scholarly journals Characteristics of the Microbial Community in the Production of Chinese Rice-Flavor Baijiu and Comparisons With the Microflora of Other Flavors of Baijiu

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuanliang Hu ◽  
Xinyi Lei ◽  
Xiaomin Zhang ◽  
Tongwei Guan ◽  
Luyao Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Scaling Analysis ◽  
Total Acid ◽  
Microbial Composition ◽  
Factors Affecting ◽  
The Core ◽  
Brewing Process ◽  
Rice Flavor

Rice-flavor baijiu is one of the four basic flavor types of Chinese baijiu. Microbial composition plays a key role in the classification of baijiu flavor types and the formation of flavor substances. In this study, we used high-throughput sequencing technology to study the changes of microbial community in the production of rice-flavor baijiu, and compared the microbial community characteristics during production of rice-, light-, and strong-flavor baijiu. The results showed that the species diversity of bacteria was much higher than that of fungi during the brewing of rice-flavor baijiu. The bacterial diversity index first increased and then decreased, while the diversity of fungi showed an increasing trend. A variety of major microorganisms came from the environment and raw rice materials; the core bacteria were Lactobacillus, Weissella, Pediococcus, Lactococcus, Acetobacter, etc., among which Lactobacillus was dominant (62.88–99.23%). The core fungi were Saccharomyces (7.06–83.50%) and Rhizopus (15.21–90.89%). Temperature and total acid content were the main physicochemical factors affecting the microbial composition. Non-metric multidimensional scaling analysis showed that during the fermentation of rice-, light-, and strong-flavor baijiu, their microbial communities formed their own distinct systems, with considerable differences among different flavor types. Compared with the other two flavor types of baijiu, in the brewing process of rice-flavor baijiu, microbial species were fewer and dominant microorganisms were prominent, which may be the main reason for the small variety of flavor substances in rice-flavor baijiu. This study provides a theoretical basis for the production of rice-flavor baijiu, and lays a foundation for studying the link between baijiu flavor formation and microorganisms.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Biogeochemical Forces Shape the Composition and Physiology of Polymicrobial Communities in the Cystic Fibrosis Lung

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Robert A. Quinn ◽  
Yan Wei Lim ◽  
Heather Maughan ◽  
Douglas Conrad ◽  
Forest Rohwer ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Microbial Community ◽  
Amino Acid ◽  
Nitrogen Cycle ◽  
High Throughput Sequencing ◽  
Survival Strategies ◽  
Novel Therapies ◽  
Amino Acid Catabolism ◽  
Respiratory Pathway ◽  
The Core

ABSTRACTThe cystic fibrosis (CF) lung contains thick mucus colonized by opportunistic pathogens which adapt to the CF lung environment over decades. The difficulty associated with sampling airways has impeded a thorough examination of the biochemical microhabitats these pathogens are exposed to. An indirect approach is to study the responses of microbial communities to these microhabitats, facilitated by high-throughput sequencing of microbial DNA and RNA from sputum samples. Microbial metagenomes and metatranscriptomes were sequenced from multiple CF patients, and the reads were assigned taxonomy and function through sequence homology to NCBI and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database hierarchies. For a comparison, saliva microbial metagenomes from the Human Microbiome Project (HMP) were also analyzed. These analyses identified that functions encoded and expressed by CF microbes were significantly enriched for amino acid catabolism, folate biosynthesis, and lipoic acid biosynthesis. The data indicate that the community uses oxidative phosphorylation as a major energy source but that terminal electron acceptors were diverse. Nitrate reduction was the most abundant anaerobic respiratory pathway, and genes for nitrate reductase were largely assigned toPseudomonasandRothia. Although many reductive pathways of the nitrogen cycle were present, the cycle was incomplete, because the oxidative pathways were absent. Due to the abundant amino acid catabolism and incomplete nitrogen cycle, the CF microbial community appears to accumulate ammonia. This finding was verified experimentally using a CF bronchiole culture model system. The data also revealed abundant sensing and transport of iron, ammonium, zinc, and other metals along with a low-oxygen environment. This study reveals the core biochemistry and physiology of the CF microbiome.IMPORTANCEThe cystic fibrosis (CF) microbial community is complex and adapts to the environmental conditions of the lung over the lifetime of a CF patient. This analysis illustrates the core functions of the CF microbial community in the context of CF lung biochemistry. There are many studies of the metabolism and physiology of individual microbes within the CF lung, but none that collectively analyze data from the whole microbiome. Understanding the core metabolism of microbes that inhabit the CF lung can provide new targets for novel therapies. The fundamental processes that CF pathogens rely on for survival may represent an Achilles heel for this pathogenic community. Novel therapies that are designed to disrupt understudied survival strategies of the CF microbial community may succeed against otherwise untreatable or antibiotic-resistant microbes.

scholarly journals Analysis of Microbial Diversity and Variation Law During Xiaoqu Baijiu Fermentation using High-throughput Sequencing Technology

2021 ◽  
Author(s):  
Qing Wang ◽  
Xiaoqing Xiang ◽  
PengFei Wu ◽  
Guoqiang Han
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Sequencing Technology ◽  
Theoretical Support ◽  
Brewing Process ◽  
Dominant Bacteria ◽  
Brewing Time

Abstract In this study, high-throughput sequencing (HTS) was used to compare and analyze the microbial diversity and variation law during the brewing process of xiaoqu Baijiu. The results showed that 34 phyla, 378 genera of bacteria and 4 phyla, 32 genera of fungi were detected. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Ascomycota and Bacteroidetes were the dominant groups. During the brewing process of xiaoqu Baijiu, the dominant bacteria were Weissella and unidentified Rickettsiales 2 days before brewing and Lactobacillus 3 days after brewing until the end of brewing. The dominant fungi were Rhizopus, Saccharomyces and Issatchenkia. The relative abundance of Rhizopus decreased with the extension of brewing time, while the relative abundance of Saccharomyces increased and became the dominant bacteria after the second day of brewing. This study revealed the diversity and variation of microbial community in the brewing process of xiaoqu Baijiu, and provide theoretical support and lay the foundation for future study on the contribution of microbial metabolism during brewing of xiaoqu Baijiu, thereby promote the development of xiaoqu baijiu industry.

scholarly journals Physicochemical Characteristics and Microbial Communities in Gochujang, a Traditional Korean Fermented Hot Pepper Paste

2021 ◽  
Vol 11 ◽  
Author(s):  
Jung-A Ryu ◽  
Eiseul Kim ◽  
Mi-Ju Kim ◽  
Shinyoung Lee ◽  
Sung-Ran Yoon ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Salt Concentration ◽  
High Throughput Sequencing ◽  
Sugar Content ◽  
Physicochemical Characteristics ◽  
Reducing Sugar ◽  
Hot Pepper ◽  
Microbial Composition ◽  
Factors Affecting ◽  
High Level

Gochujang is a Korean fermented hot pepper paste beneficial to human health by providing various nutrients. In this study, its physicochemical characteristics were identified, and its microbial communities were analyzed by high-throughput sequencing. The interrelationship between physicochemical characteristics and microbial composition was investigated to reveal the properties of gochujang before and after fermentation. After fermentation, all samples showed decreased salt concentration, pH, and reducing sugar content, while the acidity and amino-type nitrogen increased. The water content, salt concentration, amino-type nitrogen, and reducing sugar differed according to the batches of samples. Bacillus, Aerosakkonema, and Enterococcus were identified as the predominant bacterial genera. Furthermore, Aerosakkonema was the most abundant genus before fermentation; however, it was replaced by Bacillus as it decreased after fermentation. For the fungi, Aspergillus dominated before fermentation, whereas Zygosaccharomyces and Millerozyma dominated after fermentation. The high level of amino-type nitrogen in gochujang was related to the relative abundance of B. haynesii/B. licheniformis before fermentation. Additionally, the high abundance of Z. rouxii after fermentation was related to the flavor of gochujang. This comprehensive analysis of the microbial community associated with the physicochemical properties of gochujang could help in understanding the factors affecting the quality of the product.

scholarly journals Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Danyang Zheng ◽  
Yujiao Sun ◽  
Huijuan Li ◽  
Sidan Lu ◽  
Mingjun Shan ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Activated Sludge ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Public Health Issue ◽  
Activated Sludge Process ◽  
Degrading Bacteria

In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

scholarly journals Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

2015 ◽  
Vol 81 (7) ◽  
pp. 2525-2533 ◽  
Author(s):  
Daniel J. O'Sullivan ◽  
Paul D. Cotter ◽  
Orla O'Sullivan ◽  
Linda Giblin ◽  
Paul L. H. McSweeney ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Production Cycle ◽  
Microbial Composition ◽  
Temporal And Spatial Distribution ◽  
Content Type ◽  
Temporal And Spatial

ABSTRACTWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the generaThermus,Pseudoalteromonas, andBifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

scholarly journals The skin microbiome of cow-nose rays (Rhinoptera bonasus) in an aquarium touch-tank exhibit

2016 ◽  
Author(s):  
Patrick J Kearns ◽  
Jennifer L Bowen ◽  
Michael F Tlusty
Keyword(s):  
Microbial Community ◽  
New England ◽  
High Throughput Sequencing ◽  
Ventral Surface ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Microbial Composition ◽  
Human Interactions ◽  
Rhinoptera Bonasus ◽  
Public Aquarium

Public aquarium exhibits offer numerous educational opportunities for visitors while touch tank exhibits offer guests the ability to directly interact with marine life. However, despite the popularity of these exhibits, the effect of human interactions on the host-associated microbiome or the habitat microbiome remains unclear. Microbial communities, both host-associated and habitat associated can have great implications for host health and habitat function. To better understand the link between human interactions and the microbiome of a touch tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as its environment in a frequently visited touch tank exhibit at the New England Aquarium. Our analyses revealed a distinct microbial community associated with the skin of the ray that had lower diversity than the surrounding habitat. The ray skin was dominated by three orders: Burkholderiales (~55%), Flavobacteriales (~19%) and Pseudomonadales (~12%), suggesting a potentially important role of these taxa in ray health. Further, there was no difference between dorsal and ventral surface of the ray in terms of microbial composition or diversity, and a very low presence of common human-associated microbial taxa (<1.5%). Our results suggest that human contact has a minimal effect on the skin and habitat microbiome of the cow-nose ray and that the ray skin harbors a distinct and lower diversity microbial community than its environment.

scholarly journals Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1433
Author(s):  
Michele Berlanda ◽  
Giada Innocente ◽  
Barbara Simionati ◽  
Barbara Di Camillo ◽  
Sonia Facchin ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Dietary Intervention ◽  
Oral Treatment ◽  
Microbial Evolution ◽  
Rrna Gene ◽  
Gut Health ◽  
Microbial Composition ◽  
Chronic Enteropathies ◽  
Faecal Microbiome

Chronic enteropathies (CE) are gastrointestinal diseases that afflict about one in five dogs in Europe. Conventional therapeutic approaches include dietary intervention, pharmacological treatment and probiotic supplements. The patient response can be highly variable and the interventions are often not resolutive. Moreover, the therapeutic strategy is usually planned (and gradually corrected) based on the patient’s response to empirical treatment, with few indirect gut health indicators useful to drive clinicians’ decisions. The ever-diminishing cost of high-throughput sequencing (HTS) allows clinicians to directly follow and characterise the evolution of the whole gut microbial community in order to highlight possible weaknesses. In this framework, faecal microbiome transplantation (FMT) is emerging as a feasible solution to CE, based on the implant of a balanced, eubiotic microbial community from a healthy donor to a dysbiotic patient. In this study, we report the promising results of FMT carried out in a 9-year-old dog suffering from CE for the last 3 years. The patient underwent a two-cycle oral treatment of FMT and the microbiota evolution was monitored by 16S rRNA gene sequencing both prior to FMT and after the two administrations. We evaluated the variation of microbial composition by calculating three different alpha diversity indices and compared the patient and donor data to a healthy control population of 94 dogs. After FMT, the patient’s microbiome and clinical parameters gradually shifted to values similar to those observed in healthy dogs. Symptoms disappeared during a follow-up period of six months after the second FMT. We believe that this study opens the door for potential applications of FMT in clinical veterinary practice and highlights the need to improve our knowledge on this relevant topic.

scholarly journals The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260121
Author(s):  
Hiroki Morita ◽  
Satoshi Akao
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sample Size ◽  
Soil Sample ◽  
Dna Extraction ◽  
Microbial Community Structure ◽  
Diversity Index ◽  
Sample Sizes ◽  
Microbial Composition ◽  
Taxonomic Rank

To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.

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

2020 ◽  
Vol 33 (10) ◽  
pp. 1610-1616 ◽  
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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