Gut microbiota role in dietary protein metabolism and health-related outcomes: The two sides of the coin

Firmicutes primarily drive odor emission profiles in poultry manure treatments

Odor emission during livestock manure treatment poses a threat to the environment and human health. However, the odor emission profiles and related factors of commonly employed poultry manure treatments have rarely been studied. Here, we explored the odor emission profiles of 3 common poultry manure treatments in China, namely, ectopic fermentation beds (EFB), annular composting troughs (ACT) and air-drying rooms (ADR). The results revealed that the total odor concentrations in the EFB, ACT and ADR groups were 2407.67 ± 512.94, 13444.00 ± 1269.92 and 621.33 ± 59.27, respectively. The ACT had the greatest number of odorants (31), followed by the ADR (27) and the EFB (24). Methyl mercaptan, acetic acid, acetaldehyde, hydrogen sulfide, ammonia and acrolein were the key odorous compounds detected in all the treatments. ACT contained the greatest number of key odorants (11) and exhibited an extensive co-occurrence relationship with the bacterial community. The 3 poultry manure treatments exhibited significant differences in the beta diversities of the bacterial community. The phylum of most bacteria associated with key odorants was Firmicutes, and Enterococcus and Oceanobacillus were significantly positively correlated with methyl mercaptan. The bacterial functional groups were enriched in carbohydrate metabolism, amino acid metabolism and energy metabolism, and the functional genes shaped the odor emission patterns in the poultry manure treatments. Redundancy analysis demonstrated that odor emission in the 3 treatments was positively correlated with Firmicutes abundance, pH, electrical conductivity and moisture. Thus, our study provides a good understanding of odor emission profiles in poultry manure treatments and data for precise odor emission control during livestock production.

Dietary protein affects tissue accumulation of mercury and induces hepatic Phase I and Phase II enzyme expression after co-exposure with methylmercury in mice

Methylmercury (MeHg) is a ubiquitous environmental contaminant, well known for its neurotoxic effects. MeHg can interact with several nutrients in the diet and affect nutrient metabolism, however the interaction between MeHg and dietary proteins has not been thoroughly investigated. Male BALB/c mice were fed diets based on either casein, cod or chicken as protein sources, which were or were not spiked with MeHg (3.5 mg Hg kg-1). Following 13 weeks of dietary exposure to MeHg, the animals accumulated mercury in a varying degree depending on the diet, where the levels of mercury were highest in the mice fed casein and MeHg, lower in mice fed cod and MeHg, and lowest in mice fed chicken and MeHg in all tissues assessed. Assessment of gut microbiota revealed differences in microbiota composition based on the different protein sources. However, the introduction of MeHg eliminated this difference. Proteomic profiling of liver tissue uncovered the influence of the dietary protein sources on a range of enzymes related to Phase I and Phase II detoxification mechanisms, suggesting an impact of the diet on MeHg metabolism and excretion. Also, enzymes linked to pathways including methionine and glycine betaine cycling, which in turn impact the production of glutathione, an important MeHg conjugation molecule, were up-regulated in mice fed chicken as dietary protein. Our findings indicate that dietary proteins can affect expression of hepatic enzymes that potentially influence MeHg metabolism and excretion, highlighting the relevance of considering the dietary composition in risk assessment of MeHg through dietary exposure.

Untargeted metabolomics unravels distinct gut microbial metabolites derived from plant-based and animal-origin proteins using in vitro modeling

The popularity of plant-based meat alternatives (PBMAs) has sparked a contentious debate about their influence on intestinal homeostasis compared to traditional animal-based meats. This study aims to explore the changes in gut microbial metabolites (GMMs) induced by the gut microbiota on different digested patties: beef meat and pea-protein PBMA. After digesting in vitro, untargeted metabolomics revealed 32 annotated metabolites, such as carnitine and acylcarnitines correlated with beef meat, and 45 annotated metabolites, like triterpenoids and lignans, linked to our PBMA. Secondly, (un)targeted approaches highlighted differences in GMM patterns during colonic fermentations. Our findings underscore significant differences in amino acids and their derivatives. Beef protein fermentation resulted in higher production of methyl-histidine, gamma-glutamyl amino acids, indoles, isobutyric and isovaleric acids. In contrast, PBMAs exhibit a significant release of N-acyl amino acids and unique dipeptides, like phenylalanine-arginine. This research offers valuable insights into how PBMAs and animal-based proteins differently modulate intestinal microenvironments.

Recent advances in wolfberry polysaccharides and whey protein-based biopolymers for regulating the diversity of gut microbiota and its mechanism: A review

Imbalances in gut microbiota diversity are associated with various health issues, including obesity and related disorders. There is a growing interest in developing synergistic biopolymers based on wolfberry polysaccharides and whey protein to address these problems due to their potential health benefits. This review explores recent advances in understanding how functional foods based on Lycium barbarum polysaccharides (LBP) and whey protein (WP) influence gut microbiota diversity and their underlying mechanisms. We examine the impact of these biopolymers on microbial composition and functionality, focusing on their roles in improving health by regulating gut microbiota. The combined effects of WP and LBP significantly enhance gut microbiome metabolic activities and taxonomic diversity, offering promising avenues for treating obesity and related disorders.

Small intestinal microbiota: from taxonomic composition to metabolism

The small intestinal microbiota (SIM) is essential for gastrointestinal health, influencing digestion, immune modulation, and nutrient metabolism. Unlike the colonic microbiota, the SIM has been poorly characterized due to sampling challenges and ethical considerations. Current evidence suggests that the SIM consists of five core genera and additional segment-specific taxa. These bacteria closely interact with the human host, regulating nutrient absorption and metabolism. Recent work suggests the presence of two forms of small intestinal bacterial overgrowth, one dominated by oral bacteria (SIOBO) and a second dominated by coliform bacteria. Less invasive sampling techniques, omics approaches, and mechanistic studies will allow a more comprehensive understanding of the SIM, paving the way for interventions engineering the SIM towards better health.

The role of fiber in modulating plant protein-induced metabolic responses

The rising consumption of plant protein foods and the emergence of meat alternatives have prompted interest in the health benefits of such products, which contain fiber in addition to protein. This review investigates the effect of fiber on plant-based protein metabolism and evaluates its contribution to gut-derived health impacts. Plant proteins, which often come with added fiber, can have varying health outcomes. Factors such as processing and the presence of fiber and starch influence the digestibility of plant proteins, potentially leading to increased proteolytic fermentation in the gut and the production of harmful metabolites. However, fermentable fiber can counteract this effect by serving as a primary substrate for gut microbes, decreasing proteolytic activity. The increased amount of fiber, rather than the protein source itself, plays a significant role in the observed health benefits of plant-based diets in human studies. Differences between extrinsic and intrinsic fiber in the food matrix further impact protein fermentation and digestibility. Thus, in novel protein products without naturally occurring fiber, the health impact may differ from conventional plant protein sources. The influence of various fibers on plant-based protein metabolism throughout the gastrointestinal tract is not fully understood, necessitating further research.

Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.)

To reduce the use of antibiotics and chemicals in aquaculture, an edible herb, Bidens pilosa, has been selected as a multifunctional feed additive. Although there has been considerable research into the effects of B. pilosa on poultry, the wider effects of B. pilosa, particularly on the growth and gut microbiota of fish, remain largely unexplored. We aimed to investigate the interactive effects between the host on growth and the gut microbiota using transcriptomics and the gut microbiota in B. pilosa-fed tilapia. In this study, we added 0.5% and 1% B. pilosa to the diet and observed that the growth performance of tilapia significantly increased over 8 weeks of feeding. Comparative transcriptome analysis was performed on RNA sequence profiles obtained from liver and muscle tissues. Functional enrichment analysis revealed that B. pilosa regulates several pathways and genes involved in amino acid metabolism, lipid metabolism, carbohydrate metabolism, endocrine system, signal transduction, and metabolism of other amino acids. The expression of the selected growth-associated genes was validated by qRT-PCR. The qRT-PCR results indicated that B. pilosa may enhance growth performance by activating the expression of the liver igf1 and muscle igf1rb genes and inhibiting the expression of the muscle negative regulator mstnb. Both the enhancement of liver endocrine IGF1/IGF1Rb signaling and the suppression of muscle autocrine/paracrine MSTN signaling induced the expression of myogenic regulatory factors (MRFs), myod1, myog and mrf4 in muscle to promote muscle growth in tilapia. The predicted function of the gut microbiota showed several significantly different pathways that overlapped with the KEGG enrichment results of differentially expressed genes in the liver transcriptomes. This finding suggested that the gut microbiota may influence liver metabolism through the gut-liver axis in B. pilosa-fed tilapia. In conclusion, dietary B. pilosa can regulate endocrine IGF1 signaling and autocrine/paracrine MSTN signaling to activate the expression of MRFs to promote muscle growth and alter the composition of gut bacteria, which can then affect liver amino acid metabolism, carbohydrate metabolism, endocrine system, lipid metabolism, metabolism of other amino acids, and signal transduction in the host, ultimately enhancing growth performance. Our results suggest that B. pilosa has the potential to be a functional additive that can be used as an alternative to reduce antibiotic use as a growth promoter in aquaculture.

Gastrointestinal digestion of food proteins: Anticancer, antihypertensive, anti-obesity, and immunomodulatory mechanisms of the derived peptides

Food proteins and their peptides play a significant role in the important biological processes and physiological functions of the body. The peptides show diverse biological benefits ranging from anticancer to antihypertensive, anti-obesity, and immunomodulatory, among others. In this review, an overview of food protein digestion in the gastrointestinal tract and the mechanisms involved was presented. As some proteins remain resistant and undigested, the multifarious factors (e.g. protein type and structure, microbial composition, pH levels and redox potential, host factors, etc.) affecting their colonic fermentation, the derived peptides, and amino acids that evade intestinal digestion are thus considered. The section that follows focuses on the mechanisms of the peptides with anticancer, antihypertensive, anti-obesity, and immunomodulatory effects. As further considerations were made, it is concluded that clinical studies targeting a clear understanding of the gastrointestinal stability, bioavailability, and safety of food-based peptides are still warranted.

Microbial tryptophan catabolism as an actionable target via diet-microbiome interactions

In recent years, the role of microbial tryptophan (Trp) catabolism in host-microbiota crosstalk has become a major area of scientific interest. Microbiota-derived Trp catabolites positively contribute to intestinal and systemic homeostasis by acting as ligands of aryl hydrocarbon receptor and pregnane X receptor, and as signaling molecules in microbial communities. Accumulating evidence suggests that microbial Trp catabolism could be therapeutic targets in treating human diseases. A number of bacteria and metabolic pathways have been identified to be responsible for the conversion of Trp in the intestine. Interestingly, many Trp-degrading bacteria can benefit from the supplementation of specific dietary fibers and polyphenols, which in turn increase the microbial production of beneficial Trp catabolites. Thus, this review aims to highlight the emerging role of diets and food components, i.e., food matrix, fiber, and polyphenol, in modulating the microbial catabolism of Trp and discuss the opportunities for potential therapeutic interventions via specifically designed diets targeting the Trp-microbiome axis.

The use of an in vitro fecal fermentation model to uncover the beneficial role of omega-3 and punicic acid in gut microbiota alterations induced by a Western diet

The influence of gut microbiota in the onset and development of several metabolic diseases has gained attention over the last few years. Diet plays an essential role in gut microbiota modulation. Western diet (WD), characterized by high-sugar and high-fat consumption, alters gut microbiome composition, diversity index, microbial relative levels, and functional pathways. Despite the promising health effects demonstrated by polyunsaturated fatty acids, their impact on gut microbiota is still overlooked. The effect of Fish oil (omega-3 source) and Pomegranate oil (punicic acid source), and a mixture of both oils in gut microbiota modulation were determined by subjecting the oil samples to in vitro fecal fermentations. Cecal samples from rats from two different dietary groups: a control diet (CD) and a high-fat high-sugar diet (WD), were used as fecal inoculum. 16S amplicon metagenomics sequencing showed that Fish oil + Pomegranate oil from the WD group increased α-diversity. This sample can also increase the relative abundance of the Firmicutes and Bacteroidetes phylum as well as Akkermansia and Blautia, which were affected by the WD consumption. All samples were able to increase butyrate and acetate concentration in the WD group. Moreover, tyrosine concentrations, a precursor for dopamine and norepinephrine, increase in the Fish oil + Pomegranate oil WD sample. GABA, an important neurotransmitter, was also increased in WD samples. These results suggest a potential positive impact of these oils' mixture on gut-brain axis modulation. It was demonstrated, for the first time, the great potential of using a mixture of both Fish and Pomegranate oil to restore the gut microbiota changes associated with WD consumption.

Summatory Effects of Anaerobic Exercise and a 'Westernized Athletic Diet' on Gut Dysbiosis and Chronic Low-Grade Metabolic Acidosis

Anaerobic exercise decreases systemic pH and increases metabolic acidosis in athletes, altering the acid-base homeostasis. In addition, nutritional recommendations advising athletes to intake higher amounts of proteins and simple carbohydrates (including from sport functional supplements) could be detrimental to restoring acid-base balance. Here, this specific nutrition could be classified as an acidic diet and defined as 'Westernized athletic nutrition'. The maintenance of a chronic physiological state of low-grade metabolic acidosis produces detrimental effects on systemic health, physical performance, and inflammation. Therefore, nutrition must be capable of compensating for systemic acidosis from anaerobic exercise. The healthy gut microbiota can contribute to improving health and physical performance in athletes and, specifically, decrease the systemic acidic load through the conversion of lactate from systemic circulation to short-chain fatty acids in the proximal colon. On the contrary, microbial dysbiosis results in negative consequences for host health and physical performance because it results in a greater accumulation of systemic lactate, hydrogen ions, carbon dioxide, bacterial endotoxins, bioamines, and immunogenic compounds that are transported through the epithelia into the blood circulation. In conclusion, the systemic metabolic acidosis resulting from anaerobic exercise can be aggravated through an acidic diet, promoting chronic, low-grade metabolic acidosis in athletes. The individuality of athletic training and nutrition must take into consideration the acid-base homeostasis to modulate microbiota and adaptive physiological responses.

Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology

The intestine and liver are thought to metabolize dietary nutrients and regulate host nutrient homeostasis. Here, we find that the gut microbiota also reshapes the host amino acid (aa) landscape via efficiently metabolizing intestinal aa. To identify the responsible microbes/genes, we developed a metabolomics-based assay to screen 104 commensals and identified candidates that efficiently utilize aa. Using genetics, we identified multiple responsible metabolic genes in phylogenetically diverse microbes. By colonizing germ-free mice with the wild-type strain and their isogenic mutant deficient in individual aa-metabolizing genes, we found that these genes regulate the availability of gut and circulatory aa. Notably, microbiota genes for branched-chain amino acids (BCAAs) and tryptophan metabolism indirectly affect host glucose homeostasis via peripheral serotonin. Collectively, at single-gene level, this work characterizes a microbiota-encoded metabolic activity that affects host nutrient homeostasis and provides a roadmap to interrogate microbiota-dependent activity to improve human health.

A reduction in dietary crude protein with amino acid balance has no negative effects in pigs

The aim of this experiment was to evaluate the effects of low crude protein (CP) level with essential amino acids (AA) addition on growth performance, nutrient digestibility, microbiota, and volatile fatty acid composition in growing pigs. A total of 160 growing pigs (Landrace × Yorkshire × Duroc [LYD]; average initial body weight 16.68 ± 0.12 kg) were randomly allotted to one of the four treatments on the basis of initial body weight. A randomized complete block design was used to conduct this experiment in the Research Center of Animal Life Sciences at Kangwon National University. There were ten pigs/replicate with four replicates in each treatment. The treatments include; CON (Control, 17.2% dietary CP level), low protein (LP)-1.10 (15.7% dietary CP level + 1.10% lysine level), LP-1.15 (15.7% dietary CP level + 1.15% lysine level), LP1.2 (15.7% dietary CP level + 1.20% lysine level). The pigs fed CON and LP-1.2 diet showed greater final body weight than that of LP-1.1 diet (p < 0.05). Although average daily gain, average daily feed intake, and feed efficiency did not show any difference in phase 2 and 3, average daily gain and feed efficiency was significantly greater in CON and LP-1.20 in phase 1. However, the average daily feed intake did not show any difference during the experimental period. Isobutyric acid and isovaleric acid composition of LP treatments were lower than CON treatment in phase 2. Total branched chain fatty acid composition was significantly lower in LP treatment in phases 1 and 2. However, there was no significant difference among treatments in phase 3. The results of this study underscore the importance of AA supplementation when implementing a low-protein diet during the early growth phase (16-50 kg) in pigs.

Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae

The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R2 = 0.92 for the training set and R2 = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.

Crude protein content in diets associated with intestinal microbiome and metabolome alteration in Huanjiang mini-pigs during different growth stages

Introduction

Adequate crude protein (CP) content in diets plays a crucial role in the intestinal health of the animal. This study investigated the impacts of CP content in diets on the intestinal microbiome and metabolome profiles in growing Huanjiang mini-pigs.

Methods

A total of 360 pigs with similar body weight (BW) were allocated for three independent feeding trials based on three different BW stages, including (i) 5-10 kg BW, diets consisting of 14, 16, 18, 20, and 22% CP content; (ii) 10-20 kg BW, diets consisting of 12, 14, 16, 18, and 20% CP content; and (iii) 20-30 kg BW, diets consisting of 10, 12, 14, 16, and 18% CP content. These experiments lasted 28, 28, and 26 days, respectively.

Results

The results showed that the Shannon and Simpson indices were decreased (p < 0.05) in the ileum of pigs in response to the 14-18% CP compared with the 20% CP content at 5-10 kg BW stage, while diets containing 12 and 14% CP had higher Chao1 (p < 0.05) and Shannon (p = 0.054) indices compared with 18% CP at 20-30 kg BW stage. Compared with the 20% CP, the diet containing 16% CP displayed an increasing trend (p = 0.089) of Firmicutes abundance but had decreased (p = 0.056) Actinobacteria abundance in the jejunum at 5-10 kg BW stage. In addition, a diet containing 16% CP had higher Lactobacillus abundance in the jejunum and ileum compared with the 18, 20, and 22% CP, while had lower Sphingomonas and Pelomonas abundances in the jejunum and Streptococcus abundance in the ileum compared with the diet containing 22% CP (p < 0.05). Diets containing lower CP content altered differential metabolites in the small intestine at the early stage, while higher CP content had less impact.

Conclusion

These findings suggest that a diet containing lower CP content (16% CP) may be an appropriate dietary CP content for 5-10 kg Huanjiang mini-pigs, as 16% CP content in diet has shown beneficial impacts on the intestinal microbiome and metabolome profiles at the early growth stage of pigs.

Tempeh fermentation improves the nutritional and functional characteristics of Jack beans (Canavalia ensiformis (L.) DC)

The effect of two processing methods of Jack beans (i.e. cooked bean (CB) and cooked tempeh (CT)) on the in vitro digestibility of protein and starch, as well as the production of short chain fatty acids (SCFAs), γ-aminobutyric acid (GABA), and tryptophan (Trp) metabolites after in vitro colonic fermentation, was investigated. CT was obtained by fungal fermentation after cooking under acidic conditions. CT had significantly higher protein, lower digestible starch, lower total fiber, higher free phenolic compounds, and higher ash content compared to CB. CT exhibited better in vitro protein digestibility than CB and less glucose release during in vitro digestion than CB. A comparable concentration of total SCFAs and GABA was produced after in vitro fermentation of CB and CT, but CB produced more indole than CT, resulting in higher amounts of total Trp metabolites. In summary, our findings show that tempeh fermentation improves the nutritional quality of Jack beans and describe the impact of fermentation on the digestibility of nutrients and the formation of metabolites during colonic fermentation.

Short-Chain Fatty Acid (SCFA) as a Connecting Link between Microbiota and Gut-Lung Axis-A Potential Therapeutic Intervention to Improve Lung Health

The microbiome is an integral part of the human gut, and it plays a crucial role in the development of the immune system and homeostasis. Apart from the gut microbiome, the airway microbial community also forms a distinct and crucial part of the human microbiota. Furthermore, several studies indicate the existence of communication between the gut microbiome and their metabolites with the lung airways, called "gut-lung axis". Perturbations in gut microbiota composition, termed dysbiosis, can have acute and chronic effects on the pathophysiology of lung diseases. Microbes and their metabolites in lung stimulate various innate immune pathways, which modulate the expression of the inflammatory genes in pulmonary leukocytes. For instance, gut microbiota-derived metabolites such as short-chain fatty acids can suppress lung inflammation through the activation of G protein-coupled receptors (free fatty acid receptors) and can also inhibit histone deacetylase, which in turn influences the severity of acute and chronic respiratory diseases. Thus, modulation of the gut microbiome composition through probiotic/prebiotic usage and fecal microbiota transplantation can lead to alterations in lung homeostasis and immunity. The resulting manipulation of immune cells function through microbiota and their key metabolites paves the way for the development of novel therapeutic strategies in improving the lung health of individuals affected with various lung diseases including SARS-CoV-2. This review will shed light upon the mechanistic aspect of immune system programming through gut and lung microbiota and exploration of the relationship between gut-lung microbiome and also highlight the therapeutic potential of gut microbiota-derived metabolites in the management of respiratory diseases.

The effect of microbiome therapy on COVID-19-induced gut dysbiosis: A narrative and systematic review

AIMS

Emerging evidence highlights the role of COVID-19 in instigating gut dysbiosis, with repercussions on disease severity and bidirectional gut-organ communication involving the lung, heart, brain, and liver. This study aims to evaluate the efficacy of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) in addressing gut dysbiosis associated with COVID-19, as well as their impact on related disease severity and clinical outcomes.

MATERIALS AND METHODS

We systematically review 27 studies exploring the efficacy of different microbiome-modulating therapies: probiotics, prebiotics, synbiotics, and fecal microbiota transplantation as potential interventions for COVID-19.

KEY FINDINGS

The probiotics and synbiotics investigated encompassed a spectrum of eight bacterial and fungal genera, namely Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, Pediococcus, Bacillus, Saccharomyces, and Kluyveromyces. Noteworthy prebiotics employed in these studies included chestnut tannin, galactooligosaccharides, fructooligosaccharides, xylooligosaccharide, and resistant dextrin. The majority of the investigated biotics exhibited positive effects on COVID-19 patients, manifesting in symptom alleviation, inflammation reduction, and notable decreases in mortality rates. Five studies reported death rates, showing an average mortality ranging from 0 % to 11 % in the intervention groups, as compared to 3 % to 30 % in the control groups. Specifically, probiotics, prebiotics, and synbiotics demonstrated efficacy in diminishing the duration and severity of symptoms while significantly accelerating viral and symptomatic remission. FMT emerged as a particularly effective strategy, successfully restoring gut microbiota and ameliorating gastrointestinal disorders.

SIGNIFICANCE

The insights gleaned from this review significantly contribute to our broader comprehension of the therapeutic potential of biotics in addressing COVID-19-related gut dysbiosis and mitigating secondary multi-organ complications.

The Impact of Essential Amino Acids on the Gut Microbiota of Broiler Chickens

The research involving the beneficial aspects of amino acids being added to poultry feed pertaining to performance, growth, feed intake, and feed conversion ratio is extensive. Yet currently the effects of amino acids on the gut microbiota aren't fully understood nor have there been many studies executed in poultry to explain the relationship between amino acids and the gut microbiota. The overall outcome of health has been linked to bird gut health due to the functionality of gastrointestinal tract (GIT) for digestion/absorption of nutrients as well as immune response. These essential functions of the GI are greatly driven by the resident microbiota which produce metabolites such as butyrate, propionate, and acetate, providing the microbiota a suitable and thrive driven environment. Feed, age, the use of feed additives and pathogenic infections are the main factors that have an effect on the microbial community within the GIT. Changes in these factors may have potential effects on the gut microbiota in the chicken intestine which in turn may have an influence on health essentially affecting growth, feed intake, and feed conversion ratio. This review will highlight limited research studies that investigated the possible role of amino acids in the gut microbiota composition of poultry.

Regulation of Sacha Inchi protein on fecal metabolism and intestinal microorganisms in mice

Introduction

With the increasing demand for protein utilization, exploring new protein resources has become a research hotspot. Sacha Inchi Protein (SIP) is a high-quality plant protein extracted from Sacha Inchi meal. This study aimed to investigate the impact of SIP on mouse metabolomics and gut microbiota diversity and explore the underlying pathways responsible for its health benefits.

Methods

In this study, the structural composition of SIP was investigated, and the effects of SIP on fecal metabolomics and intestinal microorganisms in mice were explored by LC-MS metabolomics technology analysis and 16S rRNA gene sequencing.

Results

The results showed that SIP was rich in amino acids, with the highest Manuscript Click here to view linked References content of arginine, which accounted for 22.98% of the total amino acid content; the potential fecal metabolites of mice in the SIP group involved lipid metabolism, sphingolipid metabolism, arginine biosynthesis, and amino acid metabolism; SIP altered the microbial composition of the cecum in mice, decreased the Firmicutes/Bacteroidetes value, and It decreased the abundance of the harmful intestinal bacteria Actinobacteriota and Desulfobacterota, and increased the abundance of the beneficial intestinal bacteria Faecalibaculum, Dubosiella.

Discussion

In conclusion, SIP is a high-quality plant protein with great potential for development in lipid-lowering, intestinal health, and mental illness, providing valuable clues for further research on its health-promoting mechanisms.

Impact of Whey Protein Corona Formation around TiO2 Nanoparticles on Their Physiochemical Properties and Gastrointestinal Fate

Previously, we found that whey proteins form biomolecular coronas around titanium dioxide (TiO2) nanoparticles. Here, the gastrointestinal fate of whey protein-coated TiO2 nanoparticles and their interactions with gut microbiota were investigated. The antioxidant activity of protein-coated nanoparticles was enhanced after simulated digestion. The structure of the whey proteins was changed after they adsorbed to the surfaces of the TiO2 nanoparticles, which reduced their hydrolysis under simulated gastrointestinal conditions. The presence of protein coronas also regulated the impact of the TiO2 nanoparticles on colonic fermentation, including promoting the production of short-chain fatty acids. Bare TiO2 nanoparticles significantly increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria, but the presence of protein coronas alleviated this effect. In particular, the proportion of beneficial bacteria, such as Bacteroides and Bifidobacterium, was enhanced for the coated nanoparticles. Our results suggest that the formation of a whey protein corona around TiO2 nanoparticles may have beneficial effects on their behavior within the colon. This study provides valuable new insights into the potential impact of protein coronas on the gastrointestinal fate of inorganic nanoparticles.

Exploring the Mechanistic Interplay between Gut Microbiota and Precocious Puberty: A Narrative Review

The gut microbiota has been implicated in the context of sexual maturation during puberty, with discernible differences in its composition before and after this critical developmental stage. Notably, there has been a global rise in the prevalence of precocious puberty in recent years, particularly among girls, where approximately 90% of central precocious puberty cases lack a clearly identifiable cause. While a link between precocious puberty and the gut microbiota has been observed, the precise causality and underlying mechanisms remain elusive. This narrative review aims to systematically elucidate the potential mechanisms that underlie the intricate relationship between the gut microbiota and precocious puberty. Potential avenues of exploration include investigating the impact of the gut microbiota on endocrine function, particularly in the regulation of hormones, such as gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH). Additionally, this review will delve into the intricate interplay between the gut microbiome, metabolism, and obesity, considering the known association between obesity and precocious puberty. This review will also explore how the microbiome's involvement in nutrient metabolism could impact precocious puberty. Finally, attention is given to the microbiota's ability to produce neurotransmitters and neuroactive compounds, potentially influencing the central nervous system components involved in regulating puberty. By exploring these mechanisms, this narrative review seeks to identify unexplored targets and emerging directions in understanding the role of the gut microbiome in relation to precocious puberty. The ultimate goal is to provide valuable insights for the development of non-invasive diagnostic methods and innovative therapeutic strategies for precocious puberty in the future, such as specific probiotic therapy.

Next-generation prebiotics: Maillard-conjugates of 2'-fucosyllactose and lactoferrin hydrolysates beneficially modulate gut microbiome composition and health promoting activity in a murine model

Current prebiotics are predominantly carbohydrates. However, great competition exists among gut microbes for the scarce protein in the colon, as most consumed protein is digested and absorbed in the small intestine. Herein we evaluated in-vivo novel next-generation prebiotics: protein-containing-prebiotics, for selectively-targeted delivery of protein to colonic probiotics, to boost their growth. This system is based on micellar-particles, composed of Maillard-glycoconjugates of 2'-Fucosyllactose (2'-FL, human-milk-oligosaccharide) shell, engulfing lactoferrin peptic-then-tryptic hydrolysate (LFH) core. This core-shell structure lowers protein-core digestibility, while the prebiotic glycans are hypothesized to serve as molecular-recognition ligands for selectively targeting probiotics. To study the efficacy of this novel prebiotic, we fed C57BL/6JRccHsd mice with either 2'-FL-LFH Maillard-glycoconjugates, unconjugated components (control), or saline (blank). Administration of 2'-FL-LFH significantly increased the levels of short-chain-fatty-acids (SCFAs)-producing bacterial families (Ruminococcaceae, Lachnospiraceae) and genus (Odoribacter) and the production of the health-related metabolites, SCFAs, compared to the unconjugated components and to saline. The SCFAs-producing genus Prevotella significantly increased upon 2'-FL-LFH consumption, compared to only moderate increase in the unconjugated components. Interestingly, the plasma-levels of inflammation-inducing lipopolysaccharides (LPS), which indicate increased gut-permeability, were significantly lower in the 2'-FL-LFH group compared to the unconjugated-components and the saline groups. We found that Maillard-glycoconjugates of 2'-FL-LFH can serve as novel protein-containing prebiotics, beneficially modulating gut microbial composition and its metabolic activity, thereby contributing to host health more effectively than the conventional carbohydrate-only prebiotics.

Coffee and Microbiota: A Narrative Review

Coffee is one of the most widely consumed beverages in the world, which has important repercussions on the health of the individual, mainly because of certain compounds it contains. Coffee consumption exerts significant influences on the entire body, including the gastrointestinal tract, where a central role is played by the gut microbiota. Dysbiosis in the gut microbiota is implicated in the occurrence of numerous diseases, and knowledge of the microbiota has proven to be of fundamental importance for the development of new therapeutic strategies. In this narrative review, we thoroughly investigated the link between coffee consumption and its effects on the gut microbiota and the ensuing consequences on human health. We have selected the most significant articles published on this very interesting link, with the aim of elucidating the latest evidence about the relationship between coffee consumption, its repercussions on the composition of the gut microbiota, and human health. Based on the various studies carried out in both humans and animal models, it has emerged that coffee consumption is associated with changes in the gut microbiota, although further research is needed to understand more about this link and the repercussions for the whole organism.

Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection

Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.

Gut microbiota carbon and sulfur metabolisms support Salmonella infections

Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.

Diet, Gut Microbes, and Cancer

Gut microbes are important and may play important role in spreading cancers specially the gastrointestinal malignancies preferably colorectal cancers. Gut microbes and diet can influence the tissues in gastrointestinal tract increasing the risk of cancer spread. Insufficient nutrient intake and imbalance diet can disturb the microbiome of gastrointestinal tract causing metabolism of xenobiotics which is beneficial as well as detrimental. Dietary imbalance may also weaken the immune system which is another reason for spreading and development of cancers. The triage of gut microbiome, host immune system, and dietary patterns may help the initiation of mechanism of carcinogenesis. In addition to its role in carcinogenesis and tumor development, there is still growing evidence as to how intestinal microflora influences the efficacy and toxicity of chemotherapy and immunotherapy by the gut microbiome. It can therefore be used as a biomarker to predict treatment response or poor response and can also be modified to improve cancer treatment.

Commensal Fecal Microbiota Profiles Associated with Initial Stages of Intestinal Mucosa Damage: A Pilot Study

Progressive intestinal mucosal damage occurs over years prior to colorectal cancer (CRC) development. The endoscopic screening of polyps and histopathological examination are used clinically to determine the risk and progression of mucosal lesions. We analyzed fecal microbiota compositions using 16S rRNA gene-based metataxonomic analyses and the levels of short-chain fatty acids (SCFAs) using gas chromatography in volunteers undergoing colonoscopy and histopathological analyses to determine the microbiota shifts occurring at the early stages of intestinal mucosa alterations. The results were compared between diagnosis groups (nonpathological controls and polyps), between samples from individuals with hyperplastic polyps or conventional adenomas, and between grades of dysplasia in conventional adenomas. Some microbial taxa from the Bacillota and Euryarchaeota phyla were the most affected when comparing the diagnosis and histopathological groups. Deeper microbiota alterations were found in the conventional adenomas than in the hyperplastic polyps. The Ruminococcus torques group was enriched in both the hyperplastic polyps and conventional adenomas, whereas the family Eggerthellaceae was enriched only in the hyperplastic polyps. The abundance of Prevotellaceae, Oscillospiraceae, Methanobacteriaceae, Streptococcaceae, Christensenellaceae, Erysipelotrichaceae, and Clostridiaceae shifted in conventional adenomas depending on the grade of dysplasia, without affecting the major SCFAs. Our results suggest a reorganization of microbial consortia involved in gut fermentative processes.

Protein supplementation: the double-edged sword

Protein supplements are widely consumed by athletes as well as young adults and teenagers going to the gym and are an excellent source to increase protein intake, build muscle mass, and enhance recovery. They are available in the form of powders, gummies, protein bars, and ready-to-drink shakes and have been shown to have effects on almost every system in the body. Subjects consuming whey protein-based supplements regularly show significantly lower systolic blood pressure, while subjects who consume soy-based protein supplements have been reported to show a significant decrease in their systolic and diastolic blood pressures. Favorable effects of soy protein consumption have been observed on the serum lipid profile, with significant decreases in serum low-density lipoprotein and triglyceride levels. Lower postprandial glucose levels have been observed in diabetic subjects as well, which can be attributed to the lower glycemic index of these supplements. This can lead to an indirect decrease in diabetes-related complications. While these supplements affect the body positively, caution has to be exercised while consuming them in excess, as they have been shown to cause hyperfiltration and increased urinary calcium excretion which can, in turn, lead to chronic kidney disease development. This article focuses on the effects of protein supplementation on the human body, with emphasis on the cardiovascular, endocrine, and renal systems.

Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity

The gut microbiota contributes to the pathophysiology of non-alcoholic fatty liver disease (NAFLD). Histidine is a key energy source for the microbiota, scavenging it from the host. Its role in NAFLD is poorly known. Plasma metabolomics, liver transcriptomics, and fecal metagenomics were performed in three human cohorts coupled with hepatocyte, rodent, and Drosophila models. Machine learning analyses identified plasma histidine as being strongly inversely associated with steatosis and linked to a hepatic transcriptomic signature involved in insulin signaling, inflammation, and trace amine-associated receptor 1. Circulating histidine was inversely associated with Proteobacteria and positively with bacteria lacking the histidine utilization (Hut) system. Histidine supplementation improved NAFLD in different animal models (diet-induced NAFLD in mouse and flies, ob/ob mouse, and ovariectomized rats) and reduced de novo lipogenesis. Fecal microbiota transplantation (FMT) from low-histidine donors and mono-colonization of germ-free flies with Enterobacter cloacae increased triglyceride accumulation and reduced histidine content. The interplay among microbiota, histidine catabolism, and NAFLD opens therapeutic opportunities.

Optimizing the Gut Microbiota for Individualized Performance Development in Elite Athletes

The human gut microbiota can be compared to a fingerprint due to its uniqueness, hosting trillions of living organisms. Taking a sport-centric perspective, the gut microbiota might represent a physiological system that relates to health aspects as well as individualized performance in athletes. The athletes' physiology has adapted to their exceptional lifestyle over the years, including the diversity and taxonomy of the microbiota. The gut microbiota is influenced by several physiological parameters and requires a highly individual and complex approach to unravel the linkage between performance and the microbial community. This approach has been taken in this review, highlighting the functions that the microbial community performs in sports, naming gut-centered targets, and aiming for both a healthy and sustainable athlete and performance development. With this article, we try to consider whether initiating a microbiota analysis is practicable and could add value in elite sport, and what possibilities it holds when influenced through a variety of interventions. The aim is to support enabling a well-rounded and sustainable athlete and establish a new methodology in elite sport.

Coffee Leaf Tea Extracts Improve Hyperuricemia Nephropathy and Its Associated Negative Effect in Gut Microbiota and Amino Acid Metabolism in Rats

Hyperuricemia nephropathy (HN) is a metabolic disease characterized by tubular damage, tubulointerstitial fibrosis, and uric acid kidney stones and has been demonstrated to be associated with hyperuricemia. Coffee leaf tea is drunk as a functional beverage. However, its prevention effects on HN remain to be explored. This study showed that coffee leaf tea extracts (TE) contain 19 polyphenols, with a total content of 550.15 ± 27.58 mg GAE/g. TE decreased serum uric acid levels via inhibiting XOD activities and modulating the expression of urate transporters (GLUT9, OAT3, and ABCG2) in HN rats. TE prevented HN-induced liver and kidney damage and attenuated renal fibrosis. Moreover, it upregulated the abundance of SCFA-producing bacteria (Phascolarctobacterium, Alloprevotella, and Butyricicoccus) in the gut and reversed the amino acid-related metabolism disorder caused by HN. TE also decreased the circulating LPS and d-lactate levels and increased the fecal SCFA levels. This study supported the preliminary and indicative effect of coffee leaf tea in the prevention of hyperuricemia and HN.

Impact of Sustained Fructose Consumption on Gastrointestinal Function and Health in Wistar Rats: Glycoxidative Stress, Impaired Protein Digestion, and Shifted Fecal Microbiota

The gastrointestinal tract (GIT) is the target of assorted pathological conditions, and dietary components are known to affect its functionality and health. In previous in vitro studies, we observed that reducing sugars induced protein glycoxidation and impaired protein digestibility. To gain further insights into the pathophysiological effects of dietary sugars, Wistar rats were provided with a 30% (w/v) fructose water solution for 10 weeks. Upon slaughter, in vivo protein digestibility was assessed, and the entire GIT (digests and tissues) was analyzed for markers of oxidative stress and untargeted metabolomics. Additionally, the impact of sustained fructose intake on colonic microbiota was also evaluated. High fructose intake for 10 weeks decreased protein digestibility and promoted changes in the physiological digestion of proteins, enhancing intestinal digestion rather than stomach digestion. Moreover, at colonic stages, the oxidative stress was harmfully increased, and both the microbiota and the intraluminal colonic metabolome were modified.

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains

Motivation

ProbioMinServer is a platform designed to help researchers access information on probiotics regarding a wide variety of characteristics, such as safety (e.g. antimicrobial resistance, virulence, pathogenic, plasmid, and prophage genes) and functionality (e.g. functional classes, carbohydrate-active enzyme, and metabolite gene cluster profile). Because probiotics are functional foods, their safety and functionality are a crucial part of health care. Genomics has become a crucial methodology for investigating the safety and functionality of probiotics in food and feed. This shift is primarily attributed to the growing affordability of next-generation sequencing technologies. However, no integrated platform is available for simultaneously evaluating probiotic strain safety, investigating probiotic functionality, and identifying known phylogenetically related strains.

Results

Thus, we constructed a new platform, ProbioMinServer, which incorporates these functions. ProbioMinServer accepts whole-genome sequence files in the FASTA format. If the query genome belongs to the 25 common probiotic species collected in our database, the server performs a database search and analyzes the core-genome multilocus sequence typing. Front-end applications were implemented in JavaScript with a bootstrap framework, and back-end programs were implemented using PHP, Perl, and Python. ProbioMinServer can help researchers quickly and easily retrieve information on the safety and functionality of various probiotics.

Availability and implementation

The platform is available at https://probiomindb.imst.nsysu.edu.tw.

The microbiota-gut-brain axis in hippocampus-dependent learning and memory: current state and future challenges

A fundamental shift in neuroscience suggests bidirectional interaction of gut microbiota with the healthy and dysfunctional brain. This microbiota-gut-brain axis has mainly been investigated in stress-related psychopathology (e.g. depression, anxiety). The hippocampus, a key structure in both the healthy brain and psychopathologies, is implicated by work in rodents that suggests gut microbiota substantially impact hippocampal-dependent learning and memory. However, understanding microbiota-hippocampus mechanisms in health and disease, and translation to humans, is hampered by the absence of a coherent evaluative approach. We review the current knowledge regarding four main gut microbiota-hippocampus routes in rodents: through the vagus nerve; via the hypothalamus-pituitary-adrenal-axis; by metabolism of neuroactive substances; and through modulation of host inflammation. Next, we suggest an approach including testing (biomarkers of) the four routes as a function of the influence of gut microbiota (composition) on hippocampal-dependent (dys)functioning. We argue that such an approach is necessary to proceed from the current state of preclinical research to beneficial application in humans to optimise microbiota-based strategies to treat and enhance hippocampal-dependent memory (dys)functions.

Comparison of Neuroprotection and Regulating Properties on Gut Microbiota between Selenopeptide Val-Pro-Arg-Lys-Leu-SeMet and Its Native Peptide Val-Pro-Arg-Lys-Leu-Met In Vitro and In Vivo

Selenopeptides are promising candidates for intervening in neuroinflammation; however, the key role of selenium (Se) in selenopeptides remains poorly understood. To address this gap, we compared the neuroprotective effects of selenopeptide Val-Pro-Arg-Lys-Leu-SeMet (namely, Se-P1) and its native peptide Val-Pro-Arg-Lys-Leu-Met (namely, P1). Our results demonstrate that Se-P1 treatment exhibits superior antioxidant and antineuroinflammatory effects in PC12 cells and lipopolysaccharide (LPS)-injured mice compared to P1. Moreover, the administration of Se-P1 and P1 resulted in a shift in the gut microbiota composition. Notably, during LPS-induced injury, Se-P1 treatment demonstrated greater stability in maintaining gut microbiota composition compared to P1 treatment. Specifically, Se-P1 may have a positive impact on gut microbiota dysbiosis by modulating inflammatory-related bacteria such as enhancing Lactobacillus abundance while reducing that of Lachnospiraceae_NK4A136_group. Furthermore, the alteration of metabolites induced by Se-P1 treatment exhibited a significant correlation with gut microbiota, subsequently modulating the inflammatory-related metabolic pathways including histidine metabolism, lysine degradation, and purine metabolism. These findings suggest that organic Se contributes to the bioactivities of Se-P1 in mitigating neuroinflammation in LPS-injured mice compared to P1. These findings hold significant value for the development of potential preventive or therapeutic strategies against neurodegenerative diseases and introduce novel concepts in selenopeptide nutrition and supplementation recommendations.

Multispecies probiotic supplementation in diet with reduced crude protein levels altered the composition and function of gut microbiome and restored microbiome-derived metabolites in growing pigs

Both crude protein (CP) and probiotics can modulate the gut microbiome of the host, thus conferring beneficial effects. However, the benefits of low CP diet supplemented with multispecies probiotics on gut microbiome and its metabolites have not been investigated in pigs. Thus, we investigated the combinatory effects of low CP diet supplemented with multispecies probiotics on gut microbiome composition, function, and microbial metabolites in growing pigs. In total, 140 6 week-old piglets (Landrace × Yorkshire × Duroc) were used in this study. The pigs were divided into four groups with a 2 × 2 factorial design based on their diets: normal-level protein diet (16% CP; NP), low-level protein diet (14% CP; LP), NP with multispecies probiotics (NP-P), and LP with multispecies probiotics (LP-P). After the feeding trial, the fecal samples of the pigs were analyzed. The fecal scores were improved by the probiotic supplementation, especially in LP-P group. We also observed a probiotic-mediated alteration in the gut microbiome of pigs. In addition, LP-P group showed higher species richness and diversity compared with other groups. The addition of multispecies probiotics in low CP diet also enhanced gut microbiota metabolites production, such as short-chain fatty acids (SCFAs) and polyamines. Correlation analysis revealed that Oscillospiraceae UCG-002, Eubacterium coprostanoligenes, Lachnospiraceae NK4A136 group, and Muribaculaceae were positively associated with SCFAs; and Prevotella, Eubacterium ruminantium, Catenibacterium, Alloprevotella, Prevotellaceae NK3B31 group, Roseburia, Butyrivibrio, and Dialister were positively correlated with polyamines. Supplementation with multispecies probiotics modulated the function of the gut microbiome by upregulating the pathways for protein digestion and utilization, potentially contributing to enriched metabolite production in the gut. The results of this study demonstrate that supplementation with multispecies probiotics may complement the beneficial effects of low CP levels in pig feed. These findings may help formulate sustainable feeding strategies for swine production.

Effects of Lactiplantibacillus plantarum and Lacticaseibacillus paracasei supplementation on the faecal metabolome in children with coeliac disease autoimmunity: a randomised, double-blinded placebo-controlled clinical trial

Introduction

Coeliac disease is a lifelong immune-mediated enteropathy manifested as gluten intolerance in individuals carrying specific human leukocyte antigen (HLA) molecules. Other factors than genetics and gluten intake, however, may play a role in triggering the disease. The gut internal environment is thought to be one of these potential contributing factors, and it can be influenced throughout life.

Methods

We examine the impact of Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2 supplementation on the faecal metabolome in genetically predisposed children having tissue transglutaminase autoantibodies, i.e., coeliac disease autoimmunity. Probiotic strains were selected based on their beneficial properties, including mucosal permeability and immune modulation effects. The intervention group (n = 40) and control group (n = 38) took the probiotics or placebo daily for 6 months in a double-blinded randomised trial. Faecal samples were collected at baseline and after 3 and 6 months and analysed using the 1H NMR for metabolome. The incorporation of 16S rRNA sequencing as a supportive dataset complemented the analysis of the metabolome data.

Results

During the 6 months of intervention, the stool concentrations of 4-hydroxyphenylacetate increased in the intervention group as compared to controls, whereas concentrations of threonine, valine, leucine, isoleucine, methionine, phenylalanine, aspartate, and fumarate decreased. Additionally, a noteworthy effect on the glycine, serine, and threonine metabolic pathway has been observed.

Conclusion

The findings suggest a modest yet significant impact of the probiotics on the faecal metabolome, primarily influencing proteolytic processes in the gut.

Clinical trial registration

ClinicalTrials.gov, NCT03176095.

The Brain-Gut-Microbiota Interplay in Depression: a key to design innovative therapeutic approaches

Depression is the most prevalent mental disorder in the world associated with huge socio-economic consequences. While depressive-related symptoms are well known, the molecular mechanisms underlying disease pathophysiology and progression remain largely unknown. The gut microbiota (GM) is emerging as a key regulator of the central nervous system homeostasis by exerting fundamental immune and metabolic functions. In turn, the brain influences the intestinal microbial composition through neuroendocrine signals, within the so-called gut microbiota-brain axis. The balance of this bidirectional crosstalk is important to ensure neurogenesis, preserve the integrity of the blood-brain barrier and avoid neuroinflammation. Conversely, dysbiosis and gut permeability negatively affect brain development, behavior, and cognition. Furthermore, although not fully defined yet, changes in the GM composition in depressed patients are reported to influence the pharmacokinetics of common antidepressants by affecting their absorption, metabolism, and activity. Similarly, neuropsychiatric drugs may shape in turn the GM with an impact on the efficacy and toxicity of the pharmacological intervention itself. Consequently, strategies aimed at re-establishing the correct homeostatic gut balance (i.e., prebiotics, probiotics, fecal microbiota transplantation, and dietary interventions) represent an innovative approach to improve the pharmacotherapy of depression. Among these, probiotics and the Mediterranean diet, alone or in combination with the standard of care, hold promise for clinical application. Therefore, the disclosure of the intricate network between GM and depression will give precious insights for innovative diagnostic and therapeutic approaches towards depression, with profound implications for drug development and clinical practice.

Amino Acid-Derived Bacterial Metabolites in the Colorectal Luminal Fluid: Effects on Microbial Communication, Metabolism, Physiology, and Growth

Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply nitrogenous material to this microbial population. The bacteria in the large intestine luminal fluid release amino acids from the available proteins, and amino acids are then used for bacterial protein synthesis, energy production, and in other various catabolic pathways. The resulting metabolic intermediaries and end products can then accumulate in the colorectal fluid, and their concentrations appear to depend on different parameters, including microbiota composition and metabolic activity, substrate availability, and the capacity of absorptive colonocytes to absorb these metabolites. The aim of the present review is to present how amino acid-derived bacterial metabolites can affect microbial communication between both commensal and pathogenic microorganisms, as well as their metabolism, physiology, and growth.

Fishmeal, plant protein, and fish oil substitution with single-cell ingredients in organic feeds for European sea bass (Dicentrarchus labrax)

Single-cell ingredients (SCI) are considered promising nutrient sources which are produced using environmentally friendly biotechnological processes. The aim of the current study was to evaluate the replacement of fishmeal, plant protein sources, and fish oil with SCI in organic feeds for European sea bass (Dicentrarchus labrax). Bacterial protein, yeast protein, and microalgae were used to replace fishmeal trimmings, soya bean meal, and fish oil from trimmings. Triplicate groups (30 fish per replicate) of European sea bass (14.4 ± 2.4 g) were fed the experimental diets for 71 days. The results showed that the incorporation of SCI at all levels of inclusion significantly enhanced nutrient digestibility. Additionally, growth performance parameters were not affected by SCI inclusion, exhibiting similar or improved values. Moreover, a tendency for improved anterior and posterior gut structure was observed and a significant increase of lysozyme activity at the two highest inclusion levels of SCI was determined. Overall, the results showed that the inclusion of SCI at 15% (bacterial: yeast: algae-9.4: 4.7: 1) is possible without compromising any of the parameters evaluated. According to these findings, a higher substitution of fishmeal trimmings, plant protein sources, and fish oil from trimmings with SCI in organic diets for European sea bass (D. labrax) can be further evaluated in future studies.

Marine glycoproteins: a mine of their structures, functions and potential applications

Many bioactive compounds are reported from marine organisms, which are significantly different from those found in terrestrial organisms regarding their chemical structures and pharmacological activities. Marine glycoproteins (MGs) have aroused increasing attention as a good nutrient source owing to their potential applications in medicine, cosmetics and food. However, there is a lack of a comprehensive study on MGs to help readers understand the current state of research on marine-derived glycoproteins. The current review compiles the recent progress made on the structures and functions of MGs with future perspectives to maximize their value and applications via bibliometric analysis methods for the first time. The current research on MGs appears mostly limited to the laboratory, with no large-scale production of marine glycoproteins developed. The sugar chains are bound to proteins through covalent bonds that can readily be cleaved leading to difficultly in their separation and purification. Health effects attributed to MGs include treatment of inflammatory diseases, as well as anti-oxidant, immune modulation, anti-tumor, hypolipidemic, hypoglycemic, anti-bacterial and anti-freeze activities. This review can not only deepen the understanding of the functions of MGs, but also lay an important foundation for the further development and utilization of marine resources.

In vitro digestion models for the design of safe and nutritious foods

Responsible development of future foods requires in depth understanding of food digestion in the human body based on robust research models, ranging from in vitro models to randomized controlled human trials. This chapter overviews fundamental aspects of food digestion, namely bioaccessibility and bioavailability, and models mirroring gastric, intestinal, and colonic conditions. Second, the chapter demonstrates the potential of in vitro digestion models to help screen adverse effects of food additives, such as Titanium dioxide or carrageenan, or underpin the determinants of macro- and micronutrient digestion in different strata of the population, for example digestion of emulsions. Such efforts support rationalized design of functional foods, such as infant formulae, cheese, cereals and biscuits which are validated in vivo or in randomized controlled trials.

Modulatory Effects of A1 Milk, A2 Milk, Soy, and Egg Proteins on Gut Microbiota and Fermentation

Milk can be divided into A1 and A2 types according to β-casein variants, and there is a debate about whether A1 milk consumption exacerbates gut environments. This study examined the cecum microbiota and fermentation in mice fed A1 casein, A2 casein, mixed casein (commercial casein), soy protein isolate, and egg white. The cecum acetic acid concentration was higher, and the relative abundances of Muribaculaceae and Desulfovibrionaceae were greater in mice fed A1 versus A2 casein. The other parameters of cecum fermentation and microbiota composition were similar among the mice fed A1, A2, and mixed caseins. The differences were more distinctive among the three caseins, soy, and egg feedings. Chao 1 and Shannon indices of the cecum microbiota were lowered in egg white-fed mice, and the microbiota of mice fed milk, soy, and egg proteins were separately grouped by principal coordinate analysis. Mice fed the three caseins were characterized by a high abundance of Lactobacillaceae and Clostridiaceae, those fed soy were characterized by Corynebacteriaceae, Muribaculaceae, and Ruminococcaceae, and those fed egg white were characterized by Eggerthellaceae, Rikenellaceae, and Erysipelatoclostridiaceae. Thus, although several differences can arise between A1 and A2 caseins in terms of their modulatory effects on gut environments, the differences between milk, soy, and egg proteins can be more distinctive and are worth further consideration.

Heat-treated foxtail millet protein delayed the development of pre-diabetes to diabetes in mice by altering gut microbiota and metabolomic profiles

Millet protein has gained much attention for its beneficial effects in mitigating metabolic diseases. However, most individuals pass through a prediabetic phase before developing full-blown diabetes, and whether millet protein has hypoglycemic effects on prediabetic mice remains unclear. In the present study, heat-treated foxtail millet protein (HMP) supplementation significantly decreased fasting blood glucose and serum insulin levels, alleviated insulin resistance, and improved impaired glucose tolerance in prediabetic mice. In addition, HMP altered the intestinal flora composition, as evidenced by the reduction in the abundance of Dubosiella and Marvinbryantia and the increase in the content of Lactobacillus, Bifidobacterium, and norank_f_Erysipelotrichaceae. Moreover, HMP supplementation dramatically regulated the levels of serum metabolites (i.e., LysoPCs, 11,14,17-eicosatrienoic acid, and sphingosine) and related metabolic pathways, such as sphingolipid metabolism and pantothenate and CoA biosynthesis. In conclusion, the improvement of gut microbiota and serum metabolic profiles was related to the hypoglycemic potential of HMP in prediabetes.

Development of a simultaneous quantification method for the gut microbiota-derived core nutrient metabolome in mice and its application in studying host-microbiota interaction

The gut microbiota interacts with the host via production of various metabolites of dietary nutrients. Herein, we proposed the concept of the gut microbiota-derived core nutrient metabolome, which covers 43 metabolites in carbohydrate metabolism, glycolysis, tricarboxylic acid cycle and amino acid metabolism, and established a quantitative UPLC-Q/TOF-MS method through 3-nitrophenylhydrazine derivatization to investigate the influence of obesity on the gut microbiota in mice. All metabolites could be simultaneously analyzed via separation on a BEH C18 column within 18 min. The lower limits of quantification of most analytes were less than 1 μM. Validation results demonstrated suitability for the analysis of mouse fecal samples. The method was then applied to detect the gut microbiota-derived nutrient metabolome in the feces of high-fat diet induced obese (DIO) and ob/ob (leptin-deficient) mice, as well as obesity-prone (OP) and obesity-resistant (OR) mice. Compared to the control groups, there were 13, 23 and 10 differentially abundant metabolites detected in ob/ob, DIO and OP groups, respectively. Among them, amino acids including leucine, isoleucine, glycine, methionine, tyrosine and glutamine were co-downregulated in the obese or OP mice and exhibited inverse association with body weight. 16S rDNA analysis revealed that the genera Lactobacillus and Dubosiella were also inversely associated with body weight and positively correlated with fecal amino acids. Collectively, our work provides an effective and simplified method for simultaneous quantifying the gut microbiota-derived core nutrient metabolome in mouse feces, which could assist various future studies on host-microbiota metabolic interaction.

Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment

BACKGROUND

Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear.

RESULTS

The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation.

CONCLUSION

This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.

Demonstrating a link between diet, gut microbiota and brain: 14C radioactivity identified in the brain following gut microbial fermentation of 14C-radiolabeled tyrosine in a pig model

Background

There is a need to better understand the relationship between the diet, the gut microbiota and mental health. Metabolites produced when the human gut microbiota metabolize amino acids may enter the bloodstream and have systemic effects. We hypothesize that fermentation of amino acids by a resistant protein-primed gut microbiota could yield potentially toxic metabolites and disturb the availability of neurotransmitter precursors to the brain. However, these mechanisms are challenging to investigate via typical in vitro and clinical methods.

Methods

We developed a novel workflow using 14C radiolabeling to investigate complex nutrient-disease relationships. The first three steps of the workflow are reported here. α-Linolenic acid (ALA) was used as a model nutrient to confirm the efficacy of the workflow, and tyrosine (Tyr) was the test nutrient. 14C-Tyr was administered to male weanling pigs fed a high resistant protein diet, which primed the gut microbiota for fermenting protein. The hypotheses were; (1) that expected biodistribution of 14C-ALA would be observed, and (2) that radioactivity from 14C-Tyr, representing Tyr and other amino acids released from resistant protein following gut microbial fermentation, would be bioavailable to the brain.

Results

Radioactivity from the 14C-ALA was detected in tissues reflecting normal utilization of this essential fatty acid. Radioactivity from the 14C-Tyr was detected in the brain (0.15% of original dose).

Conclusion

Metabolites of gut-fermented protein and specifically amino acid precursors to neurotransmitters such as tyrosine, are potentially able to affect brain function. By extension, resistant proteins in the diet reaching the gut microbiota, also have potential to release metabolites that can potentially affect brain function. The high specificity of detection of 14C radioactivity demonstrates that the proposed workflow can similarly be applied to understand other key diet and health paradigms.

Study on Anti-Constipation Effects of Hemerocallis citrina Baroni through a Novel Strategy of Network Pharmacology Screening

Daylily (Hemerocallis citrina Baroni) is an edible plant widely distributed worldwide, especially in Asia. It has traditionally been considered a potential anti-constipation vegetable. This study aimed to investigate the anti-constipation effects of daylily from the perspective of gastro-intestinal transit, defecation parameters, short-chain organic acids, gut microbiome, transcriptomes and network pharmacology. The results show that dried daylily (DHC) intake accelerated the defecation frequency of mice, while it did not significantly alter the levels of short-chain organic acids in the cecum. The 16S rRNA sequencing showed that DHC elevated the abundance of Akkermansia, Bifidobacterium and Flavonifractor, while it reduced the level of pathogens (such as Helicobacter and Vibrio). Furthermore, a transcriptomics analysis revealed 736 differentially expressed genes (DEGs) after DHC treatment, which are mainly enriched in the olfactory transduction pathway. The integration of transcriptomes and network pharmacology revealed seven overlapping targets (Alb, Drd2, Igf2, Pon1, Tshr, Mc2r and Nalcn). A qPCR analysis further showed that DHC reduced the expression of Alb, Pon1 and Cnr1 in the colon of constipated mice. Our findings provide a novel insight into the anti-constipation effects of DHC.

Reducing nitrogen loss during kitchen waste composting using a bioaugmented mechanical process with low pH and enhanced ammonia assimilation

Exploring the regulation of nitrogen transformation in bioaugmented mechanical composting (BMC) process for rural kitchen waste (KW) is essential to avoid the "not-in-my-backyard" phenomenon caused by nitrogen loss. Herein, nitrogen transformation and loss in BMC versus conventional pile composting (CPC) of KW were compared. The results showed that the total nitrogen loss in the BMC was 6.87-39.32 % lower than that in the CPC. The main pathways to prevent nitrogen loss in the BMC were reducing NH₃ by avoiding a sharp increase in pH followed by transforming the preserved NH₄⁺-N into recalcitrant nitrogen reservoir via enhanced ammonia assimilation. The enriched thermophilic bacteria with mineralization capacities (e.g., Bacillus and Corynebacterium) during rapid dehydration and heating in the BMC accumulated organic acids and easy-to-use carbon sources, which could lead to lower pH and ammonia assimilation enhancement, respectively. This study provides new ideas for formulating low-cost nitrogen conservation strategies in decentralized KW composting.