Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product

Differential effects of pectin-based dietary fibre type and gut microbiota composition on in vitro fermentation outcomes

Interactions between human gut microbiota and dietary fibres (DF) are influenced by the complexity and diversity of both individual microbiota and sources of DF. Based on 480 in vitro fermentations, a full factorial experiment was performed with six faecal inocula representing two enterotypes and three DF sources with nanometer, micrometer, and millimeter length-scales (apple pectin, apple cell walls and apple particles) at two concentrations. Increasing DF size reduced substrate disappearance and fermentation rates but not biomass growth. Concentrated DF enhanced butyrate production and lactate cross-feeding. Enterotype differentiated final microbial compositions but not biomass or fermentation metabolite profiles. Individual donor microbiota differences did not influence DF type or concentration effects but were manifested in the promotion of different functional microbes within each population with the capacity to degrade the DF substrates. Overall, consistent effects (independent of donor microbiota variation) of DF type and concentration on kinetics of substrate degradation, microbial biomass production, gas kinetics and metabolite profiles were found, which can form the basis for informed design of DF for desired rates/sites and consequences of gut fermentation. These results add further evidence to the concept that, despite variations between individuals, the human gut microbiota represents a community with conserved emergent properties.

In vitro screening of the impact of dietary prebiotic components, probiotic strains, and their symbiotic combinations on colonic microbiota in children with cystic fibrosis

Children with Cystic Fibrosis (CF) are more likely to have intestinal dysbiosis due to recurrent antibiotic therapy and the conventional hypercaloric diet administered to them. This study aimed at evaluating the effect of isolated prebiotic components and probiotic strains, and their combinations as potential synbiotics, on the intestinal microbiota of CF children. A static in vitro colonic fermentation model was used by colonizing vials with faecal inoculum, a culture medium, and the substrates to be tested. Post treatment, aliquots were taken to determine ammonium, lactate, and short-chain fatty acids production and to profile the microbiota composition by 16s rRNA sequencing. At genus level, Escherichia-Shigella decreased (15.8%) with the treatment pectin + L. rhamnosus, followed by the beta-glucan + L. salivarius (15.5%). Inversely, the most increase in Bacteroides (44%) was obtained by the treatment with Pectin + L. reuteri. Lactate and acetic acid production was significantly increased with prebiotics and their combinations with L. rhamnosus and L. salivarius. In conclusion, the use of beta-glucan and pectin in combination with probiotic strains from the Lactobacillaceae family suggest potential to modulate dysbiosis and metabolic activity on CF colonic microbiota, encouraging further studies in animal studies or clinical settings to confirm the findings in vivo.

Lactobacillus acidophilus KBL409 protects against kidney injury via improving mitochondrial function with chronic kidney disease

PURPOSE

Recent advances have led to greater recognition of the role of mitochondrial dysfunction in the pathogenesis of chronic kidney disease (CKD). There has been evidence that CKD is also associated with dysbiosis. Here, we aimed to evaluate whether probiotic supplements can have protective effects against kidney injury via improving mitochondrial function.

METHODS

An animal model of CKD was induced by feeding C57BL/6 mice a diet containing 0.2% adenine. KBL409, a strain of Lactobacillus acidophilus, was administered via oral gavage at a dose of 1 × 109 CFU daily. To clarify the underlying mechanisms by which probiotics exert protective effects on mitochondria in CKD, primary mouse tubular epithelial cells stimulated with TGF-β and p-cresyl sulfate were administered with butyrate.

RESULTS

In CKD mice, PGC-1α and AMPK, key mitochondrial energy metabolism regulators, were down-regulated. In addition, mitochondrial dynamics shifted toward fission, the number of fragmented cristae increased, and mitochondrial mass decreased. These alterations were restored by KBL409 administration. KBL409 supplementation also improved defects in fatty acid oxidation and glycolysis and restored the suppressed enzyme levels involved in TCA cycle. Accordingly, there was a concomitant improvement in mitochondrial respiration and ATP production assessed by mitochondrial function assay. These favorable effects of KBL409 on mitochondria ultimately decreased kidney fibrosis in CKD mice. In vitro analyses with butyrate recapitulated the findings of animal study.

CONCLUSIONS

This study demonstrates that administration of the probiotic Lactobacillus acidophilus KBL409 protects against kidney injury via improving mitochondrial function.

Effect of replacing soybean meal with Hermetia illucens meal on cecal microbiota, liver transcriptome, and plasma metabolome of broilers

Despite the existence of a number of studies investigating the effect of insect meal on the growth performance of broilers, knowledge about the metabolic effects of insect meal in broilers is still scarce. Thus, the present study investigated the effect of partial replacement of soybean meal with Hermetia illucens (HI) larvae meal on the liver transcriptome, the plasma metabolome, and the cecal microbiota in broilers. For the study, 72 male one-day-old Cobb 500 broilers were divided into three groups and fed 3 different diets with either 0% (HI0), 7.5% (HI7.5), or 15% (HI15) defatted HI meal for 35 d. Each group consisted of 6 cages (replicates) with 4 broilers/cage. While body weight (BW) gain, feed intake, and feed:gain ratio did not differ between groups, breast muscle weight, carcass yield, and apparent ileal digestibility (AID) of 5 amino acids were higher in group HI15 than in group HI0 (P < 0.05). Indicators of α-diversity (Chao1 and Observed) in the cecal digesta were higher in groups HI15 and HI7.5 than in group HI0 (P < 0.05). The abundance of 5 families and 18 genera, all of which belonged to the Firmicutes phylum, in the cecal digesta differed among groups (P < 0.05). Concentrations of butyric acid, valeric acid, and isobutyric acid in the cecal digesta were lower in group HI15 than in the other 2 groups (P < 0.05), whereas those of total and other short-chain fatty acids were not different between groups. Liver transcriptomics revealed a total of 70 and 61 differentially expressed transcripts between groups HI15 vs. HI0 and between groups HI7.5 vs. HI0, respectively, (P < 0.05). Targeted metabolomics identified 138 metabolites, most of which were triglyceride species, being different between the 3 groups (FDR < 0.05). According to this study, dietary inclusion of HI larvae meal has no detrimental impact but increases breast muscle weight and carcass weight in broilers suggesting that HI larvae meal can be recommended as a sustainable alternative protein source for broilers.

Antiaging Effects of Human Fecal Transplants with Different Combinations of Bifidobacterium bifidum LTBB21J1 and Lactobacillus casei LTL1361 in d-Galactose-Induced Mice

The feces of healthy middle-aged and old people were first transplanted into d-galactose-induced aging mice to construct humanized aging mice with gut microbiota (FMTC) to confirm the antiaging effect of probiotics produced from centenarians. The mouse model was then treated with centenarian-derived Bifidobacterium bifidum (FMTL), Lactobacillus casei (FMTB), and their mixtures (FMTM), and young mice were used as the control. Compared with the FMTC group, the results demonstrated that the probiotics and their combinations alleviated neuronal damage, increased antioxidant capacity, decreased inflammation, and enhanced cognitive and memory functions in aging mice. In the gut microbiota, the relative abundance of Lactobacillus, Ligilactobacillus, and Akkermansia increased and that of Desulfovibrio and Colidextribacter decreased in the FMTM group compared with that in the FMTC group. The three probiotic groups displayed significant changes in 15 metabolites compared with the FMTC group, with 4 metabolites showing increased expression and 11 metabolites showing decreased expression. The groups were graded as Control > FMTM > FMTB > FMTL > FMTC using a newly developed comprehensive quantitative scoring system that thoroughly analyzed the various indicators of this study. The beneficial antiaging effects of probiotics derived from centenarians were quantitatively described using a novel perspective in this study; it is confirmed that both probiotics and their combinations exert antiaging effects, with the probiotic complex group exhibiting a larger effect.

Susceptibility to febrile malaria is associated with an inflammatory gut microbiome

Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with Plasmodium falciparum is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following Plasmodium infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. The fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., Ruminococcus gauvreauii, Ruminococcus torques, Dorea formicigenerans, Dorea longicatena, Lachnoclostridium phocaeense and Lachnoclostridium sp. YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., Anaerobutyricum hallii, Blautia producta and Sellimonas intestinalis). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.

Short-chain fatty acids: linking diet, the microbiome and immunity

The short-chain fatty acids (SCFAs) butyrate, propionate and acetate are microbial metabolites and their availability in the gut and other organs is determined by environmental factors, such as diet and use of antibiotics, that shape the diversity and metabolism of the microbiota. SCFAs regulate epithelial barrier function as well as mucosal and systemic immunity via evolutionary conserved processes that involve G protein-coupled receptor signalling or histone deacetylase activity. Indicatively, the anti-inflammatory role of butyrate is mediated through direct effects on the differentiation of intestinal epithelial cells, phagocytes, B cells and plasma cells, and regulatory and effector T cells. Intestinally derived SCFAs also directly and indirectly affect immunity at extra-intestinal sites, such as the liver, the lungs, the reproductive tract and the brain, and have been implicated in a range of disorders, including infections, intestinal inflammation, autoimmunity, food allergies, asthma and responses to cancer therapies. An ecological understanding of microbial communities and their interrelated metabolic states, as well as the engineering of butyrogenic bacteria may support SCFA-focused interventions for the prevention and treatment of immune-mediated diseases.

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.

Structure properties of Canna edulis RS3 (double enzyme hydrolysis) and RS4 (OS-starch and cross-linked starch): Influence on fermentation products and human gut microbiota

This study investigated the in vitro fermentation characteristics of different structural types of Canna edulis resistant starch (RS). RS3 was prepared through a double enzyme hydrolysis method, and RS4 (OS-starch and cross-linked starch) was prepared using octenyl succinic anhydride and sodium trimetaphosphate/sodium tripolyphosphate, respectively. The RS3 and RS4 samples were structurally analyzed using scanning electron microscopy, Fourier-transform infrared spectroscopy, differential scanning calorimetry, and X-ray diffraction analysis. This was followed by in vitro fermentation experiments. The results revealed microstructure differences in the two groups of starch samples. Compared to native starch, RS3 and RS4 exhibited a lower degree of order and endothermic energy, with lower crystallinity (RS3: 29.59 ± 1.11 %; RS4 [OS-starch]: 28.01 ± 1.32 %; RS4 [cross-linked starch]: 30.44 ± 1.73 %) than that in native starch (36.29 ± 0.89 %). The RS content was higher in RS3 (63.40 ± 2.85 %) and RS4 (OS-starch: 71.21 ± 1.28 %; cross-linked starch: 74.33 ± 0.643 %) than in native starch (57.71 ± 2.95 %). RS3 and RS4 exhibited slow fermentation rates, promoting the production of short-chain fatty acids. RS3 and cross-linked starch significantly increased the production of acetate and butyrate. Moreover, RS3 significantly promoted the abundance of Lactobacillus, while OS-starch and cross-linked starch significantly enhanced the abundance of Dorea and Coprococcus, respectively. Hence, the morphological structure and RS content of the samples greatly influenced the fermentation rate. Moreover, the different varieties of RS induced specific gut microbial regulation. Hence, they show potential applications in functional foods for tailored gut microbiota management.

Overview on biotics development

Although probiotics have been used in food products and supplements for decades, there has been a considerable increase in their use more recently. Recent technological advances have thus led to major advances in knowledge of the gut microbiota, enabling a significant development of biotics. In this review, we discuss the uses of traditional probiotics but also the discovery of next-generation probiotics that could be used as live biotherapeutics. These novel preventive and therapeutic strategies hold promise for the treatment of numerous diseases such as inflammatory bowel diseases such as Crohn's disease and ulcerative colitis. Probiotic bacteria can be consumed alone, or in combination with prebiotics as synbiotics, or mixed with other probiotic strains to form a consortium for enhanced effects. We also discuss the benefits of using postbiotics.

Assessing the causal relationship between gut microbiota and diabetic nephropathy: insights from two-sample Mendelian randomization

Background

The causal association between gut microbiota (GM) and the development of diabetic nephropathy (DN) remains uncertain. We sought to explore this potential association using two-sample Mendelian randomization (MR) analysis.

Methods

Genome-wide association study (GWAS) data for GM were obtained from the MiBioGen consortium. GWAS data for DN and related phenotypes were collected from the FinngenR9 and CKDGen databases. The inverse variance weighted (IVW) model was used as the primary analysis model, supplemented by various sensitivity analyses. Heterogeneity was assessed using Cochran's Q test, while horizontal pleiotropy was evaluated through MR-Egger regression and the MR-PRESSO global test. Reverse MR analysis was conducted to identify any reverse causal effects.

Results

Our analysis identified twenty-five bacterial taxa that have a causal association with DN and its related phenotypes (p < 0.05). Among them, only the g_Eubacterium_coprostanoligenes_group showed a significant causal association with type 1 DN (p < Bonferroni-adjusted p-value). Our findings remained consistent regardless of the analytical approach used, with all methods indicating the same direction of effect. No evidence of heterogeneity or horizontal pleiotropy was observed. Reverse MR analysis did not reveal any causal associations.

Conclusions

This study established a causal association between specific GM and DN. Our findings contribute to current understanding of the role of GM in the development of DN, offering potential insights for the prevention and treatment strategies for this condition.

The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

BACKGROUND

The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. However, there is still only limited knowledge on how the GM activity and metabolite production in the gastrointestinal tract could be influenced by pH and the pH gradient increases along the colon.

RESULTS

Here we investigate the effect of pH gradients corresponding to levels typically found in the colon on GM composition and metabolite production using substrates inulin, lactose, galactooligosaccharides (GOS), and fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) for each fecal inoculum and found that colonic pH gradients significantly influenced in vitro simulated GM structure, but the influence of fecal donor and substrate was more pronounced. Low pH regimes strongly influenced GM with the decreased relative abundance of Bacteroides spp. and increased Bifidobacterium spp. Higher in vitro simulated colonic pH promoted the production of SCFAs in a donor- and substrate-dependent manner. The butyrate producer Butyricimonas was enriched at higher pH conditions, where also butyrate production was increased for inulin. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae also increased at higher colonic pH, which was accompanied by increased production of propionate with GOS and FOS as substrates.

CONCLUSIONS

Together, our results show that colonic substrates such as dietary fibres influence GM composition and metabolite production, not only by being selectively utilized by specific microbes, but also because of their SCFA production, which in turn also influences colonic pH and overall GM composition and activity. Our work provides details about the effect of the gradients of rising pH from the proximal to distal colon on fermenting dietary substrates in vitro and highlights the importance of considering pH in GM research.

Metabolites: a converging node of host and microbe to explain meta-organism

Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.

Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus

Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand how the microbiome differs between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively. Microbiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. Two age- and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial community compositions were generated via DADA2. Metrics of microbial diversity and similarity between groups were computed. Biomarker analyses were performed to determine discriminating taxa. Bacterial co-occurrence networks were constructed to examine ecological patterns. A tight microbiota cluster was observed in the Dutch women, which overlapped with some of the SAS microbiota. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed, i.e., contained fewer inter-taxonomic correlational relationships. Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes, Odoribacter splanchnicus, and Lachnospira were enriched in the Dutch gut. Haemophilus, Bifidobacterium, and Anaerostipes hadrus discriminated the SAS gut. All but Lachnospira and certain strains of Haemophilus are known to produce SCFAs. The Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was not detected in the SAS. Among several potential gut microbial biomarkers, Haemophilus parainfluenzae likely best characterizes the ethnic minority group, which is more predisposed to T2DM. The higher prevalence of T2DM in the SAS may be associated with the gut dysbiosis observed.

Potential for New Therapeutic Approaches by Targeting Lactate and pH Mediated Epigenetic Dysregulation in Major Mental Diseases

Multiple lines of evidence have shown that lactate-mediated pH alterations in the brains of patients with neuropsychiatric diseases such as schizophrenia (SCZ), Alzheimer's disease (AD) and autism may be attributed to mitochondrial dysfunction and changes in energy metabolism. While neuronal activity is associated with reduction in brain pH, astrocytes are responsible for rebalancing the pH to maintain the equilibrium. As lactate level is the main determinant of brain pH, neuronal activities are impacted by pH changes due to the binding of protons (H+) to various types of proteins, altering their structure and function in the neuronal and non-neuronal cells of the brain. Lactate and pH could affect diverse types of epigenetic modifications, including histone lactylation, which is linked to histone acetylation and DNA methylation. In this review, we discuss the importance of pH homeostasis in normal brain function, the role of lactate as an essential epigenetic regulatory molecule and its contributions to brain pH abnormalities in neuropsychiatric diseases, and shed light on lactate-based and pH-modulating therapies in neuropsychiatric diseases by targeting epigenetic modifications. In conclusion, we attempt to highlight the potentials and challenges of translating lactate-pH-modulating therapies to clinics for the treatment of neuropsychiatric diseases.

Supplemented Infant Formula and Human Breast Milk Show Similar Patterns in Modulating Infant Microbiota Composition and Function In Vitro

The gut microbiota of healthy breastfed infants is often dominated by bifidobacteria. In an effort to mimic the microbiota of breastfed infants, modern formulas are fortified with bioactive and bifidogenic ingredients. These ingredients promote the optimal health and development of infants as well as the development of the infant microbiota. Here, we used INFOGEST and an in vitro batch fermentation model to investigate the gut health-promoting effects of a commercial infant formula supplemented with a blend containing docosahexaenoic acid (DHA) (20 mg/100 kcal), polydextrose and galactooligosaccharides (PDX/GOS) (4 g/L, 1:1 ratio), milk fat globule membrane (MFGM) (5 g/L), lactoferrin (0.6 g/L), and Bifidobacterium animalis subsp. lactis, BB-12 (BB-12) (106 CFU/g). Using fecal inoculates from three healthy infants, we assessed microbiota changes, the bifidogenic effect, and the short-chain fatty acid (SCFA) production of the supplemented test formula and compared those with data obtained from an unsupplemented base formula and from the breast milk control. Our results show that even after INFOGEST digestion of the formula, the supplemented formula can still maintain its bioactivity and modulate infants' microbiota composition, promote faster bifidobacterial growth, and stimulate production of SCFAs. Thus, it may be concluded that the test formula containing a bioactive blend promotes infant gut microbiota and SCFA profile to something similar, but not identical to those of breastfed infants.

Hydrolysed poultry byproduct meal in extruded diets for cats

Hydrolysed proteins have been shown to be potential ingredients in cat diets due to their high digestibility, presence of bioactive peptides, and relatively low antigenicity. The effects of the substitution of conventional low ash poultry byproduct meal (PBM) with hydrolysed poultry byproduct meal (HPM) as a protein source were evaluated in extruded cat diets. Five diets with similar nutrient contents were formulated: a control (CO) diet based on PBM and 4 diets with different inclusions of HPM (5%, 10%, 20%, and 30%, on an as-fed basis) replacing PBM as the protein source. The total tract apparent digestibility (CTTAD) of nutrients, faecal characteristics and microbial fermentation products, urine production and pH, nitrogen balance and urea renal excretion were evaluated using 30 healthy cats (15 males and 15 females; 4.18 ± 0.86 kg; 4.17 ± 1.38 years old), with 6 cats per diet in a complete randomised block design. When significant differences were found with the F test, the effects were evaluated by polynomial contrasts according to HPM inclusion (p < 0.05). The CTTADs of DM (89 ± 0.41%), CP (90 ± 0.36%), fat (93 ± 0.41%) and gross energy (90 ± 0.33%) were similar among treatments (p > 0.05). The faecal production, score, short-chain fatty acids and ammonia concentration were similar among treatments (p > 0.05). Isobutyric, isovaleric, valeric, and total branched-chain fatty acid contents increased quadratically (p < 0.05), with the highest level in the faeces of cats fed the diet with 20% HPM. Lactate concentration in faeces increased linearly with the inclusion of HPM (p < 0.05). Urine characteristics and urea renal excretion did not differ among treatments (p > 0.05). At 10% inclusion, HPM tended to increase the nitrogen retention of cats (p = 0.083), which may reflect the higher tryptophan, methionine, lysine, and available lysine contents of HPM in comparison to PBM. The inclusion of up to 30% HPM can be considered in cat formulations without affecting nutrient digestibility or faecal and urine characteristics. HPM tended to increase nitrogen retention and increased branched-chain fatty acids in faeces, aspects which deserves further studies.

Effects of 2'-fucosyllactose on the composition and metabolic activity of intestinal microbiota from piglets after in vitro fermentation

BACKGROUND

As indigestible carbohydrates, milk oligosaccharides possess various benefits for newborns, mainly through intestinal microbiota, among which 2'-fucosyllactose (2'-FL) is the most predominant milk oligosaccharide. However, knowledge about the fermentative characteristics of 2'-FL in the gut remains limited, especially in the small intestine. The aim of this study is to explore the differential fermentability of 2'-FL by the small and large intestinal microbiota of piglets using fructo-oligosaccharide (FOS) and lactose as controls in an in vitro batch fermentation experiment. During fermentation, microbial composition was characterized along with gas production and short-chain fatty acid production.

RESULTS

2'-Fucosyllactose showed differential fermentability in jejunal and colonic fermentation. Compared with the colon, 2'-FL produced less gas in the jejunum than in the FOS and lactose groups (P < 0.05). Meanwhile, 2'-FL exhibited a different influence on the microbial composition and metabolism in the jejunum and colon compared with FOS and lactose. In the jejunum, compared with the FOS and lactose groups, the 2'-FL group showed a higher abundance of Bacteroides, Prevotella, and Blautia, but a lower abundance of Streptococcus and Lactobacillus (P < 0.05), with a higher level of propionate and a lower level of lactate during fermentation (P < 0.05). In the colon, compared with the FOS and lactose groups, 2'-FL increased the abundance of Blautia, Faecalibacterium, and Lachnospiraceae FCS020, but decreased the abundance of Prevotella_9, Succinivibrio, and Megasphaera (P < 0.05) with an increase in acetate production (P < 0.05).

CONCLUSION

Overall, the results suggested that the small intestinal microbiota had the potential to ferment milk oligosaccharides. Meanwhile, in comparison with FOS and lactose, 2'-FL selectively stimulated the growth of propionate-producing bacteria in the jejunum and acetate-producing bacteria in the colon. These results demonstrated the differences in fermentation properties of 2'-FL by small and large intestinal microbiota and provided new evidence for the application of 2'-FL in optimizing gut microbiota. © 2023 Society of Chemical Industry.

Depression-associated gut microbes, metabolites and clinical trials

Depression is one of the most prevalent mental disorders today. Over the past decade, there has been considerable attention given to the field of gut microbiota associated with depression. A substantial body of research indicates a bidirectional communication pathway between gut microbiota and the brain. In this review, we extensively detail the correlation between gut microbiota, including Lactobacillus acidophilus and Bifidobacterium longum, and metabolites such as short-chain fatty acids (SCFAs) and 5-hydroxytryptamine (5-HT) concerning depression. Furthermore, we delve into the potential health benefits of microbiome-targeted therapies, encompassing probiotics, prebiotics, and synbiotics, in alleviating depression. Lastly, we underscore the importance of employing a constraint-based modeling framework in the era of systems medicine to contextualize metabolomic measurements and integrate multi-omics data. This approach can offer valuable insights into the complex metabolic host-microbiota interactions, enabling personalized recommendations for potential biomarkers, novel drugs, and treatments for depression.

Lactate cross-feeding between Bifidobacterium species and Megasphaera indica contributes to butyrate formation in the human colonic environment

Butyrate, a physiologically active molecule, can be synthesized through metabolic interactions among colonic microorganisms. Previously, in a fermenting trial of human fecal microbiota, we observed that the butyrogenic effect positively correlated with the increasing Bifidobacterium population and an unidentified Megasphaera species. Therefore, we hypothesized that a cross-feeding phenomenon exists between Bifidobacterium and Megasphaera, where Megasphaera is the butyrate producer, and its growth relies on the metabolites generated by Bifidobacterium. To validate this hypothesis, three bacterial species (B. longum, B. pseudocatenulatum, and M. indica) were isolated from fecal cultures fermenting hydrolyzed xylan; pairwise cocultures were conducted between the Bifidobacterium and M. indica isolates; the microbial interactions were determined based on bacterial genome information, cell growth, substrate consumption, metabolite quantification, and metatranscriptomics. The results indicated that two Bifidobacterium isolates contained distinct gene clusters for xylan utilization and expressed varying substrate preferences. In contrast, M. indica alone scarcely grew on the xylose-based substrates. The growth of M. indica was significantly elevated by coculturing it with bifidobacteria, while the two Bifidobacterium species responded differently in the kinetics of cell growth and substrate consumption. Coculturing led to the depletion of lactate and increased the formation of butyrate. An RNA-seq analysis further revealed the upregulation of M. indica genes involved in the lactate utilization and butyrate formation pathways. We concluded that lactate generated by Bifidobacterium through catabolizing xylose fueled the growth of M. indica and triggered the synthesis of butyrate. Our findings demonstrated a novel cross-feeding mechanism to generate butyrate in the human colon.IMPORTANCEButyrate is an important short-chain fatty acid that is produced in the human colon through microbial fermentation. Although many butyrate-producing bacteria exhibit a limited capacity to degrade nondigestible food materials, butyrate can be formed through cross-feeding microbial metabolites, such as acetate or lactate. Previously, the literature has explicated the butyrate-forming links between Bifidobacterium and Faecalibacterium prausnitzii and between Bifidobacterium and Eubacterium rectale. In this study, we provided an alternative butyrate synthetic pathway through the interaction between Bifidobacterium and Megasphaera indica. M. indica is a species named in 2014 and is indigenous to the human intestinal tract. Scientific studies explaining the function of M. indica in the human colon are still limited. Our results show that M. indica proliferated based on the lactate generated by bifidobacteria and produced butyrate as its end metabolic product. The pathways identified here may contribute to understanding butyrate formation in the gut microbiota.

Dietary intervention with edible film-coated multistrain probiotic Lacticaseibacilli in nondairy food matrices significantly increased the recovery of fecal viable Lacticaseibacilli and improved the performance of several colonic biomarkers among slightly malnourished preschool children

Probiotic enriched dairy products are widely consumed in Western countries for their beneficial effects on the gastrointestinal tract and overall health. The present study aims to investigate the beneficial effects of probiotic Lacticaseibacilli (LAB) strains in non-dairy food matrices. A blend of edible film-coated probiotic LAB, L. plantarum, L. paracasei, and L. rhamnosus, were incorporated into plain biscuits and dry dates. Design of the randomized controlled study: Children of both sexes (mean age 55.7 ± 14.5 months) attending kindergarten in Tersa, a poor urban Giza district, were recruited and randomized into 5 groups of equal numbers. Treatment groups: (1) placebo biscuits, (2) functional probiotic biscuits (0.18 billion colony forming units (cfu) of LAB) (3) functional probiotic + inulin biscuits (0.2 billion cfu of LAB + 2 g of chicory inulin); (4) placebo dates and (5) functional probiotic dates (0.3 billion cfu of viable multistrain LAB). The supplements were served 5 days a week and each child had to consume 21 servings of the supplement. The primary outcome was an increase in the fecal recovery of viable LAB after the intake of 21 servings (T1) compared to the respective baseline counts (T0). The secondary outcomes include the determination of fecal short-chain fatty acids (SCFA) and secretory immunoglobulin A (s-Ig A) using ELISA and fecal ammonia excretion. Results: Statistically significant % increases in the recoveries of fecal viable LAB were found among the children consuming 21 servings of supplements 2, 3, and 5 compared to the respective count at T0. Similar significant increases were found in the fecal concentrations of SCFA and s-Ig A among the children consuming 21 servings of supplements 2, 3 and 5 compared to the respective counts at T0. On the other hand, the concentration of toxic ammonia excretion decreased significantly in the feces of all children consuming probiotic-containing supplements (groups 2, 3, and 5) at T1 compared to the respective concentrations obtained at T0. Conclusion: Multistrain microencapsulated probiotic Lacticaseibacilli in functional biscuits and dry dates successfully tolerated the acidic gastric transit and exerted their bioactive action on the colonic microbiome. The synbiotic supplement exhibited a higher production rate of colonic SCFA. Probiotic-enriched products that confer definitive health benefits are convenient and do not need to be kept under refrigeration. Manipulating the composition and function of the microbiome in childhood through probiotic/+ prebiotic interventions is cost-effective with long-term beneficial health outcomes. This study was approved by the Medical Research Ethics Committee, National Research Center and registered as Clinical Trial 16/422. Written informed consent was obtained from the mothers of all participating children.

Stimbiotic supplementation and xylose-rich carbohydrates modulate broiler's capacity to ferment fibre

Stimbiotics are a new category of feed additives that can increase fibre fermentability by stimulating fibre-degrading microbiota in the gut. The aim of this study was to test, ex vivo, if the microbiota of broilers fed a stimbiotic are better able to ferment different xylose-rich substrates in an ileal and a caecal environment. The ileal and caecal contents from broiler chickens fed a stimbiotic or from a control group were used as an inoculum in the ex vivo fermentation experiment. Different xylose-rich substrates including monomeric xylose (XYL), XOS with DP 2 to 6 (XOS), short DP XOS of 2 to 3 (sDP-XOS), long DP XOS of 4 to 6 (lDP-XOS) and de-starched wheat bran (WB), were added to each ileal and caecal inoculum in fermentation vessels. Total gas, short-chain fatty acids (SCFA) production, bacterial quantification, and carbohydrate utilisation were monitored for 9 h post-inoculation. No significant interactions were observed in any of the parameters measured in either the ileal or caecal contents (p > 0.05). Stimbiotic ileal inocula resulted in higher total gas (p < 0.001) and volatile fatty acid (VFA) (p < 0.001) production, increased numbers of Lactobacillus spp. (p < 0.001), and decreased numbers of Enterococcus spp. (p < 0.01) after 9 h regardless of the xylose-rich substrate added. Stimbiotic caecal inocula resulted in a higher ratio of VFA to branched-chain fatty acids (BCFAs) by up to +9% (p < 0.05). Ileal microbiota were found to preferentially metabolise WB, while caecal microbiota favoured XOS substrates, particularly lDP-XOS. These results indicate that stimbiotics can promote the abundance of lactic acid bacteria involved in the establishment of fibre-degrading bacteria and VFA content in the gut, which could have beneficial effects on broiler performance. Further, ileal and caecal microbiota differ in their utilisation of different substrates which may impact the effectiveness of different stimbiotic products.

A modified Mediterranean-style diet enhances brain function via specific gut-microbiome-brain mechanisms

Alzheimer's disease (AD) is a debilitating brain disorder with rapidly mounting prevalence worldwide, yet no proven AD cure has been discovered. Using a multi-omics approach in a transgenic AD mouse model, the current study demonstrated the efficacy of a modified Mediterranean-ketogenic diet (MkD) on AD-related neurocognitive pathophysiology and underlying mechanisms related to the gut-microbiome-brain axis. The findings revealed that MkD induces profound shifts in the gut microbiome community and microbial metabolites. Most notably, MkD promoted growth of the Lactobacillus population, resulting in increased bacteria-derived lactate production. We discovered elevated levels of microbiome- and diet-derived metabolites in the serum as well, signaling their influence on the brain. Importantly, these changes in serum metabolites upregulated specific receptors that have neuroprotective effects and induced alternations in neuroinflammatory-associated pathway profiles in hippocampus. Additionally, these metabolites displayed strong favorable co-regulation relationship with gut-brain integrity and inflammatory markers, as well as neurobehavioral outcomes. The findings underscore the ameliorative effects of MkD on AD-related neurological function and the underlying gut-brain communication via modulation of the gut microbiome-metabolome arrays.

In vitro faecal fermentation of Tritordeum breads and its effect on the human gut health

Spontaneous fermentation of Tritordeum flour enhances the nutritional potential of this hybrid cereal. However, the effect of consumption of Tritordeum sourdough bread (SDB) on gut health remains to be elucidated. This study investigated the effect of in vitro digestion and faecal fermentation of SDB compared to that of traditional baker's yeast (BYB) Tritordeum bread. After 24-h anaerobic faecal fermentation, both SDB and BYB (1% w/v) induced an increase in the relative abundances of Bifidobacterium, Megasphaera, Mitsuokella, and Phascolarctobacterium genera compared to baseline, while concentrations of acetate and butyrate were significantly higher at 24 h for SDB compared to those for BYB. Integrity of intestinal epithelium, as assessed through in vitro trans-epithelial electrical resistance (TEER) assay, was slightly increased after incubation with SDB fermentation supernatants, but not after incubation with BYB fermentation supernatants. The SDB stimulated in vitro mucosal immune response by inducing early secretion of inflammatory cytokines, IL-6 and TNF-α, followed by downregulation of the inflammatory trigger through induction of anti-inflammatory IL-10 expression. Overall, our findings suggest that Tritordeum sourdough can modulate gut microbiota fermentation activity and positively impact the gut health.

Colorectal cancer-associated T cell receptor repertoire abnormalities are linked to gut microbiome shifts and somatic cell mutations

As with many diseases, tumor formation in colorectal cancer (CRC) is multifactorial and involves immune, environmental factors and various genetics that contribute to disease development. Accumulating evidence suggests that the gut microbiome is linked to the occurrence and development of CRC, and these microorganisms are important for immune maturation. However, a systematic perspective integrating microbial profiling, T cell receptor (TCR) and somatic mutations in humans with CRC is lacking. Here, we report distinct features of the expressed TCRβ repertoires in the peripheral blood of and CRC patients (n = 107) and healthy donors (n = 30). CRC patients have elevated numbers of large TCRβ clones and they have very low TCR diversity. The metagenomic sequencing data showed that the relative abundance of Fusobacterium nucleatum (F. nucleatum), Escherichia coli and Dasheen mosaic virus were elevated consistently in CRC patients (n = 97) compared to HC individuals (n = 30). The abundance of Faecalibacterium prausnitzii and Roseburia intestinalis was reduced in CRC (n = 97) compared to HC (n = 30). The correlation between somatic mutations of target genes (16 genes, n = 79) and TCR clonality and microbial biomarkers in CRC had been investigated. Importantly, we constructed a random forest classifier (contains 15 features) based on microbiome and TCR repertoires, which can be used as a clinical detection method to screen patients for CRC. We also analysis of F. nucleatum-specific TCR repertoire characteristics. Collectively, our large-cohort multi-omics data aimed to identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC, which is of possible etiological and diagnostic significance.

Thyroid Diseases and Intestinal Microbiome

The human microbiome plays an integral role in health. In particular, it is important for the development, differentiation, and maturation of the immune system, 70% of which resides in the intestinal mucosa. Microbiome studies conducted to date have revealed an association between disturbances in the microbiota (dysbiosis) and various pathological disorders, including changes in host immune status. Autoimmune thyroid diseases are one of the most common organ-specific autoimmune disorders, with a worldwide prevalence higher than 5%. The predominant autoimmune thyroid diseases are Hashimoto's thyroiditis and Grave's disease. Several factors, such as genetic and environmental ones, have been studied. In accordance with recent studies, it is assumed that the gut microbiome might play a significant role in triggering autoimmune diseases of the thyroid gland. However, the exact etiology has not yet been elucidated. The present review aims to describe the work carried out so far regarding the role of gut microflora in the pathogenesis of autoimmune thyroid diseases and its involvement in the appearance of benign nodules and papillary thyroid cancer. It appears that future work is needed to elucidate more precisely the mechanism for gut microbiota involvement in the development of autoimmune thyroid diseases.

The respiratory microbiome in childhood asthma

Asthma is the most prevalent noncommunicable disease in childhood, characterized by reversible airway constriction and inflammation of the lower airways. The respiratory tract consists of the upper and lower airways, which are lined with a diverse community of microbes. The composition and density of the respiratory microbiome differs across the respiratory tract, with microbes adapting to the gradually changing physiology of the environment. Over the past decade, both the upper and lower respiratory microbiomes have been implicated in the etiology and disease course of asthma, as well as in its severity and phenotype. We have reviewed the literature on the role of the respiratory microbiome in asthma, making a careful distinction between the relationship of the microbiome with development of childhood asthma and its relationship with the disease course, while accounting for age and the microbial niches studied. Furthermore, we have assessed the literature regarding the underlying asthma endotypes and the impact of the microbiome on the host immune response. We have identified distinct microbial signatures across the respiratory tract associated with asthma development, stability, and severity. These data suggest that the respiratory microbiome may be important for asthma development and severity and may therefore be a potential target for future microbiome-based preventive and treatment strategies.

Impaired gut microbiota-mediated short-chain fatty acid production precedes morbidity and mortality in people with HIV

Antiretroviral therapy (ART) has dramatically lengthened lifespan among people with HIV (PWH), but this population experiences heightened rates of inflammation-related comorbidities. HIV-associated inflammation is linked with an altered microbiome; whether such alterations precede inflammation-related comorbidities or occur as their consequence remains unknown. We find that ART-treated PWH exhibit depletion of gut-resident bacteria that produce short-chain fatty acids (SCFAs)-crucial microbial metabolites with anti-inflammatory properties. Prior reports establish that fecal SCFA concentrations are not depleted in PWH. We find that gut-microbiota-mediated SCFA production capacity is better reflected in serum than in feces and that PWH exhibit reduced serum SCFA, which associates with inflammatory markers. Leveraging stool and serum samples collected prior to comorbidity onset, we find that HIV-specific microbiome alterations precede morbidity and mortality in ART-treated PWH. Among these microbiome alterations, reduced microbiome-mediated conversion of lactate to propionate precedes mortality in PWH. Thus, gut microbial fiber/lactate conversion to SCFAs may modulate HIV-associated comorbidity risk.

Cooperative interactions between Veillonella ratti and Lactobacillus acidophilus ameliorate DSS-induced ulcerative colitis in mice

Veillonella and Lactobacillus species are key regulators of a healthy gut environment through metabolic cross-feeding, influencing lactic acid and short-chain fatty acid (SCFA) levels, which are crucial for gut health. This study aims to investigate how Veillonella ratti (V. ratti) and Lactobacillus acidophilus (LA) interact with each other and alleviate dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in a mouse model. We assess their metabolic interactions regarding carbon sources through co-culturing in a modified medium. In the in vitro experiments, V. ratti and LA were inoculated in mono-cultures and co-culture, and viable cell counts, OD600, pH, lactic acid, glucose and SCFAs were measured. For the in vivo experiment, 60 C57BL/6 mice were randomly divided into five groups and administered V. ratti and LA alone or in combination via oral gavage (1 × 109 CFU mL-1 per day per mouse) for 14 days. On the seventh day, 2.5% DSS was added to the drinking water to induce colitis. The effects of these probiotics on UC were evaluated by assessing intestinal barrier integrity and intestinal inflammation in the gut microenvironment. In vitro results demonstrated that co-culturing V. ratti with LA significantly increased viable cell numbers, lactic acid production, and SCFA production, while reducing pH and glucose levels in the medium. In vivo findings revealed that intervention with V. ratti, particularly in combination with LA, alleviated symptoms, including weight loss, colon shortening, and tissue damage. These probiotics mitigated intestinal inflammation by down-regulating pro-inflammatory molecules, such as IL-6, IL-1β, IL-γ, iNOS, and IFN-γ, as well as oxidative stress markers, including MDA and MPO. Concurrently, they upregulated the activity of anti-inflammatory enzymes, namely, SOD and GSH, and promoted the production of SCFAs. The combined intervention of V. ratti and LA significantly increased acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, and total SCFAs in cecal contents. Furthermore, the intervention of V. ratti and LA increased the abundance of beneficial bacteria, such as Akkermansia, while reducing the abundance of harmful bacteria, such as Escherichia-Shigella and Desulfovibrio, thereby mitigating excessive inflammation. These findings highlight the enhanced therapeutic effects resulting from the interactions between V. ratti and LA, demonstrating the potential of this combined probiotic approach.

Characterization of the bacterial fecal microbiota composition of pigs preceding the clinical signs of swine dysentery

Swine dysentery (SD) is a worldwide production-limiting disease of growing-finishing pigs in commercial farms. The importance of the large intestinal microbiota in the swine dysentery pathogenesis has been established, but not well characterized. The objective of this study was to characterize the fecal bacterial microbiota of pigs immediately prior to developing clinical signs of swine dysentery. A total of 60 fecal samples were collected from 15 pigs with SD. Sampling times included a time point prior to SD (d0, n=15), 2 days before mucohaemorrhagic diarrhea was observed (d-2SD, n=15), 1 day before mucohaemorrhagic diarrhea was observed (d-1SD, n=15), and the day when pigs developed mucohemorragic diarrhea (MHD, n=15). Sequencing of cpn60 amplicons was used to profile the microbiome, and analyses were performed on QIIME2. Increased Chao1 index in d-1SD and MHD samples when compared to the d0 was the only change observed in alpha diversity. No differences between sampling times on beta diversity (Bray-Curtis dissimilarity) were found. Although a small sample size was investigated, differential abundance analysis revealed that Alistipes dispar and Parabacteroides gordonii were increased in MHD fecal samples when compared to d-2SD and d-1SD. It is suggested that these taxa may play a role in the pathogenesis of SD, which is known to require the presence of Brachyspira spp. and an anaerobe for severe disease development.

Fucosylated human milk oligosaccharide-utilizing bifidobacteria regulate the gut organic acid profile of infants

Bifidobacteria are the predominant bacteria in the infant gut and have beneficial effects on host physiology. Infant cohort studies have demonstrated that a higher abundance of bifidobacteria in the gut is associated with a reduced risk of disease. Recently, bifidobacteria-derived metabolites, such as organic acid, have been suggested to play crucial roles in host physiology. This review focuses on an investigation of longitudinal changes in the gut microbiota and organic acid concentrations over 2 years of life in 12 Japanese infants and aims to identify bifidobacteria that contribute to the production of organic acid in healthy infants. Acetate, lactate, and formate, which are rarely observed in adults, are characteristically observed during breast-fed infancy. Bifidobacterium longum subspecies infantis and the symbiosis of Bifidobacterium bifidum and Bifidobacterium breve efficiently produce these organic acids through metabolization of human milk oligosaccharide (HMO) with different strategies. These findings confirmed that HMO-utilizing bifidobacteria play an important role in regulating the gut organic acid profiles of infants.

Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis

Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact on the interactions between two abundant and prevalent human gut bacteria, the primary fermenter Bacteroides thetaiotaomicron and the butyrate producer Roseburia intestinalis. By combining machine learning and flow cytometry, we found that the number of viable B. thetaiotaomicron cells decreases with glucose consumption due to acid production, while R. intestinalis survives post-glucose depletion by entering a slow growth mode. Both species attach to mucin beads, but only viable cell counts of B. thetaiotaomicron increase significantly. The number of viable co-culture cells varies significantly over time compared to those of monocultures. A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption, whereas B. thetaiotaomicron survives glucose depletion and low pH by foraging on mucin sugars. In addition, most of the mucin monosaccharides we tested inhibited the growth of R. intestinalis but not B. thetaiotaomicron. We encoded these causal relationships in a kinetic model, which reproduced the observed dynamics. In summary, we explored how R. intestinalis and B. thetaiotaomicron respond to nutrient scarcity and how this affects their dynamics. We highlight the importance of understanding bacterial metabolic strategies to effectively modulate microbial dynamics in changing conditions.

Effects of mixed fibres and essential oils blend on growth performance and intestinal barrier function of piglets challenged with enterotoxigenic Escherichia coli K88

This study was to evaluate the effects of supplementing mixed dietary fibres (MDF) and essential oils blend (EOB) either alone or in combination on growth performance and intestinal barrier function in weaned piglets challenged with enterotoxigenic Escherichia coli K88 (ETEC). Forty-two piglets (28 days old) were randomly allocated into six treatments in a 25-day experiment, and fed the basal diet (CON or ETEC) either with antibiotics (AT), MDF, EOB or MDF + EOB. On Day 22 of the experiment, pigs in CON and challenged groups (ETEC, AT, MDF, EOB and MDF + EOB) were orally administered sterile saline and ETEC containing 6 × 1010  CFU/kg body weight respectively. On Day 26, all pigs were euthanized to collect samples. Before ETEC challenge, piglets in MDF and EOB had lower diarrhoea incidence (p < 0.01) than others. After ETEC challenge, piglets in ETEC had lower average daily gain and higher diarrhoea incidence (p < 0.05) than those of CON. Furthermore, compared to CON, ETEC group increased the serum lipopolysaccharide concentration and diamine oxidase activity, and decreased mRNA levels of genes relating to barrier function (aquaporin 3, AQP3; mucin1, MUC1; zonula occludens-1, ZO-1; Occludin), and increased the concentration of cytokines (interleukin-1β/4/6/10, IL-1β/4/6/10) and secretory immunoglobulin A (sIgA) in jejunal mucosa (p < 0.05). However, these deleterious effects induced by ETEC were partly alleviated by MDF, EOB, MDF + EOB and AT. Additionally, compared to ETEC group, MDF increased Bifidobacterium abundance in cecal digesta and butyrate concentration in colonic digesta (p < 0.05). Also, EOB improved propionate concentration in cecal digesta, and MDF + EOB decreased IL-10 concentration in jejunal mucosa (p < 0.05) compared with ETEC. Conclusively, MDF and EOB either alone or in combination can improve growth performance and alleviate diarrhoea via improving intestinal barrier function of piglets after ETEC challenge, and all may serve as potential alternatives to AT for piglets.

Type of intrinsic resistant starch type 3 determines in vitro fermentation by pooled adult faecal inoculum

Resistant starch (RS) results in relatively high health-beneficial butyrate levels upon fermentation by gut microbiota. We studied how physico-chemical characteristics of RS-3 influenced butyrate production during fermentation. Six highly resistant RS-3 substrates (intrinsic RS-3, 80-95 % RS) differing in chain length (DPn 16-76), Mw distribution (PI) and crystal type (A/B) were fermented in vitro by pooled adult faecal inoculum. All intrinsic RS-3 substrates were fermented to relatively high butyrate levels (acetate/butyrate ≤ 2.5), and especially fermentation of A-type RS-3 prepared from polydisperse α-1,4 glucans resulted in the highest relative butyrate amount produced (acetate/butyrate: 1). Analysis of the microbiota composition after fermentation revealed that intrinsic RS-3 stimulated primarily Lachnospiraceae, Bifidobacterium and Ruminococcus, but the relative abundances of these taxa differed slightly depending on the RS-3 physico-chemical characteristics. Especially intrinsic RS-3 of narrow disperse Mw distribution stimulated relatively more Ruminococcus. Selected RS fractions (polydisperse Mw distribution) obtained after pre-digestion were fermented to acetate and butyrate (ratio ≤ 1.8) and stimulated Lachnospiraceae and Bifidobacterium. This study indicates that especially the α-1,4 glucan Mw distribution dependent microstructure of RS-3 influences butyrate production and microbiota composition during RS-3 fermentation.

Broiler chicken response to xylanase and fermentable xylooligosaccharide supplementation

A study was conducted to determine the effect of dietary fiber (DF), xylanase (XYL), xylooligosaccharides (XOS), and a combination of XYL and xylooligosaccharides (STBIO) on chicken growth performance, N-corrected apparent metabolizable energy (AMEn), and nutrient availability, characteristics of the gastrointestinal tract (GIT), and cecal content of short-chain fatty acids (SCFA). A 35-day experiment was performed on 1,920 as hatched Ross 308 broiler chicks, reared in 96 pens and fed ad libitum. Experimental diets were split into 2 phases: starter (0-21 d) and finisher (22-35 d). There were 2 basal diets, first contained 54% maize and in the second, 5% of the maize was replaced by wheat bran as DF. The diets were split into 4 batches: one of them was used as a control, and each of the others were supplemented either with XYL or XOS or with the STBIO. Each diet was fed to 12 pens following randomization. The data were analyzed in GenStat (20th edition) by ANOVA using a 2 × 4 factorial design. The addition of STBIO improved feed conversion ratio (FCR) and increased weight gain (WG) from 21 to 35 d and from 0 to 35 d (P < 0.05). The inclusion of DF had a negative effect on N and fat retention coefficients at 35 d as well as AMEn and dry matter retention at 21 and 35 d. At 21 d, neutral detergent fiber (NDF) retention was increased when xylanase and STBIO were added to the diet (P < 0.001) and at d 35 the highest retention was noted when the diet was supplemented with DF and XYL or STBIO (P = 0.001). There was no dietary effect on jejunum histomorphometry (P > 0.05). The addition of DF increased the concentration of cecal SCFA in particular valeric and propionic acid at 35-day-old birds (P < 0.05). It can be concluded that addition of STBIO in diet could provide benefits in terms of fiber degradation, WG, and feed efficiency.

Fecal microbiota transplantation improves hepatic fibro-inflammation via regulating oxidative stress in experimental NASH

Nonalcoholic steatohepatitis (NASH) is associated with imbalance of gut microbiome, indicating participation of gut environment in hepatic health status. Therefore, modulating gut environment via fecal microbiota transplantation (FMT) is a promising therapeutic procedure for NASH patients. However, the effect and mechanism of the FMT remains largely unknown. Here, we investigated the gut-liver axis to understand the FMT-mediated hepatic improvement in NASH. Feces from specific pathogen free mice were infused allogeneically into gastrointestinal tract of mice fed with high fat, high cholesterol and fructose (HFHCF), resulting in suppressing hepatic pathogenic events, featured by decreasing inflammatory and fibrotic mediators. The FMT elevated NF-E2-related factor 2 (NRF2), a key transcription factor that regulates antioxidant enzymes, in livers. The HFHCF-induced NASH increased intestinal permeability with abundant Facklamia and Aerococcus, an imbalanced gut environment that was significantly improved by the FMT, characterized with restoration of intestinal barrier function and an enrichment of Clostridium. Notably, the gut environment created by FMT was inferred to produce metabolites from the aromatic biogenic amine degradation pathway, specifically 4-hydroxyphenylacetic acid (4-HPA), which is known to ameliorate liver injury. We suggest that gut-derived molecules, related to hepatic improvement such as 4-HPA are the potential therapeutic agents for preventing and treating NASH.

Gut microbiota-derived short chain fatty acids act as mediators of the gut-brain axis targeting age-related neurodegenerative disorders: a narrative review

Neurodegenerative diseases associated with aging are often accompanied by cognitive decline and gut microbiota disorder. But the impact of gut microbiota on these cognitive disturbances remains incompletely understood. Short chain fatty acids (SCFAs) are major metabolites produced by gut microbiota during the digestion of dietary fiber, serving as an energy source for gut epithelial cells and/or circulating to other organs, such as the liver and brain, through the bloodstream. SCFAs have been shown to cross the blood-brain barrier and played crucial roles in brain metabolism, with potential implications in mediating Alzheimer's disease (AD) and Parkinson's disease (PD). However, the underlying mechanisms that SCFAs might influence psychological functioning, including affective and cognitive processes and their neural basis, have not been fully elucidated. Furthermore, the dietary sources which determine these SCFAs production was not thoroughly evaluated yet. This comprehensive review explores the production of SCFAs by gut microbiota, their transportation through the gut-brain axis, and the potential mechanisms by which they influence age-related neurodegenerative disorders. Also, the review discusses the importance of dietary fiber sources and the challenges associated with harnessing dietary-derived SCFAs as promoters of neurological health in elderly individuals. Overall, this study suggests that gut microbiota-derived SCFAs and/or dietary fibers hold promise as potential targets and strategies for addressing age-related neurodegenerative disorders.

Nutritional ingredients and prevention of chronic diseases by fermented koumiss: a comprehensive review

Koumiss, a traditional fermented dairy product made from fresh mare milk, is a sour beverage that contains an abundance of microbial communities, including lactic acid bacteria, yeast and others. Firstly, probiotics such as Lacticaseibacillus in koumiss can induce the secretion of immunoglobulin G in serum and interleukin-2 in the spleen while beneficial Saccharomyces can secrete antibacterial compounds such as citric acid and ascorbic acid for specific immunopotentiation. Additionally, more isoflavone in koumiss can regulate estrogen levels by binding to its receptors to prevent breast cancer directly. Bile salts can be converted into bile acids such as taurine or glycine by lactic acid bacteria to lower cholesterol levels in vivo. Butyric acid secretion would be increased to improve chronic gastrotis by regulating intestinal flora with lactic acid bacteria. Finally, SCFA and lCFA produced by Lacticaseibacillus inhibit the reproduction of pathogenic microorganisms for diarrhea prevention. Therefore, exploring the mechanisms underlying multiple physiological functions through utilizing microbial resources in koumiss represents promising avenues for ameliorating chronic diseases.

Identification of Gut Microbiota Profile Associated with Colorectal Cancer in Saudi Population

Colorectal cancer (CRC) is a significant global health concern. Microbial dysbiosis and associated metabolites have been associated with CRC occurrence and progression. This study aims to analyze the gut microbiota composition and the enriched metabolic pathways in patients with late-stage CRC. In this study, a cohort of 25 CRC patients diagnosed at late stage III and IV and 25 healthy participants were enrolled. The fecal bacterial composition was investigated using V3-V4 ribosomal RNA gene sequencing, followed by clustering and linear discriminant analysis (LDA) effect size (LEfSe) analyses. A cluster of ortholog genes' (COG) functional annotations and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed to identify enrichment pathways between the two groups. The findings showed that the fecal microbiota between the two groups varied significantly in alpha and beta diversities. CRC patients' fecal samples had significantly enriched populations of Streptococcus salivarius, S. parasanguins, S. anginosus, Lactobacillus mucosae, L. gasseri, Peptostreptococcus, Eubacterium, Aerococcus, Family XIII_AD3001 Group, Erysipelatoclostridium, Escherichia-Shigella, Klebsiella, Enterobacter, Alistipes, Ralstonia, and Pseudomonas (Q < 0.05). The enriched pathways identified in the CRC group were amino acid transport, signaling and metabolism, membrane biogenesis, DNA replication and mismatch repair system, and protease activity (Q < 0.05). These results suggested that the imbalance between intestinal bacteria and the elevated level of the predicated functions and pathways may contribute to the development of advanced CRC tumors. Further research is warranted to elucidate the exact role of the gut microbiome in CRC and its potential implications for use in diagnostic, prevention, and treatment strategies.

Topiramate alters the gut microbiome to aid in its anti-seizure effect

Introduction

There is a growing interest in the role of the gut microbiota in epilepsy, however, it is unclear if anti-seizure medications (ASMs) play a role in the gut-brain axis. To test this, we investigated the impact of the ASM topiramate on the gut microbiome of mice.

Methods

C57BL/6J mice were administered topiramate in their drinking water for 5 weeks. 16S ribosomal RNA gene sequencing was performed on fecal samples collected at 5 weeks. Analysis of alpha diversity, beta diversity, and differential abundance were performed. Cecal contents were analyzed for short-chain fatty acids (SCFAs) composition. Pentylenetetrazol (PTZ)-kindling was performed in saline, topiramate, Lactobacillus johnsonii, and topiramate and Lactobacillus johnsonii treated mice. Mice received PTZ injection every other day for a total of twelve injections, seizure activity was video monitored for 30 minutes and scored.

Results and discussion

Our study revealed that topiramate ingestion significantly increased Lactobacillus johnsonii in the gut microbiome of naïve mice. Treatment with topiramate and Lactobacillus johnsonii together, but not alone, reduced susceptibility to PTZ-induced seizures. Co-treatment also significantly increased the percent of butyrate and the abundance of butyrate-producing family Lachnospiraceae in the gut, and elevated the GABA/glutamate ratio in the cortex. Our results demonstrate that an ASM can alter the gut microbiome to aid in their anti-seizure effect in vivo and suggest the potential of the probiotic Lactobacillus johnsonii as an adjunct therapy with topiramate in reducing seizure susceptibility.

Alterations of the gut microbiota in patients with postherpetic neuralgia

Postherpetic neuralgia (PHN) is a prevalent, intricate, and intractable form of neuropathic pain. The available evidence indicates that alterations in the gut microbiota are significant environmental determinants in the development of chronic neuropathic pain. Nevertheless, the correlation between the gut microbiota and PHN remains elusive. A cross-sectional study was performed on a cohort of 27 patients diagnosed with PHN and 27 matched healthy controls. Fecal samples were collected and subjected to microbiota analysis using 16S ribosomal RNA gene sequencing. Comparable levels of bacterial richness and diversity were observed in the gut microbiota of PHN patients and healthy controls. A significant difference was observed in 37 genera between the two groups. Furthermore, the LEfSe method revealed that the abundance levels of Escherichia-Shigella, Streptococcus, Ligilactobacillus, and Clostridia_UCG-014_unclassified were elevated in PHN patients, while Eubacterium_hallii_group, Butyricicoccus, Tyzzerella, Dorea, Parasutterella, Romboutsia, Megamonas, and Agathobacter genera were reduced in comparison to healthy controls. Significantly, the discriminant model utilizing the predominant microbiota exhibited efficacy in distinguishing PHN patients from healthy controls, with an area under the curve value of 0.824. Moreover, Spearman correlation analysis demonstrated noteworthy correlations between various gut microbiota and clinical symptoms, including disease course, anxiety state, sleep quality, heat pain, pain intensity, and itching intensity. Gut microbiota dysbiosis exists in PHN patients, microbiome differences could be used to distinguish PHN patients from normal healthy individuals with high sensitivity and specificity, and altered gut microbiota are related to clinical manifestations, suggesting potentially novel prevention and therapeutic directions of PHN.

Gut-derived short-chain fatty acids bridge cardiac and systemic metabolism and immunity in heart failure

Heart failure (HF) represents a group of complex clinical syndromes with high morbidity and mortality and has a significant global health burden. Inflammation and metabolic disorders are closely related to the development of HF, which are complex and depend on the severity and type of HF and common metabolic comorbidities such as obesity and diabetes. An increasing body of evidence indicates the importance of short-chain fatty acids (SCFAs) in regulating cardiac function. In addition, SCFAs represent a unique class of metabolites and play a distinct role in shaping systemic immunity and metabolism. In this review, we reveal the role of SCFAs as a link between metabolism and immunity, which regulate cardiac and systemic immune and metabolic systems by acting as energy substrates, inhibiting the expression of histone deacetylase (HDAC) regulated genes and activating G protein-coupled receptors (GPCRs) signaling. Ultimately cardiac efficiency is improved, cardiac inflammation alleviated and cardiac function in failing hearts enhanced. In conclusion, SCFAs represent a new therapeutic approach for HF.

Fucose modifies short chain fatty acid and H2S formation through alterations of microbial cross-feeding activities

Algae are a rich but unexplored source of fibers with the potential to contribute to the next generation of prebiotics. The sulfated brown algae polysaccharide, fucoidan, is mainly composed of the deoxy-hexose L-fucose, which can be metabolized to 1,2-propanediol (1,2-PD) or lactate by gut microbes as precursors of propionate and butyrate. It was the aim of this study to investigate the impact of fucoidan on the fermentation capacity of the fecal microbiota and to compare to fucose. In batch fermentations of fecal microbiota collected from 17 donor samples, fucose promoted the production of propionate while no consistent effect was observed for commercial fucoidan and Fucus vesiculosus extract prepared in this study containing laminarin and fucoidan. H2S production was detected under all tested conditions, and levels were significantly lower in the presence of fucose in a dose-dependent manner. The addition of high fucose levels led to higher relative abundance of microbial 1,2-PD and lactate cross-feeders. Our results highlight that fucose and not fucoidan addition impacted fermentation capacity and increased the proportions of propionate and butyrate, which allows for precise modulation of intestinal microbiota activity.

Precision modulation of dysbiotic adult microbiomes with a human-milk-derived synbiotic reshapes gut microbial composition and metabolites

Manipulation of the gut microbiome using live biotherapeutic products shows promise for clinical applications but remains challenging to achieve. Here, we induced dysbiosis in 56 healthy volunteers using antibiotics to test a synbiotic comprising the infant gut microbe, Bifidobacterium longum subspecies infantis (B. infantis), and human milk oligosaccharides (HMOs). B. infantis engrafted in 76% of subjects in an HMO-dependent manner, reaching a relative abundance of up to 81%. Changes in microbiome composition and gut metabolites reflect altered recovery of engrafted subjects compared with controls. Engraftment associates with increases in lactate-consuming Veillonella, faster acetate recovery, and changes in indolelactate and p-cresol sulfate, metabolites that impact host inflammatory status. Furthermore, Veillonella co-cultured in vitro and in vivo with B. infantis and HMO converts lactate produced by B. infantis to propionate, an important mediator of host physiology. These results suggest that the synbiotic reproducibly and predictably modulates recovery of a dysbiotic microbiome.

Deep insight into oriented propionate production from food waste: Microbiological interpretation and design practice

Using mixed microbial cultures (MMCs) for oriented volatile fatty acids (VFAs) refining in an open environment is a typical challenge due to the microbial diversiform and the process complexity. Especially for carbohydrate-rich waste (such as food waste), butyrate-type fermentation is usually dominant in a single-stage MMCs anaerobic process, while the production of odd-carbon VFAs (such as propionate) is difficult although it plays a significant role in chemicals industries. In this study, firstly, we gave a new perspective on the rationality of the oriented propionate production using MMCs with lactate as feedstock by conducting in-depth microbial informatics and reaction analysis. Secondly, we verified the feasibility of the "food waste-lactate-propionate" route to reverse the original butyrate-type fermentation situation and explore mechanisms for maintaining stability. In the first stage, a defined lactate fermentation microbiome was used to produce lactate-containing broth (80% of total chemical oxygen demand) at pH=4. In the second stage, an undomesticated undefined anaerobic microbiome was used to drive propionate production (45.26% ± 2.23% of total VFAs) under optimized conditions (C/N = 100:1-200:1 and pH=5.0). The low pH environment in the first stage enhanced the lactic acid bacteria to resist the invasion of non-functional flanking bacteria, making the community stable. In the second stage, the system maintained the propionate-type fermentation due to the absence of the ecological niche of the invasive lactic acid bacteria; The selection of propionate-producing specialists was a necessary but not sufficient condition for propionate-type fermentation. At last, this study proposed an enhanced engineering strategy framework for understanding elaborate MMCs fermentation.

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

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

Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study

BACKGROUND

Compared to their healthy counterparts, patients with type 2 diabetes (T2D) can exhibit an altered gut microbiota composition, correlated with detrimental outcomes, including reduced insulin sensitivity, dyslipidemia, and increased markers of inflammation. However, a typical T2D microbiota profile is not established. The aim of this pilot study was to explore the gut microbiota and bacteria associated with prediabetes (pre-T2D) patients, and treatment naïve T2D patients, compared to healthy subjects.

METHODS

Fecal samples were collected from patients and healthy subjects (from Norway). The bacterial genomic DNA was extracted, and the microbiota analyzed utilizing the bacterial 16S rRNA gene. To secure a broad coverage of potential T2D associated bacteria, two technologies were used: The GA-map® 131-plex, utilizing 131 DNA probes complementary to pre-selected bacterial targets (covering the 16S regions V3-V9), and the LUMI-Seq™ platform, a full-length 16S sequencing technology (V1-V9). Variations in the gut microbiota between groups were explored using multivariate methods, differential bacterial abundance was estimated, and microbiota signatures discriminating the groups were assessed using classification models.

RESULTS

In total, 24 pre-T2D patients, 18 T2D patients, and 52 healthy subjects were recruited. From the LUMI-Seq™ analysis, 10 and 9 bacterial taxa were differentially abundant between pre-T2D and healthy, and T2D and healthy, respectively. From the GA-map® 131-plex analysis, 10 bacterial markers were differentially abundant when comparing pre-T2D and healthy. Several of the bacteria were short-chain fatty acid (SCFA) producers or typical opportunistic bacteria. Bacteria with similar function or associated properties also contributed to the separation of pre-T2D and T2D from healthy as found by classification models. However, limited overlap was found for specific bacterial genera and species.

CONCLUSIONS

This pilot study revealed that differences in the abundance of SCFA producing bacteria, and an increase in typical opportunistic bacteria, may contribute to the variations in the microbiota separating the pre-T2D and T2D patients from healthy subjects. However, further efforts in investigating the relationship between gut microbiota, diabetes, and associated factors such as BMI, are needed for developing specific diabetes microbiota signatures.

Examining the Interaction between Exercise, Gut Microbiota, and Neurodegeneration: Future Research Directions

Physical activity has been demonstrated to have a significant impact on gut microbial diversity and function. Emerging research has revealed certain aspects of the complex interactions between the gut, exercise, microbiota, and neurodegenerative diseases, suggesting that changes in gut microbial diversity and metabolic function may have an impact on the onset and progression of neurological conditions. This study aimed to review the current literature from several databases until 1 June 2023 (PubMed/MEDLINE, Web of Science, and Google Scholar) on the interplay between the gut, physical exercise, microbiota, and neurodegeneration. We summarized the roles of exercise and gut microbiota on neurodegeneration and identified the ways in which these are all connected. The gut-brain axis is a complex and multifaceted network that has gained considerable attention in recent years. Research indicates that gut microbiota plays vital roles in metabolic shifts during physiological or pathophysiological conditions in neurodegenerative diseases; therefore, they are closely related to maintaining overall health and well-being. Similarly, exercise has shown positive effects on brain health and cognitive function, which may reduce/delay the onset of severe neurological disorders. Exercise has been associated with various neurochemical changes, including alterations in cortisol levels, increased production of endorphins, endocannabinoids like anandamide, as well as higher levels of serotonin and dopamine. These changes have been linked to mood improvements, enhanced sleep quality, better motor control, and cognitive enhancements resulting from exercise-induced effects. However, further clinical research is necessary to evaluate changes in bacteria taxa along with age- and sex-based differences.

Spore-forming properties and enhanced oxygen tolerance of butyrate-producing Anaerostipes spp

OBJECTIVES

Butyrate producing bacteria are promising candidates for next-generation probiotics. However, they are extremely sensitive to oxygen, which is a significant obstacle to their inclusion in food matrices in a viable form. The present study characterized the spore-forming properties and stress tolerance of human gut butyrate-producing Anaerostipes spp.

METHODS

Spore formation properties in six species of Anaerostipes spp. were studied by in vitro and in silico tests.

RESULTS

Spores were observed from the cells of three species using microscopic analyses, while the remaining three did not form spores under the tested conditions. Spore-forming properties were confirmed by an ethanol treatment. The spores of Anaerostipes caccae were tolerant to oxygen and survived for 15 weeks under atmospheric conditions. Spores tolerated heat stress at 70 °C, but not at 80 °C. An in silico analysis of the conservation of potential sporulation signature genes revealed that the majority of human gut butyrate-producing bacteria were classified as potential spore formers. Comparative genomics revealed that three spore-forming Anaerostipes spp. specifically possessed the spore formation-related genes of bkdR, sodA, and splB, which may be key genes for different sporulation properties in Anaerostipes spp.

CONCLUSIONS

The present study demonstrated the enhanced stress tolerance of butyrate producing Anaerostipes spp. for future probiotic application. Presence of specific gene(s) are possibly keys for sporulation in Anaerostipes spp.