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This study is to investigate the relationship between the intestinal microbiota and urine levels of the ellagic acid-derived polyphenols, the urolithins, in a cohort of subjects following a three-week walnut dietary intervention. We longitudinally collected fecal and urine samples from 39 subjects before and after walnut consumption (2 oz per day for 21 days). 16S RNA gene sequencing was performed on fecal DNA to study the association between microbiota composition and the levels of nine urolithin metabolites, which were measured using UHPLC/Q-TOF–MS/MS. Fecal microbial composition was found to be significantly different between pre- and post-walnut intervention (beta diversity, FDR-p = 0.018; alpha diversity, p = 0.018). Roseburia, Rothia, Parasutterella, Lachnospiraceae UCG-004, Butyricicoccus, Bilophila, Eubacterium eligens, Lachnospiraceae UCG-001, Gordonibacter, Paraprevotella, Lachnospira, Ruminococcus torques, and Sutterella were identified as the 13 most significantly enriched genera after daily intake of walnuts. We observed 26 genera that were significantly associated with 7 urolithin metabolites, with 22 genera positively correlating after walnut supplementation (FDR-p ≤ 0.05). PICRUSt analysis showed that several inferred KEGG orthologs were associated with 4 urolithin metabolites after walnut intake. In this study, we found that walnut supplementation altered urolithin metabolites, which associates with specific changes in bacterial taxa and inferred functional contents. [ABSTRACT FROM AUTHOR]

Background & Aims: Intermittent fasting is a nutritional strategy that focuses on when to eat, rather than what to eat. Although the effectiveness of intermittent fasting practices in many metabolic diseases is known, its effect on microbiota and its underlying mechanism has not yet been clarified. This study aimed to investigate the effect of Ramadan fasting, one of the intermittent fasting practices, on gut microbiota and fatty acid binding protein 4 (FABP4). Methods: The study involved 10 male volunteers, 6 of whom were overweight and 4 were obese. They fasted for an average of 14-15 hours daily from dawn to sunset during the 29-day Ramadan month between 23 March - 20 April 2023 and met the inclusion criteria. The participants' nutritional and physical activity status before and during Ramadan, as well as their anthropometric measurements before and after Ramadan, intestinal microbiota, transaminases, gamma-glutamyl transferase, C reactive protein, total cholesterol (C), high-density lipoprotein (HDL) C, low-density lipoprotein C, triglycerides (TG), and FABP4 levels, were evaluated within the scope of the study. Results: The study found a statistically significant increase in both alpha and beta diversity in the intestinal microbiota following Ramadan fasting (p<0.05). The F/B ratio, Firmicutes phylum, Clostridia class, Clostridiales order, and Ruminococcaceae family exhibited statistically significant decreases, while the Bacteroidetes and Proteobacteria phyla, Bacteroidia, Alphaproteobacteria, and Erysipelotrichi classes, Bacteroidales, Erysipelotrichales, and Actinomycetales orders, Erysipelotrichaceae family and Prevotella genus, demonstrated statistically significant increases (p<0.05). Participants who achieved an average weight loss of 2.3±0.99 kg at the end of Ramadan showed a significant increase in HDL-C and a significant decrease in TG levels (p<0.05). Although FABP4 levels decreased after fasting, this difference was not statistically significant (p>0.05). Conclusion: Ramadan fasting induces weight loss, modifies gut microbiota, and improves blood lipid profile and FABP4 levels, suggesting the need for more extensive studies. [ABSTRACT FROM AUTHOR]

The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3269 compounds, 3677 reactions, and 876 modules that were obtained from 1012 manually curated scientific literature. Notably, 698 modules of these modules are new entries and cannot be found in any other databases. The database is accessible from a web application (https://enteropathway.org) that offers a metabolic diagram for graphical visualization of metabolic pathways, a customization interface, and an enrichment analysis feature for highlighting enriched modules on the metabolic diagram. Overall, Enteropathway is a comprehensive reference database that can complement widely used databases, and a tool for visual and statistical analysis in human gut microbiota studies and was designed to help researchers pinpoint new insights into the complex interplay between microbiota and host metabolism. [ABSTRACT FROM AUTHOR]

The fecal microbiota of two healthy adults was cultivated in a medium containing commercial fructooligosaccharides [FOS; 1-kestose (GF2), nystose (GF3), and 1F-fructofuranosylnystose (GF4)]. Initially, the proportions of lactobacilli in the two feces samples were only 0.42% and 0.17%; however, they significantly increased to 7.2% and 4.8%, respectively, after cultivation on FOS. Most FOS-utilizing isolates could utilize only GF2; however, Lacticaseibacillus paracasei strain Lp02 could fully consume GF3 and GF4 too. The FOS operon (fosRABCDXE) was present in Lc. paracasei Lp02 and another Lc. paracasei strain, KCTC 3510T, but fosE was only partially present in the non-FOS-degrading strain KCTC 3510T. In addition, the top six upregulated genes in the presence of FOS were fosABCDXE, particularly fosE. FosE is a β-fructosidase that hydrolyzes both sucrose and all three FOS. Finally, a genome-based analysis suggested that fosE is mainly observed in Lc. paracasei, and only 13.5% (61/452) of their reported genomes were confirmed to include it. In conclusion, FosE allows the utilization of FOS, including GF3 and GF4 as well as GF2, by some Lc. paracasei strains, suggesting that this species plays a pivotal role in FOS utilization in the human gut. Keypoints: • Lc. paracasei Lp02 could fully utilize commercial FOS including GF2, GF3 and GF4. • A specific β-fructosidase (FosE) was responsible for the utilization of three FOS molecules. • The specific β-fructosidase (FosE) was mainly observed in Lc. paracasei. [ABSTRACT FROM AUTHOR]

Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The "bottleneck" preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmodel gut commensals and not genetically manipulatable. Approaches to efficiently identify their gene transfer methodologies and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. This paper will introduce a step‐by‐step protocol to identify gene transfer conditions and build the gene manipulation tools for nonmodel gut microbes, focusing on Gram‐negative Bacteroidia and Gram‐positive Clostridia organisms. This protocol enables us to identify gene transfer methods and develop gene manipulation tools without prior knowledge of their genome sequences, by targeting bacterial 16s ribosomal RNAs or expanding their compatible replication origins combined with clustered regularly interspaced short palindromic repeats machinery. Such an efficient and generalizable approach will facilitate functional studies that causally connect gut microbiota genes to host diseases. Highlights: A protocol introducing a step‐by‐step genetic manipulation method would facilitate the investigation of those functional genes encoded by nonmodel gut commensals.The gene‐editing tools could be established in nonmodel gut Bacteroidia and Clostridia without prior knowledge of their genome information.The genetic manipulation pipeline may serve as a high‐throughput genetics screening and manipulating platform for human gut microbes. [ABSTRACT FROM AUTHOR]

A diverse array of microbes in and on the human body constitute the microbiota. These micro-residents continuously interact with the human host through the language of metabolites to dictate the host's physiology in health and illnesses. Any biotic and abiotic component ensuring a balanced host-microbiota interaction are potential microbiome therapeutic agents to overcome human diseases. Plant metabolites are continually being used to treat various illnesses. These metabolites target the host's metabolic machinery and host-gut microbiota interactions to overcome human diseases. Despite the paramount therapeutic significance of the factors affecting host-microbiota interactions, a comprehensive overview of the modulatory role of plant-derived metabolites in host-microbiota interactions is lacking. The current review puts an effort into comprehending the role of medicinal plants in gut microbiota modulation to mitigate various human illnesses. It would develop a holistic understanding of host-microbiota interactions and the role of effectors in health and diseases. Graphic Abstract [ABSTRACT FROM AUTHOR]

Humanized mice with human-like immune systems are commonly used to study immune responses to human-specific pathogens. However, one limitation of using humanized mice is their native murine gut microbiota, which significantly differs from that in humans. Given the importance of the gut microbiome to human health, these differences may profoundly impact the ability to translate results from humanized mouse studies to humans. Further, there is a critical need for improved pre-clinical models to study the complex in vivo relationships of the gut microbiome, immune system, and human disease. We previously created double humanized mice with a functional human immune system and a stable, human-like gut microbiome. Here, we characterized the engrafted human gut bacterial microbiome in our double humanized mouse model generated by transplanting fecal material from healthy human donors into the gut of humanized mice. Analysis of bacterial microbiomes in fecal samples from double humanized mice revealed they had unique 16S rRNA gene profiles consistent with those of the individual human donor samples. Importantly, transplanted human-like gut microbiomes were stable in mice for the duration of the study, extending up to 14.5 weeks post-transplant. Microbiomes of double humanized mice also harbored predicted functional capacities that more closely resembled those of the human donors than humanized mice. In conclusion, our study highlights the successful engraftment of human fecal microbiota in BLT humanized mice and underscores the stability of this model, offering a valuable platform for investigating the intricate interplay among the human gut microbiome, immune system, and various diseases in vivo. [ABSTRACT FROM AUTHOR]

Tryptamine, a neuromodulator derived from tryptophan, has been shown to significantly impact the host gut homeostasis through its production by the gut microbiota. However, the characterization of tryptamine-producing gut bacteria remains limited, the factors regulating tryptamine production largely unexplored, and its effects on the rest of the gut microbial community unknown. In this study, we screened 13 intestinal strains closely related to known tryptamine producers, characterized their production kinetics, and evaluated whether tryptophan decarboxylation to tryptamine contributes to acid stress tolerance, as shown in other amino acid-dependent acid tolerance systems. We also examined the impact of tryptamine on the composition and function of four healthy human gutmicrobiota by conducting 48-h ex vivo fecal batch fermentations. To complement the ex vivo experiments, we tested the effect of tryptamine exposure (range: 0.5-mM) on the growth of 18 intestinal strains. We identified tryptamine production in five taxa, i.e., Enterocloster asparagiformis, Blautia hansenii, Clostridium nexile, Clostridium sporogenes, and Ruminococcus gnavus,with R. gnavus DSM 108212 accumulating up to 3.4 mM tryptamine after 48 h. An increased tryptophan concentration led to higher tryptamine production. However, tryptamine production was not promoted at low pH andmay not protect cells fromacid-induced cellular damage. Exposing gut microbial communities to 2.4 mM tryptamine caused mild changes in gut microbiota function and composition. All donors showed reduced carbohydrate consumption after 5 h, leading to donor-specific alterations of short-chain fatty acids (SCFAs) (i.e., propionate, acetate, butyrate) and branched-chain fatty acids (BCFAs) (i.e., isobutyrate and isovalerate) after 48 h. Tryptamine also induced a mild change of community structure, with a consistent reduction in the phylum Bacteroidota as well as amplicon sequence variants (ASVs) related to the genera Bacteroides, Blautia, and Faecalibacterium. We confirmed the sensitivity of Bacteroides and Faecalibacterium strains in vitro at concentrations of 2 mM and above. Multiple gut commensals remained unaffected when exposed to 8 mM tryptamine. Taken together, our findings demonstrated that intestinal bacteria-derived tryptamine is a bioactive molecule that not only alters host homeostasis locally but alsomodulates the physiology of gut microbial communities. The specific mechanism through which tryptamine exerts its inhibitory effects on specific gut microbes while leaving others unaffected remains to be elucidated. [ABSTRACT FROM AUTHOR]

Background: Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed assessing their degrees of perturbation and resilience. Results: While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting important antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, treatment impact was relatively low on the fungal microbiota. At the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state like the initial one, even if the structure of the bacterial microbiota changed and the dynamics of the different components over time were rarely correlated. The observed richness of the antibiotic resistance genes repertoire was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with a concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was positively associated with the resilience of the metabolome content of the stools. Conclusions: In healthy adults, antibiotics perturb many components of the microbiota, which return close to the baseline state within 30 days. These data suggest an important role of endogenous β-lactamase-producing anaerobes in protecting the functions of the microbiota by de-activating the antibiotics reaching the colon. 64G36U-BwhYzB4Dx7Xcq3U Video Abstract [ABSTRACT FROM AUTHOR]

Green tea catechins (GTCs) are dietary polyphenols with broad bioactivities that undergo extensive microbial metabolism in the human gut. However, microbial-transferred metabolites and their health benefits are not fully understood. Herein, the microbial metabolism of GTCs by human fecal microbiota and dynamic alteration of the microbiota were integrally investigated via in vitro anaerobic fermentation. The results showed that the human gut microbiota exhibited a strong metabolic effect on GTCs via UHPLC-MS/MS analysis. A total of 35 microbial-transferred metabolites were identified, far more than were identified in previous studies. Among them, five metabolites, namely EGCG quinone, EGC quinone, ECG quinone, EC quinone, and mono-oxygenated EGCG, were identified for the first time in fermented GTCs with the human gut microbiota. Consequently, corresponding metabolic pathways were proposed. Notably, the antioxidant, α-amylase, and α-glucosidase inhibitory activities of the GTCs sample increased after fermentation compared to those of the initial unfermented sample. The results of the 16S rRNA gene sequence analysis showed that the GTCs significantly altered gut microbial diversity and enriched the abundancy of Eubacterium, Flavonifractor, etc., which may be further involved in the metabolisms of GTCs. Thus, these findings contribute to a better understanding of the interactions between GTCs and gut microbiota, as well as the health benefits of green tea consumption. [ABSTRACT FROM AUTHOR]

Polyethylene terephthalate (PET), primarily utilized for food and beverage packaging, consistently finds its way into the human gut, thereby exerting adverse effects on human health. PET hydrolases, critical for the degradation of PET, have been predominantly sourced from environmental microbial communities. Given the fact that the human gut harbors a vast and intricate consortium of microorganisms, inquiry into the presence of potential PET hydrolases within the human gut microbiota becomes imperative. In this investigation, we meticulously screened 22,156 homologous sequences that could potentially encode PET hydrolases using the hidden Markov model (HMM) paradigm, drawing from 4984 cultivated genomes of healthy human gut bacteria. Subsequently, we methodically validated the hydrolytic efficacy of five selected candidate PET hydrolases on both PET films and powders composed of micro-plastics (MPs). Notably, our study also unveiled the influence of both diverse PET MP powders and their resultant hydrolysates on the modulation of cytokine expression in macrophages. In summary, our research underscores the ubiquitous prevalence and considerable potential of the human gut microbiota in PET hydrolysis. Furthermore, our study significantly contributes to the holistic evaluation of the potential health hazards posed by PET MPs to human well-being. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiota is fundamental for human health. This complex health construct is a pivotal part of performance development in athletes. The gut microbiota plays its role in the physiology of the athlete by influencing immune function, gut barrier integrity, macro- and micronutrient absorption, muscular efficiency, and the gut-brain-axis. This article displays possible ways in which the gut microbiota affects the performance of athletes and shows practical methods to improve athletes' health and potential performance through a gut-centric approach. 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. [ABSTRACT FROM AUTHOR]

BACKGROUND: Astragali Radix (also known as Astragulus) is a traditional medicinal and edible homologous plant for tonifying Qi. Honey‐processed Astragalus is a dosage form of Astragali Radix processed with honey, which exhibited better efficacy of tonifying Qi than the raw product. Polysaccharides are their main active components. RESULTS: APS2a and HAPS2a were initially isolated from Astragulus and honey‐processed Astragulus. Both of them are highly branched acidic heteropolysaccharides containing ɑ‐configuration and β‐configuration glycosidic bonds. The molecular weight and the molecular dimension of HAPS2a decreased and the GalA contained in APS2a was converted to Gal in HAPS2a. The α‐configuration galactose residue 1,3,4‐α‐Galp in the backbone of APS2a was converted to the corresponding β‐configuration galactose residue 1,3,4‐β‐Galp in the backbone of HAPS2a and the uronic acid residue T‐α‐GalpA in the sidechain of APS2a was converted to the corresponding neutral residue T‐α‐Galp in the side chain of HAPS2a. Bioactivity results showed that HAPS2a had better probiotic effects on Bacteroides ovatus, Bacteroides thetaiotaomicron, Bifidobacterium longum and Lactobacillus rhamnosus strains than APS2a. After degradation, the molecular weights of HAPS2a and APS2a decreased with the changes in their monosaccharide composition. The contents of total short‐chain fatty acids (SCFAs) and other organic acids in HAPS2a group were higher than APS2a group. CONCLUSIONS: Two novel high‐molecular‐weight polysaccharides named APS2a and HAPS2a had different probiotic activities in vitro, which might be due to their structural differences before and after honey processing. Both of them might be possibly used as an immunopotentiator in healthy foods or dietary supplement. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4–0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9–8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L−1 NaCl (optimum 0.12 mol.L−1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood–Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T). [ABSTRACT FROM AUTHOR]

Theaflavins (TFs), the primary bioactive components in black tea, are poorly absorbed in the small intestine. However, the biological activity of TFs does not match their low bioavailability, which suggests that the gut microbiota plays a crucial role in their biotransformation and activities. In this study, we aimed to investigate the biotransferred metabolites of TFs produced by the human gut microbiota and these metabolites' function. We profiled the microbial metabolites of TFs by in vitro anaerobic human gut microbiota fermentation using liquid chromatography tandem mass spectrometry (LC-MS/MS) methods. A total of 17 microbial metabolites were identified, and their corresponding metabolic pathways were proposed. Moreover, full-length 16S rRNA gene sequence analysis revealed that the TFs altered the gut microbiota diversity and increased the relative abundance of specific members of the microbiota involved in the catabolism of the TFs, including Flavonifractor_plautii, Bacteroides_uniformis, Eubacterium_ramulus, etc. Notably, the antioxidant capacity of the TF sample increased after fermentation compared to the initial sample. In conclusion, the results contribute to a more comprehensive understanding of the microbial metabolites and antioxidant capacity of TFs. [ABSTRACT FROM AUTHOR]

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Introduction: Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRITOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. Methods: We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. Results: For validation, we used 58 sequence-confirmed strains and the CLOSTRITOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. Discussion: We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF MS. [ABSTRACT FROM AUTHOR]

Polyamines are bioactive amines that play a variety of roles, such as promoting cell proliferation and protein synthesis, and the intestinal lumen contains up to several mM polyamines derived from the gut microbiota. In the present study, we conducted genetic and biochemical analyses of the polyamine biosynthetic enzyme N-carbamoylputrescine amidohydrolase (NCPAH) that converts N-carbamoylputrescine to putrescine, a precursor of spermidine in Bacteroides thetaiotaomicron, which is one of the most dominant species in the human gut microbiota. First, ncpah gene deletion and complemented strains were generated, and the intracellular polyamines of these strains cultured in a polyamine-free minimal medium were analyzed using high-performance liquid chromatography. The results showed that spermidine detected in the parental and complemented strains was depleted in the gene deletion strain. Next, purified NCPAH-(His)6 was analyzed for enzymatic activity and found to be capable of converting N-carbamoylputrescine to putrescine, with a Michaelis constant (Km) and turnover number (kcat) of 730 µM and 0.8 s−1, respectively. Furthermore, the NCPAH activity was strongly (>80%) inhibited by agmatine and spermidine, and moderately (≈50%) inhibited by putrescine. This feedback inhibition regulates the reaction catalyzed by NCPAH and may play a role in intracellular polyamine homeostasis in B. thetaiotaomicron. [ABSTRACT FROM AUTHOR]

The study of human gut microbiota has attracted increasing interest in the fields of life science and healthcare. However, the complicated and interconnected associations between gut microbiota and human diseases are still difficult to determine in a predictive fashion. Artificial intelligence such as machine learning (ML) and deep learning can assist in processing and interpreting biological datasets. In this study, we aggregated data from different studies based on the species composition and relative abundance of gut microbiota in children with autism spectrum disorder (ASD) and typically developed (TD) individuals and analyzed the commonalities and differences of ASD-associated microbiota across cohorts. We established a predictive model using an ML algorithm to explore the diagnostic value of the gut microbiome for the children with ASD and identify potential biomarkers for ASD diagnosis. The results indicated that the Shenzhen cohort achieved a higher area under the receiver operating characteristic curve (AUROC) value of 0.984 with 97% accuracy, while the Moscow cohort achieved an AUROC value of 0.81 with 67% accuracy. For the combination of the two cohorts, the average prediction results had an AUROC of 0.86 and 80% accuracy. The results of our cross-cohort analysis suggested that a variety of influencing factors, such as population characteristics, geographical region, and dietary habits, should be taken into consideration in microbial transplantation or dietary therapy. Collectively, our prediction strategy based on gut microbiota can serve as an enhanced strategy for the clinical diagnosis of ASD and assist in providing a more complete method to assess the risk of the disorder. [ABSTRACT FROM AUTHOR]

The human gut microbiota protects the host from invading pathogens and the overgrowth of indigenous opportunistic species via a process called colonization resistance. Here, we investigated the antagonistic activity of human gut bacteria towards Candida albicans , an opportunistic fungal pathogen that can cause severe infections in susceptible individuals. Coculture batch incubations of C. albicans in the presence of faecal microbiota from six healthy individuals revealed varying levels of inhibitory activity against C. albicans. 16S rRNA gene amplicon profiling of these faecal coculture bacterial communities showed that the Bifidobacteriaceae family, and Bifidobacterium adolescentis in particular, were most correlated with antagonistic activity against C. albicans. Follow-up mechanistic studies performed under anaerobic conditions confirmed that culture supernatants of Bifidobacterium species, particularly B. adolescentis , inhibited C. albicans in vitro. Fermentation acids (FA), including acetate and lactate, present in the bifidobacterial supernatants were important contributors to inhibitory activity. However, increasing the pH of both bacterial supernatants and mixtures of FA reduced their anti- Candida effects, indicating a combinatorial effect of prevailing pH and FA. This work, therefore, demonstrates potential mechanisms underpinning gut microbiome-mediated colonization resistance against C. albicans , and identifies particularly inhibitory components such as bifidobacteria and FA as targets for further study. [ABSTRACT FROM AUTHOR]

Recently, growing attention has focused on the impact of air pollution on gut microbiota as a possible mechanism by which air pollutant exposure increased the risk for chronic diseases, as evidenced by in vivo studies demonstrating important exposure-induced alterations in the diversity and relative abundance of gut bacterial taxa. This systematic review provides updated state-of-art findings of studies examining the impact of air pollution on the human gut microbiota. Databases PubMed, Scopus, and Web of Science were searched with the following strategy: "air poll*" AND "gut micro*" OR "intestinal micro*"; moreover, a total of 10 studies were included. Overall, there is the evidence that short-term and long-term exposure to air pollutants have the potential to alter the composition and diversity of gut microbiota; some studies also correlated air pollution exposure to adverse health effects (impaired fasting glucose, adverse pregnancy outcomes, and asthma attacks) via alterations in the composition and/or function of the gut microbiota. However, the evidence on this topic is still scarce, and large cohort studies are needed globally. [ABSTRACT FROM AUTHOR]

The human gut possesses millions of microbes that define a complex microbial community. The gut microbiota has been characterized as a vital organ forming its multidirectional connecting axis with other organs. This gut microbiota axis is responsible for host-microbe interactions and works by communicating with the neural, endocrinal, humoral, immunological, and metabolic pathways. The human gut microorganisms (mostly nonpathogenic) have symbiotic host relationships and are usually associated with the host’s immunity to defend against pathogenic invasion. The dysbiosis of the gut microbiota is therefore linked to various human diseases, such as anxiety, depression, hypertension, cardiovascular diseases, obesity, diabetes, inflammatory bowel disease, and cancer. The mechanism leading to the disease development has a crucial correlation with gut microbiota, metabolic products, and host immune response in humans. The understanding of mechanisms over gut microbiota exerts its positive or harmful impacts remains largely undefined. However, many recent clinical studies conducted worldwide are demonstrating the relation of specific microbial species and eubiosis in health and disease. A comprehensive understanding of gut microbiota interactions, its role in health and disease, and recent updates on the subject are the striking topics of the current review. We have also addressed the daunting challenges that must be brought under control to maintain health and treat diseases. [ABSTRACT FROM AUTHOR]

Aim: The aim was to evaluate the impact of intermittent fasting (IF) on human body mass index (BMI) and serum lipid profile thorough constructive rectification of gut microbiota. Methods and results: Fourteen healthy women and thirty-one men were included in the study. Their blood and fecal samples were collected before and at the end of the study. Blood parameters, anthropometric values, and gut microbiology were noted to investigate the impact of intermittent fasting (IF) on human gut microbiota and physiology. Our data revealed that IF reduces the body weight and improves blood lipid profile, such as increasing high-density lipoprotein (HDL) and decreasing total cholesterol, triglycerides, and low- and very low-density lipoprotein levels. IF also decreases culturable aerobic bacterial count and increased fungal count. It was also found that the gut metagenome is altered considerably after IF. The human fecal bacterial diversity exhibited significant changes in decreased overall bacterial population, increased bacterial diversity (alpha diversity), and promoted evenness within the bacterial population at the species level. Anti-inflammatory bacteria Lactobacillus and Bifidobacterium were favorably increased, while pathogenic bacteria were decreased. Conclusion: Collectively, these results indicated that IF could improve lipid profile and body weight in humans, and the potential mechanisms might be via regulating gut microbiota. Significance and impact of the study: We demonstrated for the first time that IF improved body weight and blood lipid profile, indicating that IF could mitigate gut microbiota in humans. [ABSTRACT FROM AUTHOR]

Aims: The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. Methods and results: A library of human faecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labelled aac (6′)‐Iao and rmtI, respectively. AAC(6′)‐Iao showed the highest identity of 48% to AAC(6′)‐Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6‐disubstituted 2‐DOS aminoglycosides, whereas AAC(6′)‐Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6′)‐Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. Conclusions: Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. Significance and Impact of Study: Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6′)‐Iao. This work would contribute to the in‐depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut. [ABSTRACT FROM AUTHOR]

Brewer's spent grain (BSG) solid residues are constituted by dietary fibre, protein, sugars, and polyphenols, which can have potential effects on human health. In this study, for the first time, the flours obtained from solid residues of solid-liquid extraction (SLE) and ohmic heating extraction (OHE) were applied throughout the gastrointestinal digestion simulation (GID), in order to evaluate their prebiotic potential and in vitro human gut microbiota fermentation. The results showed that the digestion of BSG flours obtained by the different methods lead to an increase throughout the GID of total phenolic compounds (SLE: from 2.27 to 7.20 mg gallic acid/g BSG—60% ethanol:water (v/v); OHE: 2.23 to 8.36 mg gallic acid/g BSG—80% ethanol:water (v/v)) and consequently an increase in antioxidant activity (ABTS—SLE: from 6.26 to 13.07 mg ascorbic acid/g BSG—80% ethanol:water (v/v); OHE: 4.60 to 10.60 mg ascorbic acid/g BSG—80% ethanol:water (v/v)—ORAC—SLE: 3.31 to 14.94 mg Trolox/g BSG—80% ethanol:water (v/v); OHE: from 2.13 to 17.37 mg Trolox/g BSG—60% ethanol:water (v/v)). The main phenolic compounds identified included representative molecules such as vanillic and ferulic acids, vanillin and catechin, among others being identified and quantified in all GID phases. These samples also induced the growth of probiotic bacteria and promoted the positive modulation of beneficial strains (such as Bifidobacterium spp. and Lactobacillus spp.) present in human faeces. Moreover, the fermentation by human faeces microbiota also allowed the production of short chain fatty acids (acetic, propionic, and butyric). Furthermore, previous identified polyphenols were also identified during fecal fermentation. This study demonstrates that BSG flours obtained from the solid residues of SLE and OHE extractions promoted a positive modulation of gut microbiota and related metabolism and antioxidant environment associated to the released phenolic compounds. [ABSTRACT FROM AUTHOR]

The last decade has been marked by an exponential increase in the number of publications on the physiological role of the normal human gut microbiota. The idea of a symbiotic relationship between the human organism and normal microbiota of its gastrointestinal tract has been firmly established as an integral part of the current biomedical paradigm. However, the type of this symbiosis varies from mutualism to parasitism and depends on the functional state of the host organism. Damage caused to the organism by external agents can lead to the emergence of conditionally pathogenic properties in the normal gut microbiota, mediated by humoral factors and affecting the outcome of exogenous exposure. Among the substances produced by symbiotic microbiota, there are an indefinite number of compounds with systemic toxicity. Some occur in the intestinal chyme in potentially lethal amounts in the case they enter the bloodstream quickly. The quick entry of potential toxicants is prevented by the intestinal barrier (IB), a set of structural elements separating the intestinal chyme from the blood. Hypothetically, severe damage to the IB caused by exogenous toxicants can trigger a leakage and subsequent systemic redistribution of toxic substances of bacterial origin. Until recently, the impact of such a redistribution on the outcome of acute exogenous poisoning remained outside the view of toxicology. The present review addresses causal relationships between the secondary dysfunction of the IB and complications of acute poisoning. We characterize acute systemic toxicity of such waste products of the normal gut microflora as ammonia and endotoxins, and demonstrate their involvement in the formation of such complications of acute poisoning as shock, sepsis, cerebral insufficiency and secondary lung injuries. The principles of assessing the functional state of the IB and the approaches to its protection in acute poisoning are briefly considered. [ABSTRACT FROM AUTHOR]

Functional symbiotic intestinal microbiota regulates immune defense and the metabolic processing of xenobiotics in the host. The aryl hydrocarbon receptor (AhR) is one of the transcription factors mediating host–microbe interaction. An in vitro static simulation of the human colon was used in this work to analyze the evolution of bacterial populations, the microbial metabolic output, and the potential induction of AhR transcriptional activity in healthy gut ecosystems. Fifteen target taxa were explored by qPCR, and the metabolic content was chromatographically profiled using SPME-GC-MS and UPLC-FLD to quantify short-chain fatty acids (SCFA) and biogenic amines, respectively. Over 72 h of fermentation, the microbiota and most produced metabolites remained stable. Fermentation supernatant induced AhR transcription in two of the three reporter gene cell lines (T47D, HepG2, HT29) evaluated. Mammary and intestinal cells were more sensitive to microbiota metabolic production, which showed greater AhR agonism than the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) used as a positive control. Some of the SCFA and biogenic amines identified could crucially contribute to the potent AhR induction of the fermentation products. As a fundamental pathway mediating human intestinal homeostasis and as a sensor for several microbial metabolites, AhR activation might be a useful endpoint to include in studies of the gut microbiota. [ABSTRACT FROM AUTHOR]

Non-bovine milks and its products have been reported to provide exceptional nutritional properties and have lower allergenicity compared to bovine milk. Non-bovine milks contain substantial quantities of oligosaccharides, proteins, fatty acids, vitamins, minerals, and bioactive peptides. Furthermore, bioactive compounds present in non-bovine milks have been reported to enhance the human body's defense system and modulate gut microbiota. As with bovine milk, the biochemical composition of non-bovine milks varies depending on the animal breed, age, season, feed type, and environmental conditions. This review investigated non-bovine milk from goat, sheep, camel, mare, and donkeys and their nutritional composition. Special emphasis has been given to the effects of non-bovine milks on the human gut microbiome and their contribution to well-being. Finally, the conclusion and future research directions on the evaluation of non-bovine milks on human gut microbiota are outlined. The results indicated that the non-bovine milks can be used to produce various dairy products which are an alternative to bovine milk. Furthermore, non-bovine milks have been reported to enhance health-promoting bacteria, while suppressing infection-causing bacteria in the human gut microbiota. Therefore, non-bovine milks should be promoted worldwide as a healthy alternative to conventional bovine milk and more critical research is needed to explore the optimal potential of non-bovine milks. • Non-bovine milk can be used to prepare different dairy products. • Nonbovine milk contained human analogous oligosaccharide profile. • Nonbovine milk foster the growth of human gut microbiota. • Nonbovine milk could be used to develop infant milk formula. [ABSTRACT FROM AUTHOR]

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. [Display omitted] [ABSTRACT FROM AUTHOR]

Xyloglucan (XyG) is a ubiquitous plant cell wall hemicellulose that is targeted by a range of syntenic, microheterogeneous xyloglucan utilization loci (XyGUL) in Bacteroidetes species of the human gut microbiota (HGM), including Bacteroides ovatus and B. uniformis. Comprehensive biochemical and biophysical analyses have identified key differences in the protein complements of each locus that confer differential access to structurally diverse XyG side chain variants. A second, nonsyntenic XyGUL was previously identified in B. uniformis, although its function in XyG utilization compared to its syntenic counterpart was unclear. Here, complementary enzymatic product profiles and bacterial growth curves showcase the notable preference of BuXyGUL2 surface glycan-binding proteins (SGBPs) to bind full-length XyG, as well as a range of oligosaccharides produced by the glycoside hydrolase family 5 (GH5_4) endo-xyloglucanase from this locus. We use isothermal titration calorimetry (ITC) to characterize this binding capacity and pinpoint the specific contributions of each protein to nutrient capture. The high-resolution structure of BuXyGUL2 SGBP-B reveals remarkable putative binding site conservation with the canonical XyG-binding BoXyGUL SGBP-B, supporting similar roles for these proteins in glycan capture. Together, these data underpin the central role of complementary XyGUL function in B. uniformis and broaden our systems-based and mechanistic understanding of XyG utilization in the HGM. [ABSTRACT FROM AUTHOR]

National screening programs use dried blood specimens to detect metabolic disorders or aberrant protein functions that are not clinically evident in the neonatal period. Similarly, gut microbiota metabolites and immunological acute-phase proteins may reveal latent immune aberrations. Microbial metabolites interact with xenobiotic receptors (i.e., aryl hydrocarbon and pregnane-X) to maintain gastrointestinal tissue health, supported by acute-phase proteins, functioning as sensors of microbial immunomodulation and homeostasis. The delivery (vaginal or cesarean section) shapes the microbial colonization, which substantially modulates both the immune system's response and mucosal homeostasis. This study profiled microbial metabolites of the kynurenine and tryptophan pathway and acute-phase proteins in 134 neonatal dried blood specimens. We newly established neonatal blood levels of microbial xenobiotic receptors ligands (i.e., indole-3-aldehyde, indole-3-butyric acid, and indole-3-acetamide) on the second day of life. Furthermore, we observed diverse microbial metabolic profiles in neonates born vaginally and via cesarean section, potentially due to microbial immunomodulatory influence. In summary, these findings suggest the supportive role of human gut microbiota in developing and maintaining immune system homeostasis. [ABSTRACT FROM AUTHOR]

Background: Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria. Results: To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease. Conclusions: The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut. [ABSTRACT FROM AUTHOR]

Background: New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results: Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions: Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations. [ABSTRACT FROM AUTHOR]

In vitro gut models, such as the mucosal artificial colon (M-ARCOL), provide timely and cost-efficient alternatives to in vivo assays allowing mechanistic studies to better understand the role of human microbiome in health and disease. Using such models inoculated with human fecal samples may require a critical step of stool storage. The effects of preservation methods on microbial structure and function in in vitro gut models have been poorly investigated. This study aimed to assess the impact of three commonly used preserving methods, compared with fresh fecal samples used as a control, on the kinetics of lumen and mucus-associated microbiota colonization in the M-ARCOL model. Feces from two healthy donors were frozen 48 h at − 80 °C with or without cryoprotectant (10% glycerol) or lyophilized with maltodextrin and trehalose prior to inoculation of four parallel bioreactors (e.g., fresh stool, raw stool stored at − 80 °C, stool stored at − 80 °C with glycerol and lyophilized stool). Microbiota composition and diversity (qPCR and 16S metabarcoding) as well as metabolic activity (gases and short chain fatty acids) were monitored throughout the fermentation process (9 days). All the preservative treatments allowed the maintaining inside the M-ARCOL of a complex and functional microbiota, but considering stabilization time of microbial profiles and activities (and not technical constraints associated with the supply of frozen material), our results highlighted 48 h freezing at − 80 °C without cryoprotectant as the most efficient method. These results will help scientists to determine the most accurate method for fecal storage prior to inoculation of in vitro gut microbiome models. Key points: • In vitro ARCOL model reproduces luminal and mucosal human microbiome. • Short-term storage of fecal sample influences microbial stabilization and activity. • 48 h freezing at − 80°C: most efficient method to preserve microbial ecosystem. • Scientific and technical requirements: influencers of preservation method. [ABSTRACT FROM AUTHOR]

Wheat bran is a cereal rich in dietary fibers that have high levels of ferulic acid, which has prebiotic effects on the intestinal microbiota and the host. Herein we explored the effect of xylooligosaccharide, xylan, and whole wheat bran on the human gut bacteria and screened for potential ferulic acid esterase genes. Using in vitro fermentation, we analyzed the air pressure, pH-value, and short-chain fatty acid levels. We also performed 16S rRNA gene and metagenomic sequencing. A Venn diagram analysis revealed that 80% of the core operational taxonomic units (OTUs) were shared among the samples, and most of the xylooligosaccharide treatment core OTUs (319/333 OTUs) were shared with the other two treatments' core OTUs. A significant difference analysis revealed that the relative abundance of Dorea , Bilophila , and Sulfurovum in wheat bran treatment was higher than that in xylan and xylooligosaccharide treatments. The clusters of orthologous groups of proteins functional composition of all samples was similar to the microbiota composition of the control. Using metagenomic sequencing, we revealed seven genes containing the conserved residues, Gly-X-Ser-X-Gly, and the catalytic triad, Ser-His-Asp, which are thus potential ferulic acid esterase genes. All the results indicate that xylan and/or xylooligosaccharide, the main dietary fibers in wheat bran, plays a major role in in vitro fermentation by the human gut microbiota. [ABSTRACT FROM AUTHOR]

Function of mulberry leaf (Morus alba L.) polysaccharide has been reported on antitumor, immunostimulatory and anti-inflammatory effects. However, the bioactivity on human gut microbiota is unclear so far. Here, three homogenous polysaccharides named SY01-21, SY01-22, SY01-23 were isolated from mulberry leaf with molecular weight 57 kDa, 25 kDa and 7.2 kDa, respectively. The monosaccharide composition of SY01-21 contained rhamnose, galactose and arabinose in a molar ratio of 7.60:43.52:48.88. SY01-22 contained rhamnose, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 14.61:9.06:1.35:34.65:2.99:37.34. SY01-23 contained rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 23.00:4.12:24.60:5.74:17.28:1.12:24.13. Bioactivity test showed SY01-21 promoted the growth of Bacteroides cellulosilyticus (BC) while SY01-22 benefited the growth of Bacteroides ovatus (BO). Interestingly, SY01-23 boosted the growth of both BO and BC. However, Bacteroides thetaiotamicron (BT) only grew on 5 mg/mL SY01-21. Intriguingly, the growth of co-culture of BT with BO or BC was better than monoculture. This suggested that cross-feeding might exist between them. Besides, we found BO and BC generated acetate and propionate by utilizing SY01-23. The above results suggested that SY01-23 might modify human gut microbiota by driving colonization of Bacteroides in the gut to improve wellness. [Display omitted] [ABSTRACT FROM AUTHOR]

1. Bupleuri Radix (BR) is a herbal medicine traditionally used orally in oriental countries, which inevitably comes into contact with the intestinal microbiota. However, whether gut microbiota contribute to the biotransformation of BR, and/or the formation of pharmacologically active compounds remains unknown. 2. In this study, the main saikosaponins (SAPs) of Bupleurum (including saikosaponin a, b1, b2, c, d, f, h) and BR extract (BRE) were individually incubated with human fecal suspensions (HFS), and metabolic time courses of SAPs and their metabolites by human gut bacteria were systematically characterized. 3. Deglycosylation and dehydration were the main metabolic pathways identified for SAPs including newly investigated saikosaponin f (SSf) and saikosaponin h (SSh); dehydration had not been reported previously. A total of 19 dehydrated and deglycosylated metabolites of SAPs were detected and characterized, and 10 of them were newly identified. Moreover, SAPs of BRE were found to be deglycosylated to prosaikogenins. In addition, 13 metabolic pathways related to human gut microbiota were identified for phytochemicals of BRE except for SAPs. Gut microbiota may play a significant role in the biotransformation of BR in humans. [ABSTRACT FROM AUTHOR]

A new fermented food by utilizing pineapple by-products and whey protein as the matrix via co-fermentation with strains of lactic acid bacteria and yeast is developed. We investigated its impact on human well-being, focusing on the bioavailability and physiological viability of the resulting pineapple–whey protein fermented product (PWF) under simulated human gastrointestinal conditions. We evaluated PWF's potential as a prebiotic using in vitro fermentation assays, revealing that its probiotic components effectively reached the colon and functioned without hindrance. This transit triggered significant release of phenolic compounds, establishing an antioxidant-rich environment during simulated digestion. In vitro fermentation experiments showcased PWF's capacity to induce short-chain fatty acid production in the intestines, alongside its ability to influence the microbial community composition. Additionally, we explored how PWF-induced alterations in the gut microbiota might impact human health. The results suggested that PWF could potentially enhance metabolic pathways in the intestinal microbiota, thereby fostering a more favorable microbial ecosystem. • The probiotics in pineapple–whey protein fermentation product could reach the colon. • The phenols and flavonoids in product were released during in vitro study. • The product could improve intestinal flora through in vitro digestive model. • The product could promote the production of short-chain fatty acids. • The product could promote the maintenance of a more favorable microbial ecosystem. [ABSTRACT FROM AUTHOR]

Background: Human gut microbiota are important for human health and have been regarded as a "forgotten organ", whose variation is closely linked with various factors, such as host genetics, diet, pathological conditions and external environment. The diversity of human gut microbiota has been correlated with aging, which was characterized by different abundance of bacteria in various age groups. In the literature, most of the previous studies of age-related gut microbiota changes focused on individual species in the gut community with supervised methods. Here, we aimed to examine the underlying aging progression of the human gut microbial community from an unsupervised perspective. Results: We obtained raw 16S rRNA sequencing data of subjects ranging from newborns to centenarians from a previous study, and summarized the data into a relative abundance matrix of genera in all the samples. Without using the age information of samples, we applied an unsupervised algorithm to recapitulate the underlying aging progression of microbial community from hosts in different age groups and identify genera associated to this progression. Literature review of these identified genera indicated that for individuals with advanced ages, some beneficial genera are lost while some genera related with inflammation and cancer increase. Conclusions: The multivariate unsupervised analysis here revealed the existence of a continuous aging progression of human gut microbiota along with the host aging process. The identified genera associated to this aging process are meaningful for designing probiotics to maintain the gut microbiota to resemble a young age, which hopefully will lead to positive impact on human health, especially for individuals in advanced age groups. [ABSTRACT FROM AUTHOR]

Gut microbiota has been shown to have an important influence on host health. The microbial composition of the human gut microbiota is modulated by diet and other lifestyle habits and it has been reported that microbial diversity is altered in obese people. Obesity is a worldwide health problem that negatively impacts the quality of life. Currently, the widespread treatment for obesity is bariatric surgery. Interestingly, gut microbiota has been shown to be a relevant factor in effective weight loss after bariatric surgery. Since that the human gut microbiota of normal subjects differs between geographic regions, it is possible that rearrangements of the gut microbiota in dysbiosis context are also region-specific. To better understand how gut microbiota contribute to obesity, this study compared the composition of the human gut microbiota of obese and lean people from six different regions and showed that the microbiota compositions in the context of obesity were specific to each studied geographic location. Furthermore, we analyzed the functional patterns using shotgun DNA metagenomic sequencing and compared the results with other obesity-related metagenomic studies, we observed that microbial contribution to functional pathways were country-specific. Nevertheless, our study showed that although microbial composition of obese patients was country-specific, the overall metabolic functions appeared to be the same between countries, indicating that different microbiota components contribute to similar metabolic outcomes to yield functional redundancy. Furthermore, we studied the microbiota functional changes of obese patients after bariatric surgery, by shotgun metagenomics sequencing and observed that changes in functional pathways were specific to the type of obesity treatment. In all, our study provides new insights into the differences and similarities of obese gut microbiota in relation to geographic location and obesity treatments. [ABSTRACT FROM AUTHOR]

• A 1,4-β-galactan, DOP0.1-S-1 was characterized from Dioscorea opposita. • DOP0.1-S-1 could promote the growth of B. thetaiotaomicron and B. ovatus. • Bacteroides spp. produced short-chain fatty acids by using DOP0.1-S-1. Dioscorea opposita Thunb. is widely used as functional foods and traditional Chinese medicine in China for its activity of regulating function of spleen and stomach. Polysaccharides may contribute to the function of regulation. To investigate structure features and bioactivities of polysaccharides from D. opposita, the rhizome of D. opposita was extracted with boiling water, yielding crude polysaccharides DOP. A novel polysaccharide named DOP0.1-S-1 was isolated from DOP by further purification. The average molecular weight of DOP0.1-S-1 was 10,000 Da and the range was around 12,000 –1,200 Da. The carbohydrate content of DOP0.1-S-1 was 100% and no protein was detected. The monosaccharide analysis showed that DOP0.1-S-1 was mostly composed of galactose. Methylation and NMR spectra analysis indicated that DOP0.1-S-1 was a 1,4-β-galactan. Bioactivity test showed that DOP0.1-S-1 could promote the growth of B. thetaiotaomicron and B. ovatus and produce the short-chain fatty acids during the utilization of the polysaccharide. [ABSTRACT FROM AUTHOR]

Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches. [ABSTRACT FROM AUTHOR]

The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application. [ABSTRACT FROM AUTHOR]

The gut microbiota composition and its metabolites have high impact on human health. Exploitation of prebiotics and probiotics for modulation of gut microbiota can lead to promising outcomes. This study aimed to evaluate the effects of the probiotic strain Bifidobacterium longum BB-46 alone and in combination with a citric pectin from lemon on the gut microbiota from healthy adults using the Simulator of Human Intestinal Microbial Ecosystem (SHIME®). Changes in microbiota composition and in metabolic activity were assessed by the 16S rRNA gene sequencing and by analyses of short-chain fatty acids (SCFAs) and ammonium ions (NH 4 +). An increase in the relative abundances of Firmicutes (especially the members of Lachnospiraceae and Lactobacillaceae families) and Bacteroidetes was observed during treatment with B. longum BB-46 alone in all compartments of the colon. Treatment with B. longum BB-46 and pectin stimulated an increase in the proportions of genera Faecalibacterium, Eubacterium and Lactobacillus , as well as in the Ruminococcaceae family in the transverse and descending colons. Concurrently, the butyrate levels increased in these two compartments. Additionally, the combination of B. longum BB-46 and pectin reduced the abundance of proteolytic bacteria Bacteroides , Clostridium, Peptoniphilus , and Streptococcus , along with decreased NH 4 + production. No significant changes could be observed on NH 4 + production by treatment with B. longum BB-46, nor did it increase the amount of SCFAs. In this study, we observed that although each treatment was able to modulate the microbiota, the combination of B. longum BB-46 and pectin was more efficient in decreasing the intestinal NH 4 + levels and in increasing butyric acid-producing bacteria. These findings indicate that B. longum BB-46, especially when combined with the specific citric pectin, might have beneficial impact on human health. Unlabelled Image • Citric pectin combined with probiotic BB-46 modulated the human gut microbiota. • Probiotic BB-46 modified the gut microbiota differently from BB-46 combined with pectin. • Citric pectin combined with BB-46 increased intestinal butyric acid production. • Citric pectin combined with BB-46 decreased intestinal ammonium ions production. [ABSTRACT FROM AUTHOR]

Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans , and Roseburia hominis , performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections. [ABSTRACT FROM AUTHOR]

In this study, we first investigated the survival of three probiotic strains, individually and combined with acerola by-product during simulated gastrointestinal conditions. Next, we investigated the effects of acerola by-product combined with Bifidobacterium longum BB-46 on a gut microbiota model (SHIME®). Chemical composition, total phenolic compounds, antioxidant activity of the acerola by-product and microbial counts, denaturing gradient gel electrophoresis (DGGE), ammonium ions ( NH4+ ) and short-chain fatty acids (SCFAs) analysis of the SHIME® samples were performed. Acerola by-product revealed high protein and fibre, reduced lipid contents, and showed to be an excellent source of total phenolic compounds with high in vitro antioxidant activity. A decreased amount of NH4+ in the ascending colon and an increase (p < .05) in SCFAs were observed in the three regions of colon during treatment with BB-46 and acerola by-product. BB-46 combined with acerola by-product showed positive effects on the gut microbiota metabolism in SHIME® model. [ABSTRACT FROM AUTHOR]

Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species. [ABSTRACT FROM AUTHOR]

Background: Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood. Results: In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms. Conclusions: Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T). [ABSTRACT FROM AUTHOR]

Background: The importance of the gut microbiota at the early stage of life and their longitudinal effect on host health have recently been well investigated. In particular, Bifidobacterium longum subsp. longum, a common component of infant gut microbiota, appears in the gut shortly after birth and can be detected there throughout an individual's lifespan. However, it remains unclear whether this species colonizes in the gut over the long term from early infancy. Here, we investigated the long-term colonization of B. longum subsp. longum by comparing the genotypes of isolates obtained at different time points from individual subjects. Strains were isolated over time from the feces of 12 subjects followed from early infancy (the first six months of life) up to childhood (approximately six years of age). We also considered whether the strains were transmitted from their mothers' perinatal samples (prenatal feces and postnatal breast milk). Results: Intra-species diversity of B. longum subsp. longum was observed in some subjects' fecal samples collected in early infancy and childhood, as well as in the prenatal fecal samples of their mothers. Among the highlighted strains, several were confirmed to colonize and persist in single individuals from as early as 90 days of age for more than six years; these were classified as long-term colonizers. One of the long-term colonizers was also detected from the corresponding mother's postnatal breast milk. Quantitative polymerase chain reaction data suggested that these long-term colonizers persisted in the subjects' gut despite the existence of the other predominant species of Bifidobacterium. Conclusions: Our results showed that several strains belonging to B. longum subsp. longum colonized in the human gut from early infancy through more than six years, confirming the existence of long-term colonizers from this period. Moreover, the results suggested that these strains persisted in the subjects' gut while co-existing with the other predominant bifidobacterial species. Our findings also suggested the importance of microbial-strain colonization in early infancy relative to their succession and showed the possibility that probiotics targeting infants might have longitudinal effects. Trial Registration: TRN: ISRCTN25216339. Date of registration: 11/03/2016. Prospectively registered. [ABSTRACT FROM AUTHOR]