Simulated Swine Digestion and Gut Microbiota Fermentation of Hydrolyzed Copra Meal.

This study aimed to compare the effects of hydrolyzed copra meal (HCM) inclusion at 1% on its in vitro digestibility and the microbiota and cecum fermentation using the gut microbiota of weaned swine, targeting microbial community and short-chain fatty acids (SCF). For this reason, three treatments were considered: control (no copra meal), 1% non-hydrolyzed copra meal (CM), and 1% HCM. Non-defatted copra meal was hydrolyzed and analyzed (reducing sugars and total carbohydrates) in our laboratory. For digestion, microbiota identification, and fermentation assays, fresh fecal samples from two weaned pigs (1 month old) were used. Three replicates of each treatment were employed. HCM was more digestible, with approximately 0.68 g of hydrolysate recovered after simulated digestion compared to 0.82 g of hydrolysate recovered from CM. This was shown by Scanning Electron Microscope (SEM) images. Also, the three swine shared the majority of microbial species identified at the phylum and family levels. There were no differences (p > 0.05) between treatments in the microbial community and SCFA during fermentation. However, higher Chao-1 and Shannon indexes were observed in CM and HCM treatments. HCM was also found to be capable of preserving Actinobacterota and Proteobacteria at the phylum level, while at the family level, both treatments may help Lactobacillaceae, Peptostreptococcaceae, Lachnospiraceae, and Ruminococcaceae survive in the long term. Also, there was a potential trend of increasing acetic acid and butyric acid in the CM and HCM treatments. While HCM shows promise in potentially modulating the gut microbiota of weaned swine, additional research is required to investigate the effects of higher doses of HCM on swine performance parameters.

Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort.

The association between the gut mycobiome and its potential influence on host metabolism in the Thai Cohort was assessed. Two distinct predominant enterotypes, Saccharomyces (Sa) and Aspergillus/Penicillium (Ap/Pe) showed differences in gut mycobiota diversity and composition. Notably, the Sa enterotype exhibited lower evenness and richness, likely due to the prevalence of Saccharomyces, while both enterotypes displayed unique metabolic behaviors related to nutrient metabolism and body composition. Fiber consumption was positively correlated with adverse body composition and fasting glucose levels in individuals with the Sa enterotype, whereas in the Ap/Pe enterotype it was positively correlated with fat and protein intake. The metabolic functional analysis revealed the Sa enterotype associated with carbohydrate metabolism, while the Ap/Pe enterotype involved in lipid metabolism. Very interestingly, the genes involved in the pentose and glucuronate interconversion pathway, such as polygalacturonase and L-arabinose-isomerase, were enriched in the Sa enterotype signifying a metabolic capacity for complex carbohydrate degradation and utilization of less common sugars as energy sources. These findings highlight the interplay between gut mycobiome composition, dietary habits, and metabolic outcomes within the Thai cohort studies.

Synergistic activity of Limosilactobacillus reuteri KUB-AC5 and water-based plants against Salmonella challenge in a human in vitro gut model.

A synbiotic is a combination of live microorganisms and specific substrates that are selectively utilized by host microorganisms, resulting in health benefits for the host. Previous studies have demonstrated the protective effects of L. reuteri KUB-AC5 against Salmonella infection in chicken and mouse models. The probiotic activity of L. reuteri KUB-AC5 in these hosts was influenced by nutritional supplements. Water-based plants contain significant amounts of carbohydrates, particularly dietary fiber and proteins, making them potential prebiotic substrates. In this study, four water-based plants (Ulva rigida, Caulerpa lentillifera, Wolffia globosa, and Gracillaria fisheri) were screened for their ability to support the growth of L. reuteri KUB-AC5. Under monoculture testing, U. rigida exhibited the highest capacity to support the growth of L. reuteri KUB-AC5 and the production of organic acids, including acetic acid, lactic acid, and propionic acid (p ≤ 0.05). In co-culture experiments, the synbiotic combination of U. rigida and L. reuteri KUB-AC5 demonstrated the potential to eliminate Salmonella Typhimurium DMST 48437 when inoculated at 104 CFU/mL within 9 h. The synbiotic activities of U. rigida and L. reuteri KUB-AC5 were further investigated using an in vitro human gut model. Compared to the probiotic treatment, the synbiotic combination of L. reuteri KUB-AC5 and U. rigida showed significantly higher levels of L. reuteri KUB-AC5 (5.1 log copies/mL) and a reduction of S. Typhimurium by 0.8 log (CFU/ml) after 24 h (p ≤ 0.05). Synbiotic treatment also significantly promoted the production of short-chain fatty acids (SCFAs), including butyric acid, propionic acid, and acetic acid, compared to prebiotic and probiotic treatments alone (p ≤ 0.05). Furthermore, the synbiotic formulation modulated the in vitro simulated gut microbiome, enhancing putatively beneficial gut microbes, including lactobacilli, Faecalibacterium, and Blautia. Our findings demonstrated that L. reuteri KUB-AC5, in combination with U. rigida, exhibited synergistic activity, as indicated by increased viability, higher anti-pathogenicity toward Salmonella, and the ability to modulate the gut microbiome.

Exploring Longitudinal Gut Microbiome towards Metabolic Functional Changes Associated in Atopic Dermatitis in Early Childhood.

Atopic dermatitis (AD) is a prevalent inflammatory skin disease that has been associated with changes in gut microbial composition in early life. However, there are limited longitudinal studies examining the gut microbiome in AD. This study aimed to explore taxonomy and metabolic functions across longitudinal gut microbiomes associated with AD in early childhood from 9 to 30 months of age using integrative data analysis within the Thai population. Our analysis revealed that gut microbiome diversity was not different between healthy and AD groups; however, significant taxonomic differences were observed. Key gut bacteria with short-chain fatty acids (SCFAs) production potentials, such as Anaerostipes, Butyricicoccus, Ruminococcus, and Lactobacillus species, showed a higher abundance in the AD group. In addition, metabolic alterations between the healthy and AD groups associated with vitamin production and host immune response, such as biosynthesis of menaquinol, succinate, and (Kdo)2-lipid A, were observed. This study serves as the first framework for monitoring longitudinal microbial imbalances and metabolic functions associated with allergic diseases in Thai children during early childhood.

Metabolic and inflammatory profiles, gut microbiota and lifestyle factors in overweight and normal weight young thai adults.

Obesity among young adults, especially those living in developing countries is increasing. A high body mass index (BMI) is one of the major causes of several diseases worldwide, constituting an important risk factor for non-communicable diseases (NCDs). Investigations describing the relationship between BMI, clinical and gut microbiota characteristics and lifestyle factors of overweight young adults, especially from Southeast Asian countries are limited. Metabolic and inflammatory biomarkers, fecal microbiota profiles and lifestyle factors were compared between overweight Thai young adults (n = 30, mean age 33 ± 9.48) and those with normal weight (n = 30, mean age 27 ±7.50). This study was registered with the Thai Clinical Trials Registry (TCTR20220204007). Health status including body composition, fasting glucose and insulin, lipid profiles, liver and kidney function, inflammatory biomarkers, blood pressure and fecal microbiota using 16S rRNA gene sequencing data was determined. Dietary intake was assessed using a 3-day dietary record and a food frequency questionnaire (FFQ), with physical activity levels compared using the international physical activity questionnaire (IPAQ). The overweight group had significantly higher BMI, waist-hip ratio, body fat mass, % body fat, skeletal mass, triglyceride level, C-reactive protein, insulin and blood pressure, with lower levels of high-density lipoprotein cholesterol (HDL-C) and blood urea nitrogen compared to the normal weight group. Significant differences in fecal microbiota composition at the family and genus levels were observed between the two groups. In our clinical setting, we also observed that unhealthy diets with high consumption of food rich in fat and sugar, processed meat and alcohol, and physical inactivity were associated with an increased prevalence of overweight in Thai young adults. Results provided the big picture of health and lifestyle characteristics of overweight young Thai people. Young adults should be encouraged to engage in health-promoting activities that maintain healthy bodyweight.

Efficacy of Triphala extracts on the changes of obese fecal microbiome and metabolome in the human gut model.

Triphala is a mixture of tree fruits obtained from Terminalia chebula, Terminalia bellerica, and Phyllanthus emblica. It is one of the Ayurveda medicinal recipes used to treat health diseases such as obesity. The chemical composition analysis of Triphala extracts obtained from an equal portion of three fruits was performed. The contents of total phenolic compounds (62.87 ± 0.21 mg gallic acid equivalent/mL), total flavonoids (0.24 ± 0.01 mg catechin equivalent/mL), hydrolyzable tannins (177.27 ± 10.09 mg gallotannin equivalent/mL), and condensed tannins (0.62 ± 0.11 mg catechin equivalent/mL) were observed in Triphala extracts. The 1 mg/mL of Triphala extracts was applied to batch culture fermentation which contained the feces from voluntarily obese female adults (body mass index of 35.0-40.0 kg/m2) for 24 h. The extraction of DNA and metabolites was each conducted on the samples obtained from batch culture fermentation within and without Triphala extracts treatment. The 16S rRNA gene sequencing and untargeted metabolomic analysis were carried out. There was no statistically significant difference between Triphala extracts and control treatments on the changes in microbial profiles (p-value <0.05). While the metabolomic analysis showed statistically significant differences of 305 up-regulated and 23 down-regulated metabolites in the treatment of Triphala extracts when compared with the control (p-value <0.05 and fold-change ≥2) belonging to 60 pathways. The pathway analysis revealed that Triphala extracts play an important role in the activation of phenylalanine, tyrosine and tryptophan biosynthesis. In this study, phenylalanine and tyrosine were identified metabolites which involve in the regulation of energy metabolism. The treatment of Triphala extracts possesses the induction of phenylalanine, tyrosine and tryptophan biosynthesis in fecal batch culture fermentation of obese adults and therefore it can be suggested as a probable herbal medicinal recipe for obesity treatment.

Comparative genomics-based probiotic relevance of Limosilactobacillus fermentum KUB-D18.

Limosilactobacillus fermentum KUB-D18 is a heterofermentative lactic acid bacterium that its potential probiotic relevance originally isolated from the chicken intestine. This study sequenced a whole-genome of L. fermentum KUB-D18 and annotated its genes and functions in relation to probiotic properties. As a result, the genome sequence of L. fermentum KUB-D18 approximately contained 2.02 Mbps with GC content of51.7%. After annotating the genome by integrated protein and pathway databases, 2,158 protein-encoding genes were majorly annotated for metabolisms of amino acids, carbohydrates and cofactors as well as vitamins which showed a versatile metabolic capability to gastrointestinal microhabitats. According to the comparative genome analysis of L. fermentum KUB-D18 and the other related strains, L. fermentum KUB-D18 showed common characteristics e.g., folate biosynthesis and bile salt hydrolase enzymes-related cholesterol lowering effect as well as a unique gene cluster involved in metabolism of l-ascorbic acid of L. fermentum KUB-D18. Taken together, L. fermentum KUB-D18 genome provides the genetic basis towards cellular capability for further elucidating the functional mechanisms of its probiotic properties. This study serves for designing desirable targets for the development of probiotic foods and feeds.

Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5.

Limosilactobacillus reuteri KUB-AC5 displays the hallmark features of probiotic properties for food and feed industries. Optimization of cultivation condition for the industrial production is important to reach cell concentration and cost reduction. Considering the strain-specific growth physiology, metabolic capability, and essential nutrients of L. reuteri KUB-AC5, the genome-scale metabolic model (GSMM) of L. reuteri KUB-AC5 was developed. Hereby, the GSMM of iTN656 was successfully constructed which contained 656 genes, 831 metabolites, and 953 metabolic reactions. The iTN656 model could show a metabolic capability under various carbon sources and guide potentially 14 essential single nutrients (e.g., vitamin B complex and amino acids) and 2 essential double nutrients (pairwise glutamine-glutamate and asparagine-aspartate) for L. reuteri KUB-AC5 growth through single and double omission analysis. Promisingly, the iTN656 model was further integrated with transcriptome data suggesting that putative metabolic routes as preferable paths e.g., sucrose uptake, nucleotide biosynthesis, urea cycle, and glutamine transporter for L. reuteri KUB-AC5 growth. The developed GSMM offers a powerful tool for multi-level omics analysis, enabling probiotic strain optimization for biomass overproduction on an industrial scale.

In vitro gastrointestinal digestion of Lentinus squarrosulus powder and impact on human fecal microbiota.

Humans have long-used mushrooms as food and medicine, but digestion and colonic fermentation of most mushrooms, including Lentinus squarrosulus is markedly unknown. Here, nutritional profile, digestion and colonic fermentation of L. squarrosulus powder (LP) were determined. The powder contained mainly carbohydrate and protein. SEM and F-TIR analysis of the resistant hydrolysate (RH) revealed that the structure and ratio of carbohydrate and protein components were altered, and released known immunomodulation agents; beta-glucans and mannose. Both LP and RH promoted selected probiotic bacteria, especially Bifidobacterium strains. Using fecal microbiota of five volunteers (V1, V2, V3, V4 and V5), RH stimulated the microbiota of all used volunteers, via decreasing the ratio of Firmicutes/Bacteroidetes ranging from 1.3 to 8.2 times. Also, RH increased the relative abundance of vital immunomodulators; Bacteroides, Bifidobacterium, Clostridium cluster XIVa and IV, and Sutterella. Additionally, RH fermentation enriched the content of branch-chain fatty acids (BCFA) and short-chain fatty acids (SCFA), indicating protein and carbohydrate usage. Notably, propionic and butyric acids were abundant in V1, V2 and V3, while in V4 and V5, acetic and butyric acids were most enriched. Suggesting L. squarrosulus as functional mushroom to improve health and prevent diseases by enhancing gut health.

Selection of potential probiotics with cholesterol-lowering properties for probiotic yoghurt production.

From 61 lactic acid bacteria (LAB) isolates, three had good cholesterol-lowering properties, with Limosilactobacillus fermentum KUB-D18 having the highest cholesterol assimilation (68.75%) (51 µg/109 CFU). In addition, Lactiplantibacillus pentosus HM04-25 and L. pentosus HM04-3 had the two highest levels of bile salt hydrolase (BSH) activity (22.60 and 21.45 U/mL, respectively). These three strains could resist four antibiotics (aztreonam, vancomycin, teicoplanin, and nalidixic). However, fortunately, they contained no mobile antibiotic resistance genes. To evaluate the influence of probiotic strains in yoghurt production, L. fermentum KUB-D18, L. pentosus HM04-25, or L. pentosus HM04-3 were simultaneously cultured with commercial yoghurt starter (YF-L812) and incubated at 43 °C for 6 h. During yoghurt fermentation, the total bacteria in the yoghurt tended to increase from 7.39 to 8.90 log CFU/mL. The growth rates of two probiotic strains (L. pentosus HM04-25 and L. pentosus HM04-3) were stable at 6.06 to 6.62 log CFU/mL. Only the rate for L. fermentum KUB-D18 increased (to 7.5 log CFU/mL). These three probiotics did not affect the physical characteristics of yoghurt. The total soluble solids, pH, and titratable acidity values of the probiotic yoghurts were similar to the control yoghurt at 30°Brix, 4.91, and 0.90%, respectively. The firmness values of the probiotic yoghurts and the control were not significantly different (p > 0.05). Differentiation of the appearance of color, odor, flavor, and texture between the control yoghurt and the probiotic yoghurts was investigated using 56 volunteers and no significant differences were identified. Additionally, sensory evolution revealed that the acceptability of the probiotic yoghurts was higher than for the control (p ≤ 0.05). Therefore, the three probiotic strains with cholesterol-lowering properties had potential in future yoghurt production.

Analyzing Predominant Bacterial Species and Potential Short-Chain Fatty Acid-Associated Metabolic Routes in Human Gut Microbiome Using Integrative Metagenomics.

Gut microbiome plays an essential role in host health, and there is interest in utilizing diet to modulate the composition and function of microbial communities. Copra meal hydrolysate (CMH) is commonly used as a natural additive to enhance health. However, the gut microbiome is largely unknown at species level and is associated with metabolic routes involving short-chain fatty acids (SCFAs). In this study, we aimed to analyze, using integrative metagenomics, the predominant species and metabolic routes involved in SCFAs production in the human gut microbiome after treatment with CMH. The effect of CMH treatment on the Thai gut microbiome was demonstrated using 16S rRNA genes with whole-metagenome shotgun (WMGS) sequencing technology. Accordingly, these results revealed that CMH has potentially beneficial effects on the gut microbiome. Twelve predominant bacterial species, as well as their potential metabolic routes, were involved in cooperative microbiome networks under sugar utilization (e.g., glucose, mannose, or xylose) and energy supply (e.g., NADH and ATP) in relation to SCFAs biosynthesis. These findings suggest that CMH may be used as a potential prebiotic diet for modulating and maintaining the gut microbiome. To our knowledge, this is the first study to reveal the predominant bacterial species and metabolic routes in the Thai gut microbiome after treatment with potential prebiotics.

Integrative growth physiology and transcriptome profiling of probiotic Limosilactobacillus reuteri KUB-AC5.

Limosilactobacillus reuteri KUB-AC5 has been widely used as probiotic in chicken for Salmonella reduction. However, a preferable carbon source and growth phase is poorly characterized underlying metabolic responses on growth and inhibition effects of L. reuteri KUB-AC5. This study therefore aimed to investigate transcriptome profiling of L. reuteri KUB-AC5 revealing global metabolic responses when alteration of carbon sources and growth phases. Interestingly, L. reuteri KUB-AC5 grown under sucrose culture showed to be the best for fast growth and inhibition effects against Salmonella Enteritidis S003 growth. Towards the transcriptome profiling and reporter proteins/metabolites analysis, the results showed that amino acid transport via ABC systems as well as sucrose metabolism and transport are key metabolic responses at Logarithmic (L)-phase of L. reuteri KUB-AC5 growth. Considering the Stationary (S)-phase, we found the potential reporter proteins/metabolites involved in carbohydrate metabolism e.g., levansucrase and levan. Promisingly, levansucrase and levan were revealed to be candidates in relation to inhibition effects of L. reuteri KUB-AC5. Throughout this study, L. reuteri KUB-AC5 had a metabolic control in acclimatization to sucrose and energy pools through transcriptional co-regulation, which supported the cell growth and inhibition potentials. This study offers a perspective in optimizing fermentation condition through either genetic or physiological approaches for enhancing probiotic L. reuteri KUB-AC5 properties.

A randomized trial to evaluate the impact of copra meal hydrolysate on gastrointestinal symptoms and gut microbiome.

The impact of copra meal hydrolysate (CMH) on gut health was assessed by conducting a double-blinded, placebo-controlled study. Sixty healthy adult participants, aged 18-40 years were assigned to daily consume 3 g of CMH, 5 g of CMH or placebo in the form of drink powder for 21 days. Consumption of CMH at 3 g/d improved defecating conditions by reducing stool size and also relieved flatulence and bloating symptoms. Fecal samples were collected serially at the baseline before treatment, after the treatment and after a 2-week washout period. The gut microbiomes were similar among the treatment groups, with microbial community changes observed within the groups. Intake of CMH at 3 g/d led to increase microbial diversity and richness. Reduction of the ratio between Firmicutes to Bacteroidetes was observed, although it was not significantly different between the groups. The 3 g/d CMH treatment increased beneficial microbes in the group of fiber-degrading bacteria, especially human colonic Bacteroidetes, while induction of Bifidobacteriaceae was observed after the washout period. Intake of CMH led to increase lactic acid production, while 3 g/d supplement promoted the present of immunoglobulin A (IgA) in stool samples. The 3 g daily dose of CMH led to the potentially beneficial effects on gut health for healthy individuals.

ITS2 Sequencing and Targeted Meta-Proteomics of Infant Gut Mycobiome Reveal the Functional Role of Rhodotorula sp. during Atopic Dermatitis Manifestation.

Association between the gut mycobiome and atopic dermatitis was investigated in 9-12-month-old infants using metagenomics. Two groups of atopic dermatitis infants were classified according to their symptom development as outgrown (recovered) and persisted (still undergoing). The evenness and diversity of the mycobiome in the persisted group were higher than in the healthy and outgrown groups. Dysbiosis of the microbiome in the persisted group was observed by a reduction in the Ascomycota/Basidiomycota ratio. Five fungi were selected as markers from each sample group. In the persisted group, Rhodotorula sp. abundance increased significantly, while Wickerhamomyces sp. and Kodamaea sp. abundance increased in the healthy group, and Acremonium sp. and Rhizopus sp. abundance increased considerably in the outgrown group. Metaproteomic analysis revealed that the persisted group had a high abundance of fungal proteins, particularly those from Rhodotorula sp. Unique proteins such as RAN-binding protein 1 and glycerol kinase from Rhodotorula sp. were hypothesized to be related to atopic dermatitis manifestation in infants.

Anti-inflammatory Effect of Probiotic Limosilactobacillus reuteri KUB-AC5 Against Salmonella Infection in a Mouse Colitis Model.

Acute non-typhoidal salmonellosis (NTS) caused by Salmonella enterica Typhimurium (STM) is among the most prevalent of foodborne diseases. A global rising of antibiotic resistance strains of STM raises an urgent need for alternative methods to control this important pathogen. Major human food animals which harbor STM in their gut are cattle, swine, and poultry. Previous studies showed that the probiotic Limosilactobacillus (Lactobacillus) reuteri KUB-AC5 (AC5) exhibited anti-Salmonella activities in chicken by modulating gut microbiota and the immune response. However, the immunobiotic effect of AC5 in a mammalian host is still not known. Here, we investigated the anti-Salmonella and anti-inflammatory effects of AC5 on STM infection using a mouse colitis model. Three groups of C57BL/6 mice (prophylactic, therapeutic, and combined) were fed with 109 colony-forming units (cfu) AC5 daily for 7, 4, and 11 days, respectively. Then, the mice were challenged with STM compared to the untreated group. By using a specific primer pair, we found that AC5 can transiently colonize mouse gut (colon, cecum, and ileum). Interestingly, AC5 reduced STM gut proliferation and invasion together with attenuated gut inflammation and systemic dissemination in mice. The decreased STM numbers in mouse gut lumen, gut tissues, and spleen possibly came from longer AC5 feeding duration and/or the combinatorial (direct and indirect inhibitory) effect of AC5 on STM. However, AC5 attenuated inflammation (both in the gut and in the spleen) with no difference between these three approaches. This study demonstrated that AC5 confers both direct and indirect inhibitory effects on STM in the inflamed gut.

Two-stage processing for xylooligosaccharide recovery from rice by-products and evaluation of products: Promotion of lactic acid-producing bacterial growth and food application in a high-pressure process.

In this study, we attempted to maximize arabinoxylan conversion into xylooligosaccharide (XOS) from rice husk and rice straw using two saccharification processes and evaluate the promotion of lactic acid-producing bacterial growth, including an investigation of the role of prebiotics in protecting probiotic bacteria in rice drink products in a high-pressure process (HPP). Hydrothermal treatment followed by enzymatic hydrolysis was designed for XOS recovery from rice husk arabinoxylan (RH-AX) and rice straw arabinoxylan (RS-AX). The hydrothermal treatment performed at 170 °C for 20 min and 180 °C for 10 min was the optimal condition to produce XOS liquor from rice husk and rice straw, respectively. Pentopan mono BG successfully recovered XOS from rice husk and rice straw residues at 50 °C, pH 5.5, an enzyme concentration of 50 U and 100 U/g substrate for 24 h. This design converted 92.17 and 88.34% (w/w) of initial RH-AX and RS-AX into saccharides, which comprised 64.01 and 59.52% of the XOS content, respectively. Rice husk xylooligosaccharide (RH-XOS) and rice straw xylooligosaccharide (RS-XOS) had degrees of polymerization ranging from 2 to 6 with some arabino-xylooligosaccharides. RH-XOS and RS-XOS were used to examine the promotion of the growth of lactic acid-producing bacteria strains in the presence of other prebiotics. RH-XOS and RS-XOS strongly promoted the growth of Lactobacillus sakei and Lactobacillus brevis, while other species showed weak to moderate growth. This study represents the first report of the powerful effect of Lactococcus lactis KA-FF1-4 on altering the utilization of XOS but not xylose. Furthermore, for the first time, we reported the capability of XOS to protect probiotics in rice drinks under high-pressure conditions. RH-XOS and RS-XOS resulted in the highest viability of approximately 11 log cfu/mL and exhibited no significant difference compared with the non-HPP treatment. Hence, rice husk and rice straw can be utilized as alternative prebiotic sources that provide biological activity and food applications in the HPP industry.

Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults.

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.

Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.

Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics.

The infant gut microbiome consists of a complex and diverse microbial community. Comprehensive taxonomic and metabolic functional knowledge about microbial communities supports medical and biological applications, such as fecal diagnostics. Among the omics approaches available for the investigation of microbial communities, metaproteomics-based analysis is a very powerful approach; under this method, the activity of microbial communities is explored by investigating protein expression within a sample. Through use of metaproteomics, this study aimed to investigate the microbial community composition of the infant gut to identify different key proteins playing metabolic functional roles in the microbiome of healthy infants and infants with atopic dermatitis in a Thai population-based birth cohort. Here, 18 fecal samples were analyzed by liquid chromatography-tandem mass spectrometry to conduct taxonomic, functional, and pathway-based protein annotation. Accordingly, 49,973 annotated proteins out of 68,232 total proteins were investigated in gut microbiome samples and compared between the healthy and atopic dermatitis groups. Through differentially expressed proteins (DEPs) analysis, 130 significant DEPs were identified between the healthy and atopic dermatitis groups. Among these DEPs, eight significant proteins were uniquely expressed in the atopic dermatitis group. For instance, triosephosphate isomerase (TPI) in Bifidobacteriaceae in the genus Alloscardovia and demethylmenaquinone methyltransferase (DMM) in Bacteroides were shown to potentially play metabolic functional roles related to disease. PPI network analysis revealed seven reporter proteins showing metabolic alterations between the healthy and disease groups associated with the biosynthesis of ubiquinone and other quinones as well as the energy supply. This study serves as a scaffold for microbial community-wide metabolic functional studies of the infant gut microbiome in relation to allergic disease.

Lactococcus lactis KA-FF 1-4 reduces vancomycin-resistant enterococci and impacts the human gut microbiome.

Probiotic is an alternative method to treat intestinal infection disease caused by antibiotic-resistant bacteria. In this study, Lactococcus lactis KA-FF 1-4 demonstrated to have the potential to inhibit the growth of Vancomycin-resistant enterococci (VRE) by producing anti-microbial substance. In co-culture, L. lactis KA-FF 1-4 (108 CFU/mL) inhibited the growth of VRE from 103-104 CFU/mL to zero after 6 h of exposure. However, in a gut model contained human gut microbiota, this anti-VRE activity of L. lactis KA-FF 1-4 was reduced to only 3.59-6.12%. The unexpected difference in efficacy between the experimental models could be explained by the fact that the growth of L. lactis KA-FF 1-4 was stable in the gut model. Leaving aside these limitations, we observed that adding L. lactis KA-FF 1-4 into the human gut model containing VRE was able to enhance microbial richness and diversity. Specifically, a higher abundance of beneficial microbes from the group of Bifidobacterium spp. and Bacteroides fragilis. L. lactis KA-FF 1-4 also enhanced the abundance of Parabacteroides, Lactococcus, and Fusobacterium and promoted the production of lactic acid in the gut model. However, these effects were not observed in the gut model without L. lactis KA-FF 1-4. Even though this study could not demonstrate a significant anti-VRE effect of the L. lactis KA-FF 1-4 in a gut model, our results still offer evidence that L. lactis KA-FF 1-4 could positively modulate the gut microbiota by promoting the growth of beneficial microbes and their metabolite. L. lactis KA-FF 1-4 has probiotic properties to fight against VRE infection, therefore further investigation in animal model is needed.