MetaCyc Database Research Articles

Full-length 16S rRNA gene amplicon analysis of gut microbiota in pigs fed with different diets in growing and finishing stages

The present study utilized full-length 16S rRNA gene sequencing to investigate the impact of dietary protein content on the composition and function of gut microbiota, and to analyze the gut microbiota of pigs in the growing (30 kg) and finishing (120 kg) stages under different feeding conditions. The results indicated that the gut microbiota was significantly different between pigs fed high- and low-protein diets. Comparing fecal samples from pigs at 30 and 120 kg, pigs at 30 kg showed a significant increase in the relative abundance of Clostridium butyricum, whereas at 120 kg, the abundance of Lactobacillus reuteri and Lactobacillus johnsonii decreased. To access the functional profiles and metabolic pathways based on amplicon sequence variants (ASVs), the microbiome of the 120 kg exhibited significant enrichments in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to metabolism-related category, including Alanine, aspartate and glutamate metabolism, Tyrosine and Thiamin metabolism, and Inositol phosphate metabolism. Meanwhile, analysis using the MetaCyc database showed that the metabolic pathways of the 30 kg group were significantly distinct when compared to the 120 kg of fecal samples. Overall, the findings indicated that the gut microbiota composition and function in the 30 and 120 kg fecal samples were markedly shaped by different dietary protein levels.

Effect of Dietary Benzoic Acid Supplementation on Growth Performance, Rumen Fermentation, and Rumen Microbiota in Weaned Holstein Dairy Calves

Supplementation with benzoic acid (BA) in animal feed can reduce feeds’ acid-binding capacity, inhibit pathogenic bacterial growth, enhance nutrient digestion, and increase intestinal enzyme activities. This study aimed to investigate the effects of different doses of BA on the growth performance, rumen fermentation, and rumen microbiota of weaned Holstein dairy calves. Thirty-two Holstein calves at 60 days of age were randomly assigned into four groups (n = 8): a control group (fed with a basal diet without BA supplementation; CON group) and groups that were supplemented with 0.25% (LBA group), 0.50% (MBA group), and 0.75% (HBA group) BA to the basal diet (dry matter basis), respectively. The experiment lasted for 42 days, starting at 60 days of age and ending at 102 days of age, with weaning occurring at 67 days of age. Supplementation with BA linearly increased the average daily gain of the weaned dairy calves, which was significantly higher in the LBA, MBA, and HBA groups than that in the CON group. The average daily feed intake was quadratically increased with increasing BA supplementation, peaking in the MBA group. Supplementation with BA linearly decreased the feed-to-gain (F/G) ratio, but did not affect rumen fermentation parameters, except for the molar proportion of butyrate and iso-butyrate, which were linearly increased with the dose of BA supplementation. Compared with the CON group, the molar proportions of iso-butyrate in the LBA, MBA, and HBA groups and that of butyrate in the HBA group were significantly higher than those in the CON group. Supplementation with BA had no significant effect on the alpha and beta diversity of the rumen microbiota, but significantly increased the relative abundances of beneficial bacteria, such as Bifidobacterium, and reduced those of the harmful bacteria, such as unclassified_o__Gastranaerophilales and Oscillospiraceae_UCG-002, in the rumen. Functional prediction analysis using the MetaCyc database revealed significant variations in the pathways associated with glycolysis across groups, including the GLYCOLYSIS-TCA-GLYOX-BYPASS, GLYCOL-GLYOXDEG-PWY, and P105-PWY pathways. In conclusion, BA supplementation improved the composition and function of rumen microbiota, elevated the production of butyrate and iso-butyrate, and increased the growth performance of weaned Holstein dairy calves.

Novel screening approach for cancer cachexia using metagenomic gut microbiome profiling in patients with advanced non-small cell lung cancer.

12090 Background: Cancer cachexia (CC) is a multifactorial syndrome involving immune-metabolic crosstalk across multiple organs and has been associated with a negative clinical impact in patients with non-small cell lung cancer (NSCLC) amenable to immune checkpoint inhibitors (ICIs). In parallel, the gut microbiome (GM) has emerged as a key contributor to ICI response. In this study, we aimed to evaluate the association between CC and GM composition and its metabolic potentials. Methods: We collected fecal samples from 139 patients with advanced NSCLC treated with ICI. In addition to 16S rRNA sequencing for all patients, shotgun metagenomic microbiome profiling was performed for 69 patients to estimate the species-level composition and functional capacity of the GM. Cancer cachexia was diagnosed according to the international consensus based on the body weight changes over the previous six months. Survival time was calculated using the Kaplan-Meier method. GM diversity indices, differential abundance, and functional profiles based on the MetaCyc database were compared between the patients with and without CC. Results: Median progression-free survival (PFS) and overall survival (OS) were significantly shorter in the cachexia group compared to the non-cachexia group [4.5 vs. 11.5 months (p < 0.001) and 10.8 vs. 44.9 months (p < 0.01), respectively]. Both GM profiling techniques revealed a significant difference in beta diversity between both groups (p < 0.01). In addition, metagenomic analyses revealed the distinct characteristics of GM at the species level between the groups. The CC group showed an overrepresentation of the commensal bacteria, such as Escherichia coli, Ruthenibacterium lactatiformans, Hungatella hathewayi,and Eggerthella lenta, whereas the non-CC group showed an enrichment of Parabacteroides distasonis, Eubacterium rectale,and Roseburia inulinivorans. Moreover, functional analysis revealed the significantly different metabolic potentials of GM in the CC group. The CC group showed an enrichment of pathways, such as D-arabinose degradation II, L-lysine degradation, and octan oxidation. Finally, the clustering of patients based on significant metabolic pathways or gene reactions provided a high predictive ability to discriminate between patients with and without CC. Conclusions: The shotgun metagenomic approach allowed for the characterization of the altered gut microbes and their metabolic potentials in patients with CC. Stratification based on the GM profiles may be useful as a novel screening method for CC, which is progressive and may involve more multistage pathology than identified by the conventional approach.

Metformin-induced changes of the gut microbiota in patients with type 2 diabetes mellitus: results from a prospective cohort study.

The influence of the microbiota on hypoglycemic agents is becoming more apparent. The effects of metformin, a primary anti-diabetes drug, on gut microbiota are still not fully understood. This prospective cohort study aims to investigate the longitudinal effects of metformin on the gut microbiota of 25 treatment-naïve diabetes patients, each receiving a daily dose of 1500 mg. Microbiota compositions were analyzed at baseline, and at 1, 3, and 6 months of medication using 16S rRNA gene sequencing. Prior to the 3-month period of metformin treatment, significant improvements were noted in body mass index (BMI) and glycemic-related parameters, such as fasting blood glucose (FPG) and hemoglobin A1c (HbA1c), alongside homeostasis model assessment indices of insulin resistance (HOMA-IR). At the 3-month mark of medication, a significant reduction in the α-diversity of the gut microbiota was noted, while β-diversity exhibited no marked variances throughout the treatment duration. The Firmicutes to Bacteroidetes ratio. markedly decreased. Metformin treatment consistently increased Escherichia-Shigella and decreased Romboutsia, while Pseudomonas decreased at 3 months. Fuzzy c-means clustering identified three longitudinal trajectory clusters for microbial fluctuations: (i) genera temporarily changing, (ii) genera continuing to decrease (Bacteroides), and (iii) genera continuing to increase(Lachnospiraceae ND3007 group, [Eubacterium] xylanophilum group, Romboutsia, Faecalibacterium and Ruminococcaceae UCG-014). The correlation matrix revealed associations between specific fecal taxa and metformin-related clinical parameters HbA1c, FPG, Uric Acid (UA), high-density lipoproteincholesterol (HDL-C), alanine aminotransferase (ALT), hypersensitive C-reactive protein (hs-CRP), triglyceride (TG) (P < 0.05). Metacyc database showed that metformin significantly altered 17 functional pathways. Amino acid metabolism pathways such as isoleucine biosynthesis predominated in the post-treatment group. Metformin's role in glucose metabolism regulation may primarily involve specific alterations in certain gut microbial species rather than an overall increase in microbial species diversity. This may suggest gut microbiota targets in future studies on metabolic abnormalities caused by metformin.

Characteristics and metabolic potential of biliary microbiota in patients with giant common bile duct stones.

Endoscopic retrograde cholangiopancreatography (ERCP) is an effective minimally invasive operation for the management of choledocholithiasis, while successful extraction is hampered by large diameter of stones. Emerging studies have revealed the close correlation between biliary microbiota and common bile duct stones (CBDS). In this study, we aimed to investigate the community characteristics and metabolic functions of biliary microbiota in patients with giant CBDS. Eligible patients were prospectively enrolled in this study in First Affiliated Hospital of Soochow University from February 2022 to October 2022. Bile samples were collected through ERCP. The microbiota was analyzed using 16S rRNA sequencing. Metabolic functions were predicted by PICRUSTs 2.0 calculation based on MetaCyc database. Bile acids were tested and identified using ultra performance liquid chromatography-tandem mass spectrometry. A total of 26 patients were successfully included into final analysis, 8 in giant stone (GS) group and 18 in control group. Distinct biliary microbial composition was identified in patients with giant CBDS, with a significantly higher abundance of Firmicutes at phylum level. The unique composition at genus level mainly consisted of Enterococcus, Citrobacter, Lactobacillus, Pyramidobacter, Bifidobacterium and Shewanella. Pyramidobacter was exclusively found in GS group, along with the absence of Robinsoniella and Coprococcus. The contents of free bile acids were significantly higher in GS group, including cholic acid (98.39μmol/mL vs. 26.15μmol/mL, p=0.035), chenodesoxycholic acid (54.69μmol/mL vs. 5.86μmol/mL, p=0.022) and ursodeoxycholic acid (2.70μmol/mL vs. 0.17μmol/mL, p=0.047). Decreasing tendency of conjugated bile acids were also observed. Metabolic pathways concerning cholelithiasis were abundant in GS group, including geranylgeranyl diphosphate biosynthesis, gluconeogenesis, glycolysis and L-methionine biosynthesis. This study demonstrated the community structure and metabolic potential of biliary microbiota in patients with giant CBDS. The unique biliary microbial composition holds valuable predictive potential for clinical conditions. These findings provide new insights into the etiology of giant CBDS from the perspective of biliary microbiota.

THU075 Sex And Age Specificity Of Correlations Among IGF-1, GH, And Duodenal Microbial Diversity Predicting TMA Biosynthesis

Abstract Disclosure: N. Tal: None. G. Leite: None. G. Barlow: None. W. Morales: None. R. de Souza Santos: None. M. Pimentel: None. R. Mathur: None. Varied gut microbial profiles and functional potentials may increase or decrease cardiovascular (CVD) disease risk. Trimethylamine (TMA), a known bacterial metabolite associated with red meat ingestion, is linked to increased CVD risk and morbidity through its liver-transformed form trimethylamine N-oxide (TMAO). As the somatotroph axis is also linked both to the microbiome and CVD morbidity, we explored the relationships between the duodenal microbiome, microbial pathways, IGF-1 and GH levels. Methods: Female (F) and male (M) subjects undergoing upper endoscopy without colon prep were enrolled and completed a medical history including CV conditions and risk factors such as exercise and diet. Whole blood was collected and duodenal aspirates obtained using a double lumen sterile catheter. Microbial DNA was extracted and 16S sequenced. Analyses were performed with CLC Microbial Module. Predicted pathways were identified using MetaCyc Database. Fasting circulating GH, IGF-1 (Luminex FLEXMAP) and cholesterol fractions (Cobas 400) were measured. Results: 177 subjects were grouped by age (sex and BMI, P=NS): 18-35yrs (N=21, F=11), 36-50yrs (N=29, F=15), 51-65yrs (N=69, F=38) and 66-80yrs (N=58, F=28). IGF-1 levels gradually decreased in older subjects (P&amp;lt;0.0001). In older M (66-80yrs), GH correlated positively with IGF-1 (R=0.371, P=0.044) and negatively with duodenal microbial diversity (R=-0.517, P=0.003). M and F had similar CVD risks (hypertension, smoking, exercise habits, obesity, LDL levels and weekly red meat consumption [P=NS for all]). In M only: 1) GH levels correlated with overall number of CV conditions (R=0.339, P=0.001), 2) Red meat consumption correlated with GH (R=0.353, P=0.002) and predicted microbial TMA biosynthesis from L-carnitine (R=0.272, P=0.009), and 3) Higher IGF-1 correlated with predicted microbial TMA production from L-carnitine (R=0.208, P=0.05) and predicted microbial conversion of TMA to TMAO (R=0.257, P=0.018). Duodenal relative abundance (RA) of Prevotellaceae (which positively impacts duodenal microbial diversity) inversely correlated with both GH (R=-0.174, P=0.019) and predicted TMA production (R=-0.174, P=0.019). Positive associations among Prevotellaceae and duodenal diversity (R=0.570, P&amp;lt;0.0001) and inverse associations with TMA production (R=-0.354, P=0.029) were stronger in older M (66-80yrs). In M, Prevotellaceae RA decreased gradually with age (P=0.023). Conclusion: IGF-1 and GH levels exhibit differential relationships with the duodenal microbiome and cardiovascular risk. In males, IGF-1 levels strongly associate with duodenal microbial pathways linked to TMA production and conversion to TMAO. Red meat consumption is linked to GH levels and to predicted TMA biosynthesis pathways. The microbial family Prevotellaceae appears to mitigate predicted TMA production and its relative abundance is lower in older men. Presentation: Thursday, June 15, 2023

Regulating effects of chlorinated drinking water on cecal microbiota of broiler chicks

In this study, 2 types of drinking water were provided to broiler chicks to evaluate the relationship between the bacterial load of drinking water and cecal microbiota. One type of drinking water was untreated, while the other type was daily treated with sodium dichlorocyanurate (50 mg/L). A total of 240 broiler chicks were divided into 2 groups based on their initial body weight. There were 6 replicates in each group, and each replicate cage contained 20 birds. Each cage was assigned to a different floor of the battery cage. On the final day, water samples were collected from each replicate cage at the opening of the drinking cup height, and one bird was selected from each replicate cage to obtain cecal content samples for measuring microbiota composition using the 16S rRNA technique. We found that drinking water treated with sodium dichlorocyanurate significantly reduced the richness and diversity of microbiota and diminished/disappeared most gram-negative bacteria. Broiler chicks that consumed chlorinated drinking water exhibited changes in the composition of cecal microbiota, with Alistipes serving as the marker species in the cecal content of broiler chicks that consumed untreated water, whereas AF12 served as the marker species in the cecal content of broiler chicks that consumed chlorinated drinking water. Functional prediction using the MetaCyc database and species composition analysis of metabolic pathways showed that changes in 7 metabolic pathways were related to the abundance of Providencia. Therefore, we concluded that chlorinated drinking water reduced the bacterial load in drinking water, thereby altering the cecal microbiota composition and regulating the metabolic activity of broiler chicks.

Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs

Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.

Effect of purple sweet potato-derived anthocyanins on heat stress response in Wenchang chickens and preliminary mechanism study

This study was conducted to investigate the beneficial effect of purple sweet potato anthocyanins (PSPA) on growth performance, oxidative status, immune response, intestinal morphology, and intestinal flora homeostasis in heat-stressed Wenchang chickens. A total of 100 Wenchang chickens (50-day-old) were randomly assigned to 5 groups, including the thermoneutral environment (TN) group (26°C); high-temperature stressed (HS) group (33°C ± 1°C); low-dose PSPA treatment (L_HS) group (8 mg/kg body weight, 33°C ± 1°C); medium-dose PSPA treatment (M_HS) group and high-dose PSPA treatment (H_HS) group (16 mg/kg and 32 mg/kg body weight, respectively, 33°C ± 1°C). The results showed that PSPA reversed the adverse effects of heat stress on growth performance, meat quality, and carcass characteristics. And the effect was associated with the concentration of PSPA partially. Heat stress increased the serum lipids of Wenchang chickens. LDL-C, TG, TC, and FFA in the serum were significantly decreased, and HDL-C and LPS in the serum were increased by PSPA treatment. The digestive enzymes in duodenal chyme were significantly (P < 0.05) increased by PSPA treatment. And PSPA treatment significantly (P < 0.05) enhanced the redox status by improving antioxidant parameters (GSH-Px and SOD) and decreasing the MDA level in the serum and liver. Moreover, the level of inflammatory cytokines was significantly (P < 0.05) regulated by PSPA treatment compared to the HS group. The villus length and goblet cell numbers after PSPA treatment were significantly higher than HS group. Furthermore, PSPA also played protection on the intestine structure by decreasing the level of D-LA and DAO. 16S rRNA sequencing revealed the microbial composition was altered by PSPA, and Acetanaerobacterium and Oscillibacter were dominant in the H_HS group. Microbial functional prediction indicated that function pathways based on KEGG and metacyc database were regulated by PSPA, and intestinal flora correlated with metabolic function significantly. The spearman correlation analysis showed that Saccharibacteria and Clostridium_IV correlated with the serum lipids, antioxidant, and inflammatory cytokines. Collectively, these findings suggest that PSPA has a positive effect against heat stress in poultry.

A new metabolic model of Drosophila melanogaster and the integrative analysis of Parkinson's disease.

High conservation of the disease-associated genes between flies and humans facilitates the common use of Drosophila melanogaster to study metabolic disorders under controlled laboratory conditions. However, metabolic modeling studies are highly limited for this organism. We here report a comprehensively curated genome-scale metabolic network model of Drosophila using an orthology-based approach. The gene coverage and metabolic information of the draft model derived from a reference human model were expanded via Drosophila-specific KEGG and MetaCyc databases, with several curation steps to avoid metabolic redundancy and stoichiometric inconsistency. Furthermore, we performed literature-based curations to improve gene-reaction associations, subcellular metabolite locations, and various metabolic pathways. The performance of the resulting Drosophila model (8,230 reactions, 6,990 metabolites, and 2,388 genes), iDrosophila1 (https://github.com/SysBioGTU/iDrosophila), was assessed using flux balance analysis in comparison with the other currently available fly models leading to superior or comparable results. We also evaluated the transcriptome-based prediction capacity of iDrosophila1, where differential metabolic pathways during Parkinson's disease could be successfully elucidated. Overall, iDrosophila1 is promising to investigate system-level metabolic alterations in response to genetic and environmental perturbations.

Correlation between caries activity and salivary microbiota in preschool children.

Early childhood caries (ECC) is the most common chronic infectious oral disease in preschool children worldwide. It is closely related to the caries activity (CA) of children. However, the distribution characteristics of oral saliva microbiomes in children with different CA are largely underexplored. The aim of this study was to investigate the microbial community in saliva of preschool children with different CA and caries status, and to analyze the difference of microbial community in saliva of children with different CA and its correlation with ECC. Subjects were divided into 3 groups based on the Cariostat caries activity test: Group H, high CA (n=30); Group M, medium CA (n = 30); Group L, low CA (n=30). Questionnaire survey was used to explore the related influencing factors of CA. According to the caries status (on the basis of decayed mising filled teeth), these subjects were divided into caries-free group (dmft=0, n=19), caries-low group (0 < dmft ≤ 4, n=27) and caries-high group (dmft > 4, n=44). Microbial profiles of oral saliva were analyzed using 16S rRNA gene sequencing. There were significant differences in the microbial structure (P < 0.05). Scardovia and Selenomonas were the biomarkers of both H group and high caries group. The genus Abiotrophia and Lautropia were the biomarkers of both the L group and the low caries group, while the Lactobacillus and Arthrospira spp. were significantly enriched in the M group. The area under the ROC curve of the combined application of dmft score, age, frequency of sugary beverage intake, and the genus Scardovia, Selenomonas, and Campylobacter in screening children with high CA was 0.842. Moreover, function prediction using the MetaCyc database showed that there were significant differences in 11 metabolic pathways of salivary microbiota among different CA groups. Certain bacteria genera in saliva such as Scardovia and Selenomonas may be helpful in screening children with high CA.

Altered dental plaque microbiota correlated with salivary inflammation in female methamphetamine users.

Poor oral health is the most immediate and overlooked hazard of methamphetamine abuse in humans. Previous studies have reported methamphetamine-associated alterations in saliva microbiota, but the cause of methamphetamine-induced alterations in the oral microenvironment remains unclear. The present study aimed to investigate the alterations in dental plaque microbiota in methamphetamine users, and to explore their relationship with local immune inflammation in the oral cavity. This may provide new ideas on the development of methamphetamine-related oral microenvironment changes. Questionnaires and samples were obtained from 30 female methamphetamine users and 15 sex- and age-matched healthy controls. Microbial profiles of supragingival dental plaque were analyzed using 16S rRNA gene sequencing. Inflammatory factors in saliva were measured using enzyme-linked immunosorbent assay. Methamphetamine users had worse oral self-evaluation. Compared with healthy controls, methamphetamine users showed no differences in oral dental plaque microbial diversity but exhibited differences in the relative abundance of several microbial taxa. At the phylum level, a higher abundance of Proteobacteria and a lower abundance of Firmicutes were detected in methamphetamine users. Moreover, function prediction using the MetaCyc database showed that 33 pathways were significantly upregulated in methamphetamine users; Only the glycolytic (Pyrococcus) pathway was enriched in the C group. Importantly, salivary inflammatory factors showed complex significant associations with bacterial genera in methamphetamine users. Specifically, the genus Neisseria was positively correlated with IL-17 levels in saliva, and both were high in methamphetamine users. In contrast, the genus Streptococcus, with a lower abundance, was positively correlated with lower IL-10 levels. Overall, This study is the first to provide evidence for a link between altered dental plaque microbiota and salivary inflammation in methamphetamine users. Further elucidation of the interactions between methamphetamine use and oral microenvironment would be beneficial for appropriate interventions to improve oral health.

Comparison of gut microbiota in male MAFLD patients with varying liver stiffness.

PurposeIn this study, we examined the changes to the composition and function of the gut microbiota from patients with metabolic dysfunction-associated fatty liver disease (MAFLD).We compared patients in a case group (liver stiffness (LSM) ≥ 7.4 kPa) with a matched control group (LSM < 7.4 kPa) and investigated the correlation between characteristics of the microbiota and other biochemical indicators. MethodsThe study looked at a total of 85 men with MAFLD, 17 of whom were in the case group and 68 of whom were in the control group. We measured waist circumference, blood pressure, and body mass index, as well as clinical parameters including liver stiffness, enzyme levels, cholesterol levels, and fat attenuation. Whole-genome shotgun sequencing technology and the MetaCyc database were then used to detect the composition and major pathways of the gut microbiota for each patient. Statistical analyses were performed, including the chi-square test, the student’s t-test, the Wilcoxon rank-sum test, and the Mann–Whitney test. ResultsWhole-genome sequencing showed that the composition of the gut microbiota in patients with an LSM of above 7.4 kPa was significantly different to that of the control group. There were seven bacterial species that were different between the two groups. Prevotella copri, Phascolarctobacterium succinatutens, Eubacterium biforme, and Collinsella aerofaciens were enriched in the case group (P < 0.05). Conversely, Bacteroides coprocola, Bacteroides stercoris and Clostridiales bacterium 1_7_47FAA were decreased in the case group (P < 0.05). Furthermore, after removing low abundance pathways, a total of 32 microbial pathways were found to be significantly different between the two groups. Most pathways enriched in the case group over the control were related to biosynthesis of metabolites including amino acids, vitamins, nucleosides, and nucleotides. Conclusion. The composition and function of the gut microbiota in patients with increased liver stiffness are significantly altered. This observation may provide new avenues to better understand the mechanism of liver fibrosis.

Maternal Administration Of Probiotic Lactobacilli Since Pre-Conception Programs Offspring Gut Microbiota Functions

ObjectivesProbiotics intake may be considered beneficial by prospective and pregnant mothers but their effects on offspring development are underexplored. The maternal gut microbiota is a determinant of early offspring gut microbial colonization patterns and pre-conception may be a critical period. Our aim was to assess the programming effects of a probiotic Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus R0052 mixture, which is known to support intestinal homeostasis in infancy, on the temporal dynamics of offspring gut microbiota functions.MethodsFemale C57BL/6 specific pathogen free mice received sterile or probiotic-supplemented water starting one week before mating and until weaning (postnatal day, PND, 21). Offspring remained on their respective mother's treatment from PND 21 to 36. Offspring cecal microbiota was profiled at PND 14, 21, and 36 by 16S rRNA (V3-V4) gene amplicon sequencing and metabolic pathways were inferred with PICRUSt2 and the MetaCyc database. Data analysis and clustering were conducted with DESeq2-Wald test and hclust in R.Results355 MetaCyc pathways were predicted and collapsed into 48 functional classes; 10 of these accounted for more than 80% of the total pathway relative abundance, including various biosynthetic as well as carbohydrate and protein degradation pathways. With time, 113 and 55 pathways were altered (q-values < 0.01) in the control and probiotic groups, respectively, but only control samples clustered by age. At PND 14 and 21,195 and 39 pathways were differentially represented in the probiotic group vs. controls, but none at PND 36. Age-dependent pathways altered by probiotic supplementation belonged to biosynthesis (Amino Acid, Nucleoside and Nucleotide, Cofactor, Electron Carrier, and Vitamin) and degradation (Carbohydrate, Nucleoside and Nucleotide, Secondary Metabolite Degradation, C1 Compound Utilization and Assimilation) functional classes.ConclusionsMaternal probiotic supplementation accelerates the establishment of gut microbiota metabolic functions necessary to process host diet as well as for the synthesis of metabolites relevant for host health in the juvenile offspring.Funding SourcesNSERC; Lallemand Health Solutions; Lawson Family Chair in Microbiome Research.

Contrasting summer versus winter dynamic microbial communities and their environmental driving factors in the solid-state saccharification process of Fuyu-flavor Baijiu

The seasonal spontaneous fermentation depends on the assembly of specific microbiota. However, a knowledge gap remains regarding the seasonal dynamics of microbial community and functionality. This study aimed to investigate the differences in microbial community dynamics during the saccharification process of Fuyu-flavor Baijiu in winter versus summer by employing high-throughput sequencing. It also explored the driving effects of environmental variables on the microbial succession. The environmental temperature of saccharification in summer (29 ± 1 °C) was strikingly different in winter (14 ± 1 °C), leading to a longer incubation time in winter fermentation. The dominant bacterial genera displayed in the early stage of the summer saccharification process were Staphylococcus, unclassified Enterobacteriaceae, and Weissella, whereas the dominant genus was Weissella during the middle stage and Lactobacillus during the late stage of saccharification. In contrast, unclassified Enterobacteriaceae and Weissella were dominant genera throughout the winter saccharification process. In the fungal community, Rhizopus was the dominant genus in summer and winter saccharification. Principal coordinate analysis revealed that the changes in the environmental temperature in winter versus summer had distinct impacts on the microbial community structure. Also, temperature was the key factor driving the succession of bacterial community, whereas pH was the main factor driving the succession of dominant fungi. Predictive gene functionality of bacterial and fungal communities was computed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 against Kyoto Encyclopedia of Genes and Genomes (KEGG) database and MetaCyc database, respectively. Correlation networks were constructed to better understand the relationships between dominant microbial genera and physicochemical factors during the saccharification process. These results provided new insights into the Baijiu fermentation technology and allowed a theoretical basis for exploring effective management strategies regarding traditional fermentation in response to complex seasonal factors.

Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711

BackgroundMetabolism including anabolism and catabolism is a prerequisite phenomenon for all living organisms. Anabolism refers to the synthesis of the entire compound needed by a species. Catabolism refers to the breakdown of molecules to obtain energy. Many metabolic pathways are undisclosed and many organism-specific enzymes involved in metabolism are misplaced. When predicting a specific metabolic pathway of a microorganism, the first and foremost steps is to explore available online databases. Among many online databases, KEGG and MetaCyc pathway databases were used to deduce trehalose metabolic network for bacteria Variovorax sp. PAMC28711. Trehalose, a disaccharide, is used by the microorganism as an alternative carbon source.ResultsWhile using KEGG and MetaCyc databases, we found that the KEGG pathway database had one missing enzyme (maltooligosyl-trehalose synthase, EC 5.4.99.15). The MetaCyc pathway database also had some enzymes. However, when we used RAST to annotate the entire genome of Variovorax sp. PAMC28711, we found that all enzymes that were missing in KEGG and MetaCyc databases were involved in the trehalose metabolic pathway.ConclusionsFindings of this study shed light on bioinformatics tools and raise awareness among researchers about the importance of conducting detailed investigation before proceeding with any further work. While such comparison for databases such as KEGG and MetaCyc has been done before, it has never been done with a specific microbial pathway. Such studies are useful for future improvement of bioinformatics tools to reduce limitations.

Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers

BackgroundThe gut microbiome is associated with the response to immunotherapy for different cancers. However, the impact of the gut microbiome on hepatobiliary cancers receiving immunotherapy remains unknown. This study aims...

Web Alert: Amino acids from microbes for biotechnology: An annotated selection of World Wide Web sites relevant to the topics in microbial biotechnology.

https://www.ajinomoto.com/aboutus/amino-acids/how-amino-acids-are-made This website is maintained by a major company in Japan that produces amino acids via microbial fermentation processes. https://www.sciencedirect.com/science/article/pii/S0734975017301052 This is a review article that focuses on the specificity of the processes used in fermentation to make amino acids via different microbial strains. https://link.springer.com/content/pdf/10.1007%2F978-4-431-56520-8.pdf This is a book on microbial amino acid fermentations. It is comprehensive and covers the history, examples of processes, recent advances and future prospects for the field. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=Stickland-Oxidative This page of the MetaCyc database links to reactions that comprise the oxidative branch of the amino acid fermentation metabolism known as the Stickland reactions. https://www.nature.com/articles/ja2017142.pdf?origin=ppub This review article in the Journal of Antibiotics provides a very clear and concise overview of microbial amino acid production. It focuses on the microorganisms, the scale and the economic impacts of these processes. https://www.frontiersin.org/articles/10.3389/fmicb.2018.00683/full While most commercially relevant amino acids are in the L-form, there is increasing evidence of the importance of D-amino acids in the physiology of microorganisms. https://www.nature.com/articles/s41587-019-0345-2 Detecting specific proteinogenic amino acids electrically is described in this report. The method can provide a new, fast way to sequence proteins. https://www.pnas.org/content/115/20/5093 Amino acids have traditionally been derived on scale via microbes that overproduce specific amino acids that they excrete into fermentation broths. This paper describes the potential to use biomass and specific catalysts to produce a number of α-amino acids. If scalable and economically feasible, these methods could compete with the current microbial fermentation processes used in industry. https://www.nature.com/articles/s41598-018-21926-5 This study investigated the high level production of L-valine by Corynebacterium glutamicum. https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/469/ Corynebacterium glutamicum is the single most used and useful bacterium for producing amino acids. Its genome sequence was first publicly reported in 2003, and currently, dozens of genomes of C. glutamicum strains have been sequenced. Links to the genomes are provided here. https://biocyc.org/CORYNE/organism-summary Metabolic pathways for Corynebacterium glutamicum are provided here. https://link.springer.com/chapter/10.1007/978-3-030-39267-3_10 This review article discusses metabolic engineering of Corynebacterium glutamicum for enhanced amino acid production. The methods covered in this report range from classical mutagenesis, genetic engineering of single genes and systems biology approaches. https://www.biotechnologynotes.com/amino-acids/industrial-production-of-amino-acids-by-microorganism-and-fermentation/13820 This site provides a good basic overview of the range of amino acid products, the microorganisms used and parameters such as yield. https://www.prnewswire.com/news-releases/global-feed-amino-acids-market-overview-2021-with-profiles-of-56-companies--industry-guide-containing-contact-details-for-219-companies-301303039.html This site describes the industrial demand for amino acids and the major global players in their production. https://www.sciencedirect.com/science/article/pii/S2214030120300122 This report describes a selection and bio-sensing system to enhance the production of amino acids by Lactococcus lactis.

Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases.

Metabolic models have been proven to be useful tools in system biology and have been successfully applied to various research fields in a wide range of organisms. A relatively complete metabolic network is a prerequisite for deriving reliable metabolic models. The first step in constructing metabolic network is to harmonize compounds and reactions across different metabolic databases. However, effectively integrating data from various sources still remains a big challenge. Incomplete and inconsistent atomistic details in compound representations across databases is a very important limiting factor. Here, we optimized a subgraph isomorphism detection algorithm to validate generic compound pairs. Moreover, we defined a set of harmonization relationship types between compounds to deal with inconsistent chemical details while successfully capturing atom-level characteristics, enabling a more complete enabling compound harmonization across metabolic databases. In total, 15,704 compound pairs across KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc databases were detected. Furthermore, utilizing the classification of compound pairs and EC (Enzyme Commission) numbers of reactions, we established hierarchical relationships between metabolic reactions, enabling the harmonization of 3856 reaction pairs. In addition, we created and used atom-specific identifiers to evaluate the consistency of atom mappings within and between harmonized reactions, detecting some consistency issues between the reaction and compound descriptions in these metabolic databases.

Effects of Aleurone Supplementation on Glucose-Insulin Metabolism and Gut Microbiome in Untrained Healthy Horses.

Aleurone, a layer of the bran fraction, is deemed to be responsible for the positive health effects associated with the consumption of whole-grain products. Studies on rodents, pigs, and humans report beneficial effects of aleurone in five main areas: the reduction of oxidative stress, immunomodulatory effects, modulation of energy management, digestive health, and the storage of vitamins and minerals. Our study is the first aleurone supplementation study performed in horses. The aim of this study was to investigate the effect of an increase in the dose levels of aleurone on the postprandial glucose-insulin metabolism and the gut microbiome in untrained healthy horses. Seven adult Standardbred horses were supplemented with four different dose levels of aleurone (50, 100, 200, and 400 g/day for 1 week) by using a Latin square model with a 1-week wash out in between doses. On day 7 of each supplementation week, postprandial blood glucose-insulin was measured and fecal samples were collected. 16S ribosomal RNA (rRNA) gene sequencing was performed and QIIME2 software was used for microbiome analysis. Microbial community function was assessed by using the predictive metagenome analysis tool Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and using the Metacyc database of metabolic pathways. The relative abundancies of a pathway were analyzed by using analysis of composition of microbiomes (ANCOM) in R. There was a significant dose-dependent increase in the postprandial time to peak of glucose (p = 0.030), a significant delay in the time to peak of insulin (p = 0.025), and a significant decrease in both the insulin peak level (p = 0.049) and insulin area under the curve (AUC) (p = 0.019) with increasing dose levels of aleurone, with a consideration of 200 g being the lowest significant dose. Alpha diversity and beta diversity of the fecal microbiome showed no significant changes. Aleurone significantly decreased the relative abundance of the genera Roseburia, Shuttleworthia, Anaerostipes, Faecalibacter, and Succinovibrionaceae. The most pronounced changes in the relative abundance at phyla level were seen in Firmicutes and Verrucomicrobia (downregulation) and Bacteroidetes and Spirochaetes (upregulation). The PICRUSt analysis shows that aleurone induces a downregulation of the degradation of L-glutamate and taurine and an upregulation of the three consecutive pathways of the phospholipid membrane synthesis of the Archaea domain. The results of this study suggest a multimodal effect of aleurone on glucose-insulin metabolism, which is most likely to be caused by its effect on feed texture and subsequent digestive processing; and a synergistic effect of individual aleurone components on the glucose-insulin metabolism and microbiome composition and function.