scholarly journals Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America

2021 ◽  
Vol 9 (5) ◽  
pp. 1060
Author(s):  
Keisha Harrison ◽  
Chris Curtin
Keyword(s):  
Microbial Community ◽  
North America ◽  
High Throughput Sequencing ◽  
Solid Phase ◽  
Taxonomic Diversity ◽  
Acetic Acid Bacterium ◽  
Sampling Procedure ◽  
Starter Cultures ◽  
Microbial Composition ◽  
Spatial Homogeneity

Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of the fermenting tea and represents an interphase environment, where embedded microbes gain access to oxygen as well as nutrients in the tea. To date, various yeast and bacteria have been reported to exist within the SCOBY, with little consensus as to which species are essential and which are incidental to Kombucha production. In this study, we used high-throughput sequencing approaches to evaluate spatial homogeneity within a single commercial SCOBY and taxonomic diversity across a large number (n = 103) of SCOBY used by Kombucha brewers, predominantly in North America. Our results show that the most prevalent and abundant SCOBY taxa were the yeast genus Brettanomyces and the bacterial genus Komagataeibacter, through careful sampling of upper and lower SCOBY layers. This sampling procedure is critical to avoid over-representation of lactic acid bacteria. K-means clustering was used on metabarcoding data of all 103 SCOBY, delineating four SCOBY archetypes based upon differences in their microbial community structures. Fungal genera Zygosaccharomyces, Lachancea and Starmerella were identified as the major compensatory taxa for SCOBY with lower relative abundance of Brettanomyces. Interestingly, while Lactobacillacae was the major compensatory taxa where Komagataeibacter abundance was lower, phylogenic heat-tree analysis infers a possible antagonistic relationship between Starmerella and the acetic acid bacterium. Our results provide the basis for further investigation of how SCOBY archetype affects Kombucha fermentation, and fundamental studies of microbial community assembly in an interphase environment.

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.

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

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.

scholarly journals Microbiome Analysis Exploring Taxonomic Diversity in Kasaragod Dwarf and Holstein Crossbred Cattle

2021 ◽  
Author(s):  
Deepthi M ◽  
Kumar Arvind ◽  
Rituja Saxena ◽  
Joby Pulikkan ◽  
Vineet K Sharma ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Marker Gene ◽  
Taxonomic Diversity ◽  
Crossbred Cattle ◽  
Microbial Composition ◽  
Indigenous Cattle ◽  
Animal Products ◽  
Unifrac Distance ◽  
Unweighted Unifrac ◽  
Principle Coordinate Analysis

Abstract The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf cattle, a unique non-descriptive native cattle of Kerala, India, are noted for their unique qualities, such as low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. However, owing to the higher milk yield, Holstein crossbred cattle are given more importance over Kasaragod Dwarf. The hindgut microbiota plays a major role in various biological processes such as the digestion, vitamins synthesis, and immunity in cattle. In this study, we compared the hindgut microbiota of the Kasaragod Dwarf with the highly found, Holstein crossbred utilizing 16S rRNA high-throughput sequencing for a better understanding of the relationship between the host and microbial community. Four replicates of each 20 samples comprising two cattle type (n=10) were sequenced and analyzed. Marker gene-based taxonomic analysis affirmed variations in their microbial composition. Principle Coordinate Analysis (PCoA) using weighted and unweighted UniFrac distance matrices showed the distinct microbial architecture of the two cattle type. Random Forest analysis further confirmed the distinctness and revealed the signature taxa in K-Dwarf. The study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in Kasaragod Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in Kasaragod Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of Kasaragod Dwarf cattle gut microbiome profiling. This study is pivotal towards developing genetic resources for the microbial population in K-Dwarf and how it could be differentiated from Holstein crossbred cattle.

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 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 Microbial Community Succession and Its Environment Driving Factors During Initial Fermentation of Maotai-Flavor Baijiu

2021 ◽  
Vol 12 ◽  
Author(s):  
Fei Hao ◽  
Yuwei Tan ◽  
Xibin Lv ◽  
Liangqiang Chen ◽  
Fan Yang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Solid State ◽  
Environmental Factors ◽  
Fermentation Process ◽  
High Throughput Sequencing ◽  
Driving Forces ◽  
Great Influence ◽  
Community Succession ◽  
Microbial Succession ◽  
Microbial Composition

The microbial composition and environmental factors can take a great influence on community succession during the solid-state fermentation (SSF) of Maotai-flavor Baijiu. In this paper, high-throughput sequencing was used to reveal the dominant microorganisms and the evolution process of microbial community structure in the initial fermentation of Maotai-flavor Baijiu. The correlation analysis was carried out for the relationship between physicochemical factors and fermented microbes. The results showed that microorganisms were obviously enriched and the diversity of bacteria and fungi showed a downward trend during the heap fermentation process of Maotai-flavor Baijiu. However, the diversity of fungi in the pit fermentation process increased. Generally, Lactobacillus, Pichia, and Saccharomyces were the dominant microorganisms in the initial fermentation of Maotai-flavor Baijiu. According to the redundancy analysis, we found that reducing sugar was the key driving factor for microbial succession in the heap fermentation, while acidity, alcohol, and temperature were the main driving forces in pit fermentation. This study revealed the microbial succession and its related environmental factors in the initial fermentation of Maotai-flavor Baijiu, which will enrich our knowledge of the mechanism of solid-state liquor fermentation.

scholarly journals Flavor Composition and Microbial Community Structure of Mianning Ham

2021 ◽  
Vol 11 ◽  
Author(s):  
Lin Chen ◽  
Zhengli Wang ◽  
Lili Ji ◽  
Jiamin Zhang ◽  
Zhiping Zhao ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
High Throughput ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Solid Phase ◽  
Debaryomyces Hansenii ◽  
Culture Method ◽  
Quality Parameters ◽  
Staphylococcus Equorum

Mianning ham, a traditional Chinese dry-cured ham, is protected by national geographical indications. To understand the surface and internal flavor composition and microbial community structure of Mianning ham, solid phase microextraction-gas chromatography (SPME-GC-MS) technology and Illumina high-throughput sequencing were utilized. The results showed that a total of 60 flavor substances were identified in the hams. Forty-nine kinds of flavorings were identified on the surface, including 14 aldehydes, 6 ketones, 10 alcohols, 5 esters, 7 hydrocarbons, 5 acids, and 2 other compounds. Thirty-six kinds of internal flavorings were identified, including 13 aldehydes, 4 ketones, 6 alcohols, 3 esters, 5 hydrocarbons, 4 acids and 1 other type. Decanal (34.91 μg/g) was the most prevalent compound on the surface, followed by n-hexanol (24.99 μg/g), n-hexanal (20.20 μg/g), and n-octyl (16.14 μg/g). n-Hexanal (20.74 μg/g) was the most common compound internally, followed by non-aldehyde (5.70 μg/g), 1-octene-3-alcohol (3.54 μg/g), and inverse-2-octenal (2.77 μg/g). Penicillium lanosum, Penicillium nalgiovense, Debaryomyces hansenii, Staphylococcus equorum, and Erwinia tasmaniensis were isolated from the surfaces of the hams by the traditional culture method. By Illumina high-throughput sequencing, three fungal phyla were identified. Ascomycota was the dominant phylum followed by Basidiomycota. At the genus level, 11 fungi were identified, of which Aspergillus was the dominant fungus, followed by Penicillium and Wallemia. These findings provide fundamental knowledge regarding the microorganisms and flavor compounds in Mianning ham, which will help industrial processors develop effective strategies for standardizing quality parameters.

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.

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