression and restricted cubic spline were utilized to substantiate the research objectives.

Results

The overall prevalence of risk for PAD was 7.9, 51% in males and 49% in females. After multivariable adjustment, lower thiamine intake was significantly and nonlinearly associated with higher risks of PAD among participants. Furthermore, we discovered L-shaped associations (p = 0.082) between thiamine intake and the risk of PAD, with an inflection point at 0.66 mg/day. Accordingly, in the threshold effect analysis, there was an inverse association between dietary thiamine intake and the risk in participants with dietary thiamine intake <0.65 mg/day. Compared to participants with thiamine intake below the inflection points, those with higher levels had a 31% lower risk for PAD (OR, 0.69; 95% CI: 0.51, 0.95). Further subgroup analysis showed no significant interactions between the subgroups (all p values for interaction were > 0.05).

Conclusion

A non-linear association was revealed, showing that low and high levels of thiamine intake were associated with an increased the risk of peripheral artery disease in American adults. The inflection point at 0.66 mg/day and lower risk of PAD at 0.65-1.13mg/day of dietary thiamine intake may represent intervention targets for lowering the risk of PAD. The findings of this study require further validation and confirmation.

Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders

1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.

Emerging Targets and Treatments for Sarcopenia: A Narrative Review

BACKGROUND

Sarcopenia is characterized by the progressive loss of skeletal muscle mass, strength, and function, significantly impacting overall health and quality of life in older adults. This narrative review explores emerging targets and potential treatments for sarcopenia, aiming to provide a comprehensive overview of current and prospective interventions.

METHODS

The review synthesizes current literature on sarcopenia treatment, focusing on recent advancements in muscle regeneration, mitochondrial function, nutritional strategies, and the muscle-microbiome axis. Additionally, pharmacological and lifestyle interventions targeting anabolic resistance and neuromuscular junction integrity are discussed.

RESULTS

Resistance training and adequate protein intake remain the cornerstone of sarcopenia management. Emerging strategies include targeting muscle regeneration through myosatellite cell activation, signaling pathways, and chronic inflammation control. Gene editing, stem cell therapy, and microRNA modulation show promise in enhancing muscle repair. Addressing mitochondrial dysfunction through interventions aimed at improving biogenesis, ATP production, and reducing oxidative stress is also highlighted. Nutritional strategies such as leucine supplementation and anti-inflammatory nutrients, along with dietary modifications and probiotics targeting the muscle-microbiome interplay, are discussed as potential treatment options. Hydration and muscle-water balance are emphasized as critical in maintaining muscle health in older adults.

CONCLUSIONS

A combination of resistance training, nutrition, and emerging therapeutic interventions holds potential to significantly improve muscle function and overall health in the aging population. This review provides a detailed exploration of both established and novel approaches for the prevention and management of sarcopenia, highlighting the need for further research to optimize these strategies.

Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk

Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group. Here, we investigated the beneficial potential of Bifidobacterium breve DSM 32583 isolated from human milk. We show that in vitro B. breve DSM 32583 exhibited several characteristics considered fundamental for beneficial bacteria, including survival in conditions simulating those present in the digestive tract, adherence to human epithelial cell lines, and inhibition of growth of potentially pathogenic microorganisms. Its antibiotic resistance patterns were comparable to those of known beneficial bifidobacterial strains, and its genome did not contain plasmids nor virulence-associated genes. These results suggest that B. breve DSM 32583 is a potential probiotic candidate.

The Effect of Dietary Types on Gut Microbiota Composition and Development of Non-Communicable Diseases: A Narrative Review

INTRODUCTION

The importance of diet in shaping the gut microbiota is well established and may help improve an individual's overall health. Many other factors, such as genetics, age, exercise, antibiotic therapy, or tobacco use, also play a role in influencing gut microbiota.

AIM

This narrative review summarizes how three distinct dietary types (plant-based, Mediterranean, and Western) affect the composition of gut microbiota and the development of non-communicable diseases (NCDs).

METHODS

A comprehensive literature search was conducted using the PubMed, Web of Science, and Scopus databases, focusing on the keywords "dietary pattern", "gut microbiota" and "dysbiosis".

RESULTS

Both plant-based and Mediterranean diets have been shown to promote the production of beneficial bacterial metabolites, such as short-chain fatty acids (SCFAs), while simultaneously lowering concentrations of trimethylamine-N-oxide (TMAO), a molecule associated with negative health outcomes. Additionally, they have a positive impact on microbial diversity and therefore are generally considered healthy dietary types. On the other hand, the Western diet is a typical example of an unhealthy nutritional approach leading to an overgrowth of pathogenic bacteria, where TMAO levels rise and SCFA production drops due to gut dysbiosis.

CONCLUSION

The current scientific literature consistently highlights the superiority of plant-based and Mediterranean dietary types over the Western diet in promoting gut health and preventing NCDs. Understanding the influence of diet on gut microbiota modulation may pave the way for novel therapeutic strategies.

Molecular cross-talk among human intestinal bifidobacteria as explored by a human gut model

Bifidobacteria are well known as common and abundant colonizers of the human gut and are able to exert multiple beneficial effects on their host, although the cooperative and competitive relationships that may occur among bifidobacterial strains are still poorly investigated. Therefore, to dissect possible molecular interactions among bifidobacterial species that typically colonize the human gut, three previously identified bifidobacterial prototypes, i.e., B. bifidum PRL2010, B. breve PRL2012, and B. longum PRL2022 were cultivated individually as well as in bi- and tri-association in a human gut-simulating medium. Transcriptomic analyses of these co-associations revealed up-regulation of genes predicted to be involved in the production of extracellular structures including pili (i.e., flp pilus assembly TadE protein gene), exopolysaccharides (i.e., GtrA family protein gene) and teichoic acids (i.e., ABC transporter permease), along with carbohydrate, amino acid and vitamin metabolism-related genes (i.e., exo-alpha-sialidase; beta-galactosidase and pyridoxamine kinase), suggesting that co-cultivation of bifidobacteria induces a response, in individual bifidobacterial strains, aimed at enhancing their proliferation and survival, as well as their ability to cooperate with their host to promote their persistence. Furthermore, exposure of the selected prototypes to human cell line monolayers unveiled the ability of the bifidobacterial tri-association to communicate with their host by increasing the expression of genes involved in adherence to/interaction with intestinal human cells. Lastly, bifidobacterial tri-association promoted the transcriptional upregulation of genes responsible for maintaining the integrity and homeostasis of the intestinal epithelial barrier.

The Role of Host Genetics and Intestinal Microbiota and Metabolome as a New Insight into IBD Pathogenesis

Inflammatory bowel disease (IBD) is an incurable, chronic disorder of the gastrointestinal tract whose incidence increases every year. Scientific research constantly delivers new information about the disease and its multivariate, complex etiology. Nevertheless, full discovery and understanding of the complete mechanism of IBD pathogenesis still pose a significant challenge to today's science. Recent studies have unanimously confirmed the association of gut microbial dysbiosis with IBD and its contribution to the regulation of the inflammatory process. It transpires that the altered composition of pathogenic and commensal bacteria is not only characteristic of disturbed intestinal homeostasis in IBD, but also of viruses, parasites, and fungi, which are active in the intestine. The crucial function of the microbial metabolome in the human body is altered, which causes a wide range of effects on the host, thus providing a basis for the disease. On the other hand, human genomic and functional research has revealed more loci that play an essential role in gut homeostasis regulation, the immune response, and intestinal epithelial function. This review aims to organize and summarize the currently available knowledge concerning the role and interaction of crucial factors associated with IBD pathogenesis, notably, host genetic composition, intestinal microbiota and metabolome, and immune regulation.

Comparative genome analysis of microbial strains marketed for probiotic interventions: an extension of the Integrated Probiotic Database

Background: Members of the Bifidobacterium genus and lactobacilli are the most commonly used probiotics to promote human health. In this context, genome-based in silico analyses have been demonstrated as a fast and reliable tool for identifying and characterizing health-promoting activities imputed to probiotics. Methods: This study is an extension of the Integrated Probiotic Database (IPDB) previously created on probiotics of the genus Bifidobacterium, facilitating a comprehensive understanding of the genetic characteristics that contribute to the diverse spectrum of beneficial effects of probiotics. The strains integrated into this new version of the IPDB, such as various lactobacilli and strains belonging to the species Streptococcus thermophilus (S. thermophilus) and Heyndrickxia coagulans (H. coagulans) (formerly Bacillus coagulans), were selected based on the labels of probiotic formulations currently on the market and using the bacterial strains whose genome had already been sequenced. On these bacterial strains, comparative genome analyses were performed, mainly focusing on genetic factors that confer structural, functional, and chemical characteristics predicted to be involved in microbe-host and microbe-microbe interactions. Results: Our investigations revealed marked inter- and intra-species variations in the genetic makeup associated with the biosynthesis of external structures and bioactive metabolites putatively associated with microbe- and host-microbe interactions. Conclusion: Although genetic differences need to be confirmed as functional or phenotypic differences before any probiotic intervention, we believe that considering these divergences will aid in improving effective and personalized probiotic-based interventions.

The communication mechanism of the gut-brain axis and its effect on central nervous system diseases: A systematic review

Gut microbiota is involved in intricate and active metabolic processes the host's brain function, especially its role in immune responses, secondary metabolism, and symbiotic connections with the host. Gut microbiota can promote the production of essential metabolites, neurotransmitters, and other neuroactive chemicals that affect the development and treatment of central nervous system diseases. This article introduces the relevant pathways and manners of the communication between the brain and gut, summarizes a comprehensive overview of the current research status of key gut microbiota metabolites that affect the functions of the nervous system, revealing those adverse factors that affect typical communication between the brain-gut axis, and outlining the efforts made by researchers to alleviate these neurological diseases through targeted microbial interventions. The relevant pathways and manners of communication between the brain and gut contribute to the experimental design of new treatment plans and drug development. The factors that may cause changes in gut microbiota and affect metabolites, as well as current intervention methods are summarized, which helps improve gut microbiota brain dialogue, prevent adverse triggering factors from interfering with the gut microbiota system, and minimize neuropathological changes.

Host-Gut Microbiota Metabolic Interactions and Their Role in Precision Diagnosis and Treatment of Gastrointestinal Cancers

The critical role of the gut microbiome in gastrointestinal cancers is becoming increasingly clear. Imbalances in the gut microbial community, referred to as dysbiosis, are linked to increased risks for various forms of gastrointestinal cancers. Pathogens like Fusobacterium and Helicobacter pylori relate to the onset of esophageal and gastric cancers, respectively, while microbes such as Porphyromonas gingivalis and Clostridium species have been associated with a higher risk of pancreatic cancer. In colorectal cancer, bacteria such as Fusobacterium nucleatum are known to stimulate the growth of tumor cells and trigger cancer-promoting pathways. On the other hand, beneficial microbes like Bifidobacteria offer a protective effect, potentially inhibiting the development of gastrointestinal cancers. The potential for therapeutic interventions that manipulate the gut microbiome is substantial, including strategies to engineer anti-tumor metabolites and employ microbiota-based treatments. Despite the progress in understanding the influence of the microbiome on gastrointestinal cancers, significant challenges remain in identifying and understanding the precise contributions of specific microbial species and their metabolic products. This knowledge is essential for leveraging the role of the gut microbiome in the development of precise diagnostics and targeted therapies for gastrointestinal cancers.