Comparative Evaluation of Microbiota Dynamics and Metabolites Correlation Between Spontaneous and Inoculated Fermentations of Nanfeng Tangerine Wine

Understanding the evolution of microorganisms and metabolites during wine fermentation is essential for controlling its production. The structural composition and functional capacity of the core microbiota determine the quality and quantity of fruit wine. Nanfeng tangerine wine fermentation involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this product fermentation remain unclear. Therefore, high-throughput sequencing (HTS) and headspace-gas chromatography-mass spectrometry (HS/GC-MS) were employed to reveal the core functional microbiota for the production of volatile flavors during spontaneous fermentation (SF) and inoculated fermentation (IF) with Saccharomyces cerevisiae of Nanfeng tangerine wine. A total of 13 bacterial and 8 fungal genera were identified as the core microbiota; Lactobacillus and Acetobacter were the dominant bacteria in SF and IF, respectively. The main fungal genera in SF and IF were Hanseniaspora, Pichia, and Saccharomyces with a clear succession. In addition, the potential correlations analysis between microbiota succession and volatile flavor dynamics revealed that Lactobacillus, Acetobacter, Hanseniaspora, and Saccharomyces were the major contributors to the production of the volatile flavor of Nanfeng tangerine wine. The results of the present study provide insight into the effects of the core functional microbiota in Nanfeng tangerine wine and can be used to develop effective strategies for improving the quality of fruit wines.

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Correlation: Between Autochthonous Microbial Diversity and Volatile Metabolites During the Fermentation of Nongxiang Daqu

Frontiers in Microbiology ◽

10.3389/fmicb.2021.688981 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuke Deng ◽

Dan Huang ◽

Baolin Han ◽

Xinqian Ning ◽

Dong Yu ◽

...

Keyword(s):

Microbial Diversity ◽

High Throughput Sequencing ◽

Vital Role ◽

Partial Least Square ◽

Least Square ◽

Gas Chromatography Mass Spectrometry ◽

Volatile Flavor Compounds ◽

Volatile Metabolites ◽

Partial Least Square Analysis ◽

Volatile Flavor

Daqu is an important saccharifying and fermenting agent. It provides various microorganisms and enzymes for the fermentation of Baijiu and plays a vital role in the formation of Baijiu flavor. However, it is difficult to obtain information on microbial growth and metabolism in time for Daqu production. Therefore, the “Qu Xiang” obtained by smelling is an important index in the traditional production process to evaluate the microbial fermentation in the process of Daqu-making, “Qu Xiang” mainly represents the volatile flavor compounds in Daqu. The microbial diversity and volatile metabolites on 0, 6, 16, and 29 days of the fermentation process were measured using high-throughput sequencing and gas chromatography–mass spectrometry. Significant differences were found in the composition of the microbial community. Pseudomonas, Weissella, Bacillus, and Pelomonas were the main bacterial genera. Alternaria, Rhizopus, and Pichia are the main fungal genera. A total of 32 differential volatile metabolites were detected in samples at four time points using differential metabolic analysis. The correspondence of prevailing microorganisms with differential metabolites distinguished by Spearman correlation and two-way orthogonal partial least square analysis show that Saccharopolyspora exhibited a significant connection for the 12 differential metabolites. A significant positive correlation was observed between Rhizomucor and 13 different metabolites. These findings further understanding of the metabolism of microorganisms in Daqu fermentation and also help to control the microorganisms in the Daqu-making process, to obtain more stable Baijiu products.

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Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese

Applied and Environmental Microbiology ◽

10.1128/aem.02097-14 ◽

2014 ◽

Vol 80 (19) ◽

pp. 6243-6255 ◽

Cited By ~ 48

Author(s):

Ilaria De Pasquale ◽

Raffaella Di Cagno ◽

Solange Buchin ◽

Maria De Angelis ◽

Marco Gobbetti

Keyword(s):

Microbial Ecology ◽

Relative Abundance ◽

Solid Phase ◽

Volatile Component ◽

Streptococcus Thermophilus ◽

Gas Chromatography Mass Spectrometry ◽

Microbial Succession ◽

Content Type ◽

Core Microbiota ◽

Pasta Filata

ABSTRACTPyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated byFirmicutes(53%),Proteobacteria(39%),Bacteroidetes(7.8%),Actinobacteria(0.06%), andFusobacteria(0.03%), with heterogeneity at the genus level. The primary starterStreptococcus thermophilusdominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance ofStreptococcussp. and especiallySt. thermophilusdecreased, while that ofLactobacillus casei,Lactobacillussp., and especiallyLactobacillus paracaseiincreased consistently. Despite the lower relative abundance compared toSt. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which seemed to be the main factor responsible for cheese ripening.

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Different Distribution of Soil Core Microbiota in two Places of Huabei Plain, Central China

10.20944/preprints202101.0402.v1 ◽

2021 ◽

Author(s):

Luan Wang ◽

Qian Zhang ◽

Hongtao Mei ◽

Xiaohan Cui ◽

Meijie Wang ◽

...

Keyword(s):

Microbial Diversity ◽

Human Activity ◽

High Throughput Sequencing ◽

Central China ◽

Soil Core ◽

Limited Information ◽

Soil Microbiota ◽

Core Microbiota ◽

Soil Nutrition ◽

The Core

Soils harbor diverse bacteria, and these bacteria play important roles in soil nutrition cycling and carbon storage. Numerous investigations of soil microbiota had been performed, and the core microbiota in different soil or vegetation soil types had been described. However, the complexity of soil environments and relatively limited information of many geographic areas had attracted great attention on comprehensive exploration of soil microbes in enormous types of soil. To reveal the core soil microbiota in Huabei plain, soil samples from metropolis and countryside regions in the Huabei plain were investigated using high-throughput sequencing strategy. The results showed that the most dominant bacteria are Proteobacteria (38.34%), Actinobacteria (20.56%), and Acidobacteria (15.18%). At the genus-level, the most abundant known genera are Gaiella (3.66%), Sphingomonas (3.6%), Acidobacteria Gp6 (2.1%), and Arthrobacter (2%). Moreover, several dominant operational taxanomy units (OTU), such as OTU_3 and OTU_17, were identified to be associated with the soil environment. Microbial distributions of the metropolis samples were different from the countryside samples, which may reflect the environments in the countryside were more diverse than in the metropolis. Microbial diversity and evenness were higher in the metropolis than in the countryside, which might due to the fact that human activity increased the microbial diversity in the metropolis. The soil core microbiota of the Huabei plain were complex, and microbial distributions in the Huabei plain might be mainly affected by the human activity and environmental factors, not by the distance. Our data highlights the soil core microbiota in Huabei Plain, and provides insights for future soil microbiota distribution studies in central China.

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Effects of husbandry systems and Chinese indigenous chicken strain on cecum microbial diversity

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.19.0157 ◽

2020 ◽

Vol 33 (10) ◽

pp. 1610-1616 ◽

Cited By ~ 1

Author(s):

Xiuxue Dong ◽

Bing Hu ◽

Wenlong Wan ◽

Yanzhang Gong ◽

Yanping Feng

Keyword(s):

Microbial Diversity ◽

High Throughput Sequencing ◽

Stocking Density ◽

Operational Taxonomic Unit ◽

Indigenous Chicken ◽

Microbial Composition ◽

Core Microbiota ◽

Free Range ◽

The Core ◽

Individual Cage

Objective: This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions.Methods: A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment.Results: i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens.Conclusion: The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

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Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

Microorganisms ◽

10.3390/microorganisms9030617 ◽

2021 ◽

Vol 9 (3) ◽

pp. 617

Author(s):

Zhenbing Wu ◽

Qianqian Zhang ◽

Yaoyao Lin ◽

Jingwen Hao ◽

Shuyi Wang ◽

...

Keyword(s):

Relative Abundance ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

High Throughput Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Gastrointestinal Mucosa ◽

Gastrointestinal Microbiota ◽

Linear Discriminant ◽

Intestinal Microbes ◽

Nile Tilapia Oreochromis Niloticus

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia–Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia–Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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Effects of pH shock on microaerobic activated sludge system with a graphene oxide/nano-magnetic powder composite

Nordic Pulp & Paper Research Journal ◽

10.1515/npprj-2020-0022 ◽

2020 ◽

Vol 35 (3) ◽

pp. 457-463

Author(s):

Huixia Lan ◽

Xiangzhi Wang ◽

Shixin Qi ◽

Da Yang ◽

Hao Zhang

Keyword(s):

Graphene Oxide ◽

Activated Sludge ◽

High Throughput Sequencing ◽

Impact Resistance ◽

Magnetic Powder ◽

Blank Group ◽

Activated Sludge System ◽

Ph Shock ◽

Dominant Bacteria ◽

The Impact

AbstractUsing the acclimated activated sludge from the pulping middle-stage effluent, the effect of pH shock on the micro-oxygen activated sludge system with a nano-magnetic powder/graphene oxide composite was studied. The results showed that the removal rates of chemical oxygen demand (CODCr) and ultraviolet adsorption at 254 nm (UV254) decreased. Also, the sludge settling performance was poor due to the impact of pH, but the impact resistance of nano-magnetic powder/graphene oxide group (MGO group) was higher and the recovery was faster. Results of high throughput sequencing indicated that the diversity of microbial community was reduced by the impact of pH, but it was significantly higher in MGO group than in the blank group. The dominant bacteria after pH shock or recovery in both of the system had a large difference. The percentage of the dominant bacteria in the MGO group was higher than that in the blank group. The MGO group had higher electron transfer system (ETS) activity which made the system having a strong pH impact resistance.

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Flavor and Metabolite Profiles of Meat, Meat Substitutes, and Traditional Plant-Based High-Protein Food Products Available in Australia

Foods ◽

10.3390/foods10040801 ◽

2021 ◽

Vol 10 (4) ◽

pp. 801

Author(s):

Kornelia Kaczmarska ◽

Matthew Taylor ◽

Udayasika Piyasiri ◽

Damian Frank

Keyword(s):

Mass Spectrometry ◽

Solid Phase ◽

Food Products ◽

High Protein ◽

Gas Chromatography Mass Spectrometry ◽

Protein Food ◽

Volatile Flavor ◽

Orbitrap Mass Spectrometry ◽

Metabolite Profiles

Demand for plant-based proteins and plant-based food products is increasing globally. This trend is driven mainly by global population growth and a consumer shift towards more sustainable and healthier diets. Existing plant-based protein foods and meat mimetics often possess undesirable flavor and sensory properties and there is a need to better understand the formation of desirable meat-like flavors from plant precursors to improve acceptance of novel high-protein plant foods. This study aimed to comprehensively characterize the non-volatile flavor metabolites and the volatiles generated in grilled meat (beef, chicken, and pork) and compare these to commercially available meat substitutes and traditional high-protein plant-based foods (natto, tempeh, and tofu). Solid phase microextraction with gas-chromatography mass-spectrometry was used for elucidation of the flavor volatilome. Untargeted characterization of the non-volatile metabolome was conducted using Orbitrap mass spectrometry and Compound DiscovererTM datamining software. The study revealed greater diversity and higher concentrations of flavor volatiles in plant-based foods in comparison to grilled meat, although the odor activity of specific volatiles was not considered. On average, the total amount of volatiles in plant-based products were higher than in meat. A range of concentrations of free amino acids, dipeptide, tripeptides, tetrapeptides, nucleotides, flavonoids, and other metabolites was identified in meat and plant-based foods.

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Analysis of Microbial Community Structure and Volatile Compounds in the Pit Mud Used for Manufacturing Taorong-type Baijiu Based on High-Throughput Sequencing

10.21203/rs.3.rs-1097837/v1 ◽

2021 ◽

Author(s):

Yanbo Liu ◽

Mengxiao Sun ◽

Pei Hou ◽

Wenya Wang ◽

Xiangkun Shen ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Qualitative Analysis ◽

Volatile Compounds ◽

High Throughput ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Solid Phase ◽

Gas Chromatography Mass Spectrometry ◽

Pit Mud

Abstract In this study, the pit mud used in manufacturing Taorong-type Baijiu was collected from the upper, middle, lower and bottom layers of pits in Henan Yangshao Liquor Co., LTD. Besides, high-throughput sequencing (HTS) technology was adopted to analyze the microbial community structure of the pit mud. In addition, the volatile compounds in the pit mud were subjected to preliminarily qualitative analysis through headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The results of HTS demonstrated that there were 5, 3, 5 and 5 dominant bacterial phyla (including 11, 11, 9 and 8 dominant bacterial genera) and 3, 3, 3 and 3 dominant fungal phyla (including 4, 7, 7 and 5 dominant fungal genera) in the pit mud from F-S (upper), G-Z (middle), H-X (lower) and I-D (bottom), respectively. The qualitative analysis results of volatile compounds demonstrated that a total of 78 kinds of volatile compounds were detected in the pit mud, including 46, 45, 39 and 49 kinds in the pit mud from F-S, G-Z, H-X and I-D, respectively. Ester and acid were the two main components in the pit mud. Meanwhile, the correlation between microorganisms and main volatile compounds in the pit mud was analyzed. Moreover, Lentimicrobium, Syner-01 and Blvii28_wastewater-sludge group were found for the first time in the pit mud used for manufacturing Taorong-type Baijiu. The findings of this study could provide a theoretical foundation for improving the quality of pit mud and the flavor of Taorong-type Baijiu.

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