Dynamic Evolution and Correlation between Metabolites and Microorganisms during Manufacturing Process and Storage of Fu Brick Tea

Fu brick tea (FBT) is one of the major brands of dark tea. Microbial fermentation is considered the key step in the development of the special characteristics of FBT. The systemic corelationship of the microbiome and metabolomics during manufacture of Fu brick tea is not fully understood. In this study, we comprehensively explored the microbiome and metabolite dynamic evolution during the FBT manufacturing processes, and revealed decisive factors for the quality and safety of FBT based on the grouped methods of metabolomics combined with biochemical measurements, microbiome sequencing combined with quantitative polymerase chain reaction (PCR), and multiplex analysis. Both the microbiome and quantitative PCR showed that fungi displayed concentrated distribution characteristics in the primary dark tea samples, while bacterial richness increased during the flowering processes and ripening period. All microorganism species, as well as dominant fungi and bacteria, were identified in the distinct processes periods. A total of 178 metabolites were identified, and 34 of them were characterized as critical metabolites responsible for metabolic changes caused by the corresponding processes. Metabolic analysis showed that most metabolites were decreased during the FBT manufacturing processes, with the exception of gallic acid. Multivariate analysis verified that the critical metabolites were correlated with specific dominant microbial species. All the top fungal species except unclassified_g_ Aspergillus showed positive correlations with six critical metabolites (L-The, epigallocatechin (EGC), Gln, tea polyphenol (TP), tea polysaccharides (TPs) and caffeine). Five of the top bacteria species (Cronobacter, Klebsiella, Pantoea, Pluralibacter, and unclassified_ f_Entero-bacteriaceae) showed positive correlations with epigallocatechins and tea polyphenols, while the other 11 top bacterial species correlated negatively with all the critical metabolites. The content of amino acids, tea polyphenols, tea polysaccharides, and flavonoids was reduced during microbial fermentation. In conclusion, our results reveal that microbial composition is the critical factor in changing the metabolic profile of FBT. This discovery provides a theoretical basis for improving the quality of FBT and enhancing its safety.

Download Full-text

The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients

Science ◽

10.1126/science.aao3290 ◽

2018 ◽

Vol 359 (6371) ◽

pp. 104-108 ◽

Cited By ~ 693

Author(s):

Vyara Matson ◽

Jessica Fessler ◽

Riyue Bao ◽

Tara Chongsuwat ◽

Yuanyuan Zha ◽

...

Keyword(s):

Metastatic Melanoma ◽

Antitumor Immunity ◽

Human Cancer ◽

Quantitative Polymerase Chain Reaction ◽

Bacterial Species ◽

Bifidobacterium Longum ◽

Tumor Control ◽

Microbial Composition ◽

Stool Samples ◽

Melanoma Patients

Anti–PD-1–based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients’ microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria. A significant association was observed between commensal microbial composition and clinical response. Bacterial species more abundant in responders included Bifidobacterium longum, Collinsella aerofaciens, and Enterococcus faecium. Reconstitution of germ-free mice with fecal material from responding patients could lead to improved tumor control, augmented T cell responses, and greater efficacy of anti–PD-L1 therapy. Our results suggest that the commensal microbiome may have a mechanistic impact on antitumor immunity in human cancer patients.

Download Full-text

Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches

Biotechnology for Biofuels ◽

10.1186/s13068-021-01968-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Anna Detman ◽

Michał Bucha ◽

Laura Treu ◽

Aleksandra Chojnacka ◽

Łukasz Pleśniak ◽

...

Keyword(s):

Microbial Communities ◽

Methane Production ◽

Bacterial Species ◽

Stable Carbon Isotope ◽

Anaerobic Sludge ◽

Methane Formation ◽

Microbial Composition ◽

Fermentation Products ◽

Core Microbiome ◽

Specific Species

Abstract Background During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. Results Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%–67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. Conclusions In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

Download Full-text

Functional Characterization and Diversity of Ammonia-Oxidizing Microorganisms in Streams South of the Dabie Mountains, China

10.20944/preprints201812.0154.v1 ◽

2018 ◽

Author(s):

Amjed Ginawi ◽

Wang Lixiao ◽

Huading Wang ◽

Bingbing Yu ◽

Yan Yunjun

Keyword(s):

Quantitative Polymerase Chain Reaction ◽

Functional Characterization ◽

Physiological Adaptation ◽

Ammonia Oxidizing Bacteria ◽

Dabie Mountains ◽

Natural Habitats ◽

Environmental Pressures ◽

Microbial Structures ◽

Ammonia Oxidizing Archaea ◽

Positive Correlations

Ammonia-oxidizing microorganism communities are abundant and functionally efficacious in nitrification. However, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) groups complicate this process in subtropical streams. This study investigates the abundance of ammonia-oxidizing communities south of the Dabie Mountains, China, using quantitative polymerase chain reaction (qPCR). Clone libraries were utilized to analyze the abundance and microbial structures of AOA and AOB in sediments. Such analysis may provide strong evidence reflecting the links within the environment. The results show that AOB had a lower abundance of copies of the ammonia-oxidizing gene (amoA) than AOA. Interestingly, the AOA and AOB community compositions were correlated with ecological characteristics. The dissolved oxygen (DO) and oxidation-reduction potential (ORP) had significant positive correlations, whereas the phosphorus within the structure had a negative correlation with the abundance of both groups. Our study shows that it might adopt some species related to Nitrosotalea clusters that can resist comparably higher pH (toward pH 6.5). Together, these results imply that the physiological adaptation of microbial guilds to environmental pressures in ammonia-oxidizing archaea might allow them to have a more substantial function of ammonia-oxidizing communities in natural habitats.

Download Full-text

Oral Dextran Sulfate Sodium Administration Induces Peripheral Spondyloarthritis Features in SKG Mice Accompanied by Intestinal Bacterial Translocation and Systemic Th1 and Th17 Cell Activation.

10.21203/rs.3.rs-1071333/v1 ◽

2021 ◽

Author(s):

Yuya Tabuchi ◽

Masao Katsushima ◽

Yuri Nishida ◽

Mirei Shirakashi ◽

Hideaki Tsuji ◽

...

Keyword(s):

Bacterial Translocation ◽

Whole Blood ◽

Th17 Cell ◽

Cell Activation ◽

Dextran Sulfate ◽

Dextran Sulfate Sodium ◽

Quantitative Polymerase Chain Reaction ◽

Bacterial Species ◽

Bacterial Dna ◽

Anti Fungal

Abstract Background: Spondyloarthritis (SpA) is an autoimmune and autoinflammatory musculoskeletal disease characterised by systemic enthesitis. Recent research has focused on subclinical inflammatory bowel disease (IBD) in SpA pathogenesis. SKG mice, harbouring the Zap70 W163C mutation, increase autoreactive Th17 cells intrinsically, and show SpA features, including enteritis, after peritoneal injection of β-1,3- glucan under SPF conditions. In a conventional environment, they exhibit spontaneous arthritis with fungal factors. This study aimed to clarify whether oral dextran sulfate sodium (DSS) administration, utilised in IBD model mice, can provoke SpA features in SKG mice under SPF conditions, focusing on the relationship between gut microorganisms and SpA pathogenesis.Methods: SKG and BALB/c mice were administered oral DSS, and their body weights, arthritis, and enthesitis scores were recorded. In another cohorts, antibiotics (meropenem and vancomycin) or an anti-fungal agent (amphotericin B) were administered orally before DSS administration. The splenic Th1 and Th17 cell populations were examined before and after DSS administration using flow cytometry. Furthermore, the amount of circulating bacterial DNA in whole blood was measured by absolute quantitative polymerase chain reaction (qPCR), and the number and characteristics of bacterial species corresponding to these circulating DNA were analised by next-generation sequencing (NGS).Results: Ankle enthesitis as a peripheral SpA feature was elicited in half of DSS-administered SKG mice, and none of the BALB/c mice. Pre-administration of antibiotics suppressed enthesitis, whilst an anti-fungal agent could not. Th1 and Th17 cell levels in the spleen increased after DSS administration, and this was suppressed by pre-administration of antibiotics. SKG mice have a larger amount of bacterial DNA in whole blood than BALB/c mice before and one day after the initiation of DSS administration. The number of bacterial species in whole blood increased after DSS administration in SKG and BALB/c mice. Some genera and species significantly specific to the DSS-treated SKG mice group were also detected. Conclusion: Oral DSS administration alone elicited peripheral enthesitis in SKG mice with bacterial translocation accompanied by increased splenic Th1 and Th17 cell levels. Pre-administration of antibiotics ameliorated these DSS-induced SpA features. These findings suggest that intestinal bacterial leakage plays a pivotal role in SpA pathogenesis.

Download Full-text

Study on a Fermented Whole Wheat: Phenolic Content, Activity on PTP1B Enzyme and In Vitro Prebiotic Properties

Molecules ◽

10.3390/molecules24061120 ◽

2019 ◽

Vol 24 (6) ◽

pp. 1120 ◽

Cited By ~ 3

Author(s):

Diletta Balli ◽

Maria Bellumori ◽

Paolo Paoli ◽

Giuseppe Pieraccini ◽

Monica Di Paola ◽

...

Keyword(s):

Lactobacillus Reuteri ◽

Tyrosine Phosphatase ◽

Bacterial Species ◽

Food Ingredient ◽

Microbial Composition ◽

Acidic Hydrolysis ◽

Inhibitory Power ◽

Methyl Ferulate ◽

First Time

Fermented cereals, staple foods in Asia and Africa, are recently receiving a growing interest in Western countries. The object of this work is the characterization of a fermented wheat used as a food ingredient and dietary supplement. To this aim, the phenolic composition, the activity on protein tyrosine phosphatase 1B (PTP1B), an enzyme overexpressed in type-II diabetes, the in vitro prebiotic properties on Lactobacillus reuteri and the microbial composition were investigated. Basic and acidic hydrolysis were tested for an exhaustive recovery of bound phenols: the acidic hydrolysis gave best yields. Methyl ferulate and neocarlinoside were identified for the first time in wheat. The inhibitory power of the extracts of several batches were investigated on PTP1B enzyme. The product was not able to inhibit the enzyme, otherwise, for the first time, a complete inhibition was observed for schaftoside, a major C-flavonoid of wheat. The microbial composition was assessed identifying Lactobacillus, Enterococcus, and Pediococcus as the main bacterial species. The fermented wheat was a suitable substrate for the grown of L. reuteri, recognized for its health properties in the human gut. The proposed method for phenols is easier compared to those based on strong basic hydrolysis; our results assessed the bound phenols as the major fraction, differently from that suggested by the literature for fermented cereals.

Download Full-text

Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs

Scientific Reports ◽

10.1038/s41598-019-55825-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Frédérique Chaucheyras-Durand ◽

Aurélie Ameilbonne ◽

Pauline Auffret ◽

Mickaël Bernard ◽

Marie-Madeleine Mialon ◽

...

Keyword(s):

Positive Impact ◽

Bacterial Species ◽

Animal Health ◽

Microbial Colonization ◽

Feed Additive ◽

Gut Development ◽

Host Animal ◽

Microbial Composition ◽

Rumen Microbiota ◽

Live Yeast

AbstractRumen microbiota is of paramount importance for ruminant digestion efficiency as the microbial fermentations supply the host animal with essential sources of energy and nitrogen. Early separation of newborns from the dam and distribution of artificial milk (Artificial Milking System or AMS) could impair rumen microbial colonization, which would not only affect rumen function but also have possible negative effects on hindgut homeostasis, and impact animal health and performance. In this study, we monitored microbial communities in the rumen and the feces of 16 lambs separated from their dams from 12 h of age and artificially fed with milk replacer and starter feed from d8, in absence or presence of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. Microbial groups and targeted bacterial species were quantified by qPCR and microbial diversity and composition were assessed by 16S rDNA amplicon sequencing in samples collected from birth to 2 months of age. The fibrolytic potential of the rumen microbiota was analyzed with a DNA microarray targeting genes coding for 8 glycoside hydrolase (GH) families. In Control lambs, poor establishment of fibrolytic communities was observed. Microbial composition shifted as the lambs aged. The live yeast supplement induced significant changes in relative abundances of a few bacterial OTUs across time in the rumen samples, among which some involved in crucial rumen function, and favored establishment of Trichostomatia and Neocallimastigaceae eukaryotic families. The supplemented lambs also harbored greater abundances in Fibrobacter succinogenes after weaning. Microarray data indicated that key cellulase and hemicellulase encoding-genes were present from early age in the rumen and that in the Supplemented lambs, a greater proportion of hemicellulase genes was present. Moreover, a higher proportion of GH genes from ciliate protozoa and fungi was found in the rumen of those animals. This yeast combination improved microbial colonization in the maturing rumen, with a potentially more specialized ecosystem towards efficient fiber degradation, which suggests a possible positive impact on lamb gut development and digestive efficiency.

Download Full-text

Structural changes in gut microbiome after Ramadan fasting: a pilot study

Beneficial Microbes ◽

10.3920/bm2019.0039 ◽

2020 ◽

Vol 11 (3) ◽

pp. 227-233

Author(s):

C. Ozkul ◽

M. Yalinay ◽

T. Karakan

Keyword(s):

Microbial Community ◽

Pilot Study ◽

Structural Changes ◽

Bacterial Species ◽

Shannon Index ◽

Microbial Community Analysis ◽

Intermittent Fasting ◽

Microbial Composition ◽

Ramadan Fasting ◽

Significant Difference

It has been largely accepted that dietary changes have an effect on gut microbial composition. In this pilot study we hypothesised that Ramadan fasting, which can be considered as a type of time-restricted feeding may lead to changes in gut microbial composition and diversity. A total of 9 adult subjects were included in the study. Stool samples were collected before (baseline) and at the end of the Ramadan fasting (after 29 days). Following the construction of an 16S rRNA amplicon library, the V4 region was sequenced using the Illumina Miseq platform. Microbial community analysis was performed using the QIIME program. A total of 27,521 operational taxonomic units (OTUs) with a 97% similarity were determined in all of the samples. Microbial richness was significantly increased after Ramadan according to observed OTU results (P=0.016). No significant difference was found in terms of Shannon index or phylogenetic diversity metrics of alpha diversity. Microbial community structure was significantly different between baseline and after Ramadan samples according to unweighted UniFrac analysis (P=0.025). LEfSe analysis revealed that Butyricicoccus, Bacteroides, Faecalibacterium, Roseburia, Allobaculum, Eubacterium, Dialister and Erysipelotrichi were significantly enriched genera after the end of Ramadan fasting. According to random forest analysis, the bacterial species most affected by the Ramadan fasting was Butyricicoccus pullicaecorum. Despite this is a pilot study with a limited sample size; our results clearly revealed that Ramadan fasting, which represents an intermittent fasting regime, leads to compositional changes in the gut microbiota.

Download Full-text

Human milk oligosaccharide categories define the microbiota composition in human colostrum

Beneficial Microbes ◽

10.3920/bm2016.0185 ◽

2017 ◽

Vol 8 (4) ◽

pp. 563-567 ◽

Cited By ~ 44

Author(s):

J. Aakko ◽

H. Kumar ◽

S. Rautava ◽

A. Wise ◽

C. Autran ◽

...

Keyword(s):

Gut Microbiota ◽

Human Milk ◽

Bifidobacterium Longum ◽

Microbiota Composition ◽

Microbial Composition ◽

Human Colostrum ◽

Human Milk Oligosaccharide ◽

Positive Correlations ◽

Microbial Groups ◽

And Staphylococcus Aureus

Human milk oligosaccharides (HMOs) are structurally diverse unconjugated glycans with a composition unique to each lactating mother. While HMOs have been shown to have an impact on the development of infant gut microbiota, it is not well known if HMOs also already affect milk microbial composition. To address this question, we analysed eleven colostrum samples for HMO content by high-pressure liquid chromatography and microbiota composition by quantitative PCR. Higher total HMO concentration was associated with higher counts of Bifidobacterium spp. (ρ=0.63, P=0.036). A distinctive effect was seen when comparing different HMO groups: positive correlations were observed between sialylated HMOs and Bifidobacterium breve (ρ=0.84, P=0.001), and non-fucosylated/non-sialylated HMOs and Bifidobacterium longum group (ρ=0.65, P=0.030). In addition to associations between HMOs and bifidobacteria, positive correlations were observed between fucosylated HMOs and Akkermansia muciniphila (ρ=0.70, P=0.017), and between fucosylated/sialylated HMOs and Staphylococcus aureus (ρ=0.75, P=0.007). Our results suggest that the characterised HMOs have an effect on specific microbial groups in human milk. Both oligosaccharides and microbes provide a concise inoculum for the compositional development of the infant gut microbiota.

Download Full-text

Microbial Antagonists of Foodborne Pathogens on Fresh, Minimally Processed Vegetables

Journal of Food Protection ◽

10.4315/0362-028x-65.12.1909 ◽

2002 ◽

Vol 65 (12) ◽

pp. 1909-1915 ◽

Cited By ~ 102

Author(s):

KAREN M. SCHUENZEL ◽

MARK A. HARRISON

Keyword(s):

Foodborne Pathogens ◽

Inhibitory Activity ◽

Bacterial Species ◽

Microbiological Analysis ◽

Microbial Composition ◽

Minimally Processed ◽

Naturally Occurring ◽

Bacterial Microbiota ◽

Bacterial Enumeration ◽

Minimally Processed Vegetables

On many types of raw or minimally processed foods, the bacterial microbiota is often composed of mixed species. The activities of one bacterial species may influence the growth and activities of others that are present. The objective of this project was to evaluate the microbial composition of fresh and minimally processed vegetables to determine if naturally occurring bacteria on produce are competitive with or antagonistic to potentially encountered pathogens. Naturally occurring bacteria were obtained from ready-to-eat salad vegetables on four occasions to allow for seasonal variation. Minimally processed vegetables were sampled at various stages in their processing from raw vegetables to packaged products. Some portions were analyzed microbiologically within 24 h, while other portions were stored refrigerated and analyzed after 72 h. Microbiological analysis was conducted for bacterial enumeration and to obtain isolates. An agar spot method was used to screen isolates for antimicrobial activity against Staphylococcus aureus ATCC 27664, Escherichia coli O157:H7 E009, Listeria monocytogenes LCDC 81–861, and Salmonella Montevideo. Of the 1,180 isolates screened for inhibitory activity, 37 (3.22%) were found to have various degrees of inhibitory activity against at least one test pathogen. Many isolates showed inhibitory activity against all four pathogens. The isolates with the most extensive inhibition were removed from finished lettuce piece shreds. Of the 37 inhibitory isolates, 34 (91.9%) were gram negative. All isolates with inhibitory activity are able to multiply at both 4 and 10°C.

Download Full-text

Nutritional Immunity and Antibiotic Drug Treatments Influence Microbial Composition but Fail to Eliminate Urethral Catheter Biofilms in Recurrently Catheterized Patients

10.1101/637819 ◽

2019 ◽

Author(s):

Yanbao Yu ◽

Harinder Singh ◽

Tamara Tsitrin ◽

Keehwan Kwon ◽

Shiferaw Bekele ◽

...

Keyword(s):

Immune Responses ◽

Metal Ion ◽

Bacterial Species ◽

Anaerobic Bacteria ◽

Effector Proteins ◽

Emerging Pathogens ◽

Microbial Composition ◽

Antibiotic Drug ◽

Drug Treatments ◽

Cellular Import

AbstractPolymicrobial biofilms that form on indwelling urethral catheters used by neurogenic bladder patients are known to recur following catheter replacements. Uropathogens dominate in catheter biofilms (CBs), grow and disperse as multi-cellular aggregates. Their microbial complexity, the characteristics of host immune responses and the molecular crosstalk in this ecosystem are incompletely understood. By surveying eight patients over up to six months with meta-omics analysis methods, we shed new light on the longitudinal microbial dynamics in CBs and the microbial-host crosstalk. There was evidence of chronic innate immune responses in all patients. Pathogens dominated the microbial contents.Proteus mirabilisoften out-competed other species in cases of salt encrustation of catheters. The examination of proteomes in CBs and associated urinary pellets revealed many abundant bacterial systems for transition metal ion (TMI) acquisition. TMIs are sequestered by effector proteins released by activated neutrophils and urothelial cells, such as lactotransferrin and calgranulins, which were abundant in the host proteomes. We identified positive quantitative correlations among systems responsible for siderophore biosynthesis, TMI/siderophore uptake and TMI cellular import in bacterial species, suggesting competition for TMIs to support their metabolism and growth in CBs.Enterococcus faecaliswas prevalent as a cohabitant of CBs and expressed three lipoproteins with apparent TMI acquisition functions. Fastidious anaerobic bacteria such asVeillonella,Actinobaculum, andBifidobacteriumgrew in CB communities that appeared to be oxygen starved. Finally, antibiotic drug treatments were shown to influence microbial composition of CBs but failed to prevent re-colonization of urethral catheters with persisting and/or drug-resistant newly emerging pathogens.

Download Full-text